From 76073b912b371c3940087897aecdce4430b7aa1d Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Wed, 23 Sep 2020 16:40:55 -0400 Subject: [PATCH] 16827: Update the generated API to Arvados 2.0 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- sdk/R/R/Arvados.R | 4821 ++++++++++++++---------------------------- sdk/R/R/autoGenAPI.R | 12 +- 2 files changed, 1581 insertions(+), 3252 deletions(-) diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R index 744cb3c296..528a606650 100644 --- a/sdk/R/R/Arvados.R +++ b/sdk/R/R/Arvados.R @@ -1,130 +1,60 @@ -#' users.get -#' -#' users.get is a method defined in Arvados class. -#' -#' @usage arv$users.get(uuid) -#' @param uuid The UUID of the User in question. -#' @return User object. -#' @name users.get -NULL - -#' users.create -#' -#' users.create is a method defined in Arvados class. -#' -#' @usage arv$users.create(user, ensure_unique_name = "false") -#' @param user User object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return User object. -#' @name users.create -NULL - -#' users.update -#' -#' users.update is a method defined in Arvados class. -#' -#' @usage arv$users.update(user, uuid) -#' @param user User object. -#' @param uuid The UUID of the User in question. -#' @return User object. -#' @name users.update -NULL - -#' users.delete -#' -#' users.delete is a method defined in Arvados class. -#' -#' @usage arv$users.delete(uuid) -#' @param uuid The UUID of the User in question. -#' @return User object. -#' @name users.delete -NULL - -#' users.current -#' -#' users.current is a method defined in Arvados class. -#' -#' @usage arv$users.current(NULL) -#' @return User object. -#' @name users.current -NULL - -#' users.system -#' -#' users.system is a method defined in Arvados class. -#' -#' @usage arv$users.system(NULL) -#' @return User object. -#' @name users.system -NULL - -#' users.activate -#' -#' users.activate is a method defined in Arvados class. -#' -#' @usage arv$users.activate(uuid) -#' @param uuid -#' @return User object. -#' @name users.activate -NULL +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 -#' users.setup +#' api_clients.get #' -#' users.setup is a method defined in Arvados class. +#' api_clients.get is a method defined in Arvados class. #' -#' @usage arv$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 +#' @usage arv$api_clients.get(uuid) +#' @param uuid The UUID of the ApiClient in question. +#' @return ApiClient object. +#' @name api_clients.get NULL -#' users.unsetup +#' api_clients.create #' -#' users.unsetup is a method defined in Arvados class. +#' api_clients.create is a method defined in Arvados class. #' -#' @usage arv$users.unsetup(uuid) -#' @param uuid -#' @return User object. -#' @name users.unsetup +#' @usage arv$api_clients.create(apiclient, +#' ensure_unique_name = "false", cluster_id = NULL) +#' @param apiClient ApiClient object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @param cluster_id Create object on a remote federated cluster instead of the current one. +#' @return ApiClient object. +#' @name api_clients.create NULL -#' users.update_uuid +#' api_clients.update #' -#' users.update_uuid is a method defined in Arvados class. +#' api_clients.update is a method defined in Arvados class. #' -#' @usage arv$users.update_uuid(uuid, new_uuid) -#' @param uuid -#' @param new_uuid -#' @return User object. -#' @name users.update_uuid +#' @usage arv$api_clients.update(apiclient, +#' uuid) +#' @param apiClient ApiClient object. +#' @param uuid The UUID of the ApiClient in question. +#' @return ApiClient object. +#' @name api_clients.update NULL -#' users.merge +#' api_clients.delete #' -#' users.merge is a method defined in Arvados class. +#' api_clients.delete is a method defined in Arvados class. #' -#' @usage arv$users.merge(new_owner_uuid, -#' new_user_token, redirect_to_new_user = NULL) -#' @param new_owner_uuid -#' @param new_user_token -#' @param redirect_to_new_user -#' @return User object. -#' @name users.merge +#' @usage arv$api_clients.delete(uuid) +#' @param uuid The UUID of the ApiClient in question. +#' @return ApiClient object. +#' @name api_clients.delete NULL -#' users.list +#' api_clients.list #' -#' users.list is a method defined in Arvados class. +#' api_clients.list is a method defined in Arvados class. #' -#' @usage arv$users.list(filters = NULL, +#' @usage arv$api_clients.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") +#' count = "exact", cluster_id = NULL, bypass_federation = NULL) #' @param filters #' @param where #' @param order @@ -133,8 +63,10 @@ NULL #' @param limit #' @param offset #' @param count -#' @return UserList object. -#' @name users.list +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @return ApiClientList object. +#' @name api_clients.list NULL #' api_client_authorizations.get @@ -152,9 +84,10 @@ NULL #' api_client_authorizations.create is a method defined in Arvados class. #' #' @usage arv$api_client_authorizations.create(apiclientauthorization, -#' ensure_unique_name = "false") +#' ensure_unique_name = "false", cluster_id = NULL) #' @param apiClientAuthorization ApiClientAuthorization object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @param cluster_id Create object on a remote federated cluster instead of the current one. #' @return ApiClientAuthorization object. #' @name api_client_authorizations.create NULL @@ -209,7 +142,7 @@ NULL #' @usage arv$api_client_authorizations.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") +#' count = "exact", cluster_id = NULL, bypass_federation = NULL) #' @param filters #' @param where #' @param order @@ -218,111 +151,173 @@ NULL #' @param limit #' @param offset #' @param count +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only #' @return ApiClientAuthorizationList object. #' @name api_client_authorizations.list NULL -#' containers.get +#' authorized_keys.get #' -#' containers.get is a method defined in Arvados class. +#' authorized_keys.get is a method defined in Arvados class. #' -#' @usage arv$containers.get(uuid) -#' @param uuid The UUID of the Container in question. -#' @return Container object. -#' @name containers.get +#' @usage arv$authorized_keys.get(uuid) +#' @param uuid The UUID of the AuthorizedKey in question. +#' @return AuthorizedKey object. +#' @name authorized_keys.get NULL -#' containers.create +#' authorized_keys.create #' -#' containers.create is a method defined in Arvados class. +#' authorized_keys.create is a method defined in Arvados class. #' -#' @usage arv$containers.create(container, -#' ensure_unique_name = "false") -#' @param container Container object. +#' @usage arv$authorized_keys.create(authorizedkey, +#' ensure_unique_name = "false", cluster_id = NULL) +#' @param authorizedKey AuthorizedKey object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return Container object. -#' @name containers.create +#' @param cluster_id Create object on a remote federated cluster instead of the current one. +#' @return AuthorizedKey object. +#' @name authorized_keys.create NULL -#' containers.update +#' authorized_keys.update #' -#' containers.update is a method defined in Arvados class. +#' authorized_keys.update is a method defined in Arvados class. #' -#' @usage arv$containers.update(container, +#' @usage arv$authorized_keys.update(authorizedkey, #' uuid) -#' @param container Container object. -#' @param uuid The UUID of the Container in question. -#' @return Container object. -#' @name containers.update +#' @param authorizedKey AuthorizedKey object. +#' @param uuid The UUID of the AuthorizedKey in question. +#' @return AuthorizedKey object. +#' @name authorized_keys.update NULL -#' containers.delete +#' authorized_keys.delete #' -#' containers.delete is a method defined in Arvados class. +#' authorized_keys.delete is a method defined in Arvados class. #' -#' @usage arv$containers.delete(uuid) -#' @param uuid The UUID of the Container in question. -#' @return Container object. -#' @name containers.delete +#' @usage arv$authorized_keys.delete(uuid) +#' @param uuid The UUID of the AuthorizedKey in question. +#' @return AuthorizedKey object. +#' @name authorized_keys.delete NULL -#' containers.auth +#' authorized_keys.list #' -#' containers.auth is a method defined in Arvados class. +#' authorized_keys.list is a method defined in Arvados class. #' -#' @usage arv$containers.auth(uuid) -#' @param uuid -#' @return Container object. -#' @name containers.auth +#' @usage arv$authorized_keys.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact", cluster_id = NULL, bypass_federation = NULL) +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @return AuthorizedKeyList object. +#' @name authorized_keys.list NULL -#' containers.lock +#' collections.get #' -#' containers.lock is a method defined in Arvados class. +#' collections.get is a method defined in Arvados class. #' -#' @usage arv$containers.lock(uuid) -#' @param uuid -#' @return Container object. -#' @name containers.lock +#' @usage arv$collections.get(uuid) +#' @param uuid The UUID of the Collection in question. +#' @return Collection object. +#' @name collections.get NULL -#' containers.unlock +#' collections.create #' -#' containers.unlock is a method defined in Arvados class. +#' collections.create is a method defined in Arvados class. #' -#' @usage arv$containers.unlock(uuid) -#' @param uuid -#' @return Container object. -#' @name containers.unlock +#' @usage arv$collections.create(collection, +#' ensure_unique_name = "false", cluster_id = NULL) +#' @param collection Collection object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @param cluster_id Create object on a remote federated cluster instead of the current one. +#' @return Collection object. +#' @name collections.create NULL -#' containers.secret_mounts +#' collections.update #' -#' containers.secret_mounts is a method defined in Arvados class. +#' collections.update is a method defined in Arvados class. #' -#' @usage arv$containers.secret_mounts(uuid) -#' @param uuid -#' @return Container object. -#' @name containers.secret_mounts +#' @usage arv$collections.update(collection, +#' uuid) +#' @param collection Collection object. +#' @param uuid The UUID of the Collection in question. +#' @return Collection object. +#' @name collections.update NULL -#' containers.current +#' collections.delete #' -#' containers.current is a method defined in Arvados class. +#' collections.delete is a method defined in Arvados class. #' -#' @usage arv$containers.current(NULL) -#' @return Container object. -#' @name containers.current +#' @usage arv$collections.delete(uuid) +#' @param uuid The UUID of the Collection in question. +#' @return Collection object. +#' @name collections.delete NULL -#' containers.list +#' collections.provenance #' -#' containers.list is a method defined in Arvados class. +#' collections.provenance is a method defined in Arvados class. #' -#' @usage arv$containers.list(filters = NULL, +#' @usage arv$collections.provenance(uuid) +#' @param uuid +#' @return Collection object. +#' @name collections.provenance +NULL + +#' collections.used_by +#' +#' collections.used_by is a method defined in Arvados class. +#' +#' @usage arv$collections.used_by(uuid) +#' @param uuid +#' @return Collection object. +#' @name collections.used_by +NULL + +#' collections.trash +#' +#' collections.trash is a method defined in Arvados class. +#' +#' @usage arv$collections.trash(uuid) +#' @param uuid +#' @return Collection object. +#' @name collections.trash +NULL + +#' collections.untrash +#' +#' collections.untrash is a method defined in Arvados class. +#' +#' @usage arv$collections.untrash(uuid) +#' @param uuid +#' @return Collection object. +#' @name collections.untrash +NULL + +#' collections.list +#' +#' collections.list is a method defined in Arvados class. +#' +#' @usage arv$collections.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") +#' count = "exact", cluster_id = NULL, bypass_federation = NULL, +#' include_trash = NULL, include_old_versions = NULL) #' @param filters #' @param where #' @param order @@ -331,62 +326,116 @@ NULL #' @param limit #' @param offset #' @param count -#' @return ContainerList object. -#' @name containers.list +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @param include_trash Include collections whose is_trashed attribute is true. +#' @param include_old_versions Include past collection versions. +#' @return CollectionList object. +#' @name collections.list NULL -#' api_clients.get +#' containers.get #' -#' api_clients.get is a method defined in Arvados class. +#' containers.get is a method defined in Arvados class. #' -#' @usage arv$api_clients.get(uuid) -#' @param uuid The UUID of the ApiClient in question. -#' @return ApiClient object. -#' @name api_clients.get +#' @usage arv$containers.get(uuid) +#' @param uuid The UUID of the Container in question. +#' @return Container object. +#' @name containers.get NULL -#' api_clients.create +#' containers.create #' -#' api_clients.create is a method defined in Arvados class. +#' containers.create is a method defined in Arvados class. #' -#' @usage arv$api_clients.create(apiclient, -#' ensure_unique_name = "false") -#' @param apiClient ApiClient object. +#' @usage arv$containers.create(container, +#' ensure_unique_name = "false", cluster_id = NULL) +#' @param container Container object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return ApiClient object. -#' @name api_clients.create +#' @param cluster_id Create object on a remote federated cluster instead of the current one. +#' @return Container object. +#' @name containers.create NULL -#' api_clients.update +#' containers.update #' -#' api_clients.update is a method defined in Arvados class. +#' containers.update is a method defined in Arvados class. #' -#' @usage arv$api_clients.update(apiclient, +#' @usage arv$containers.update(container, #' uuid) -#' @param apiClient ApiClient object. -#' @param uuid The UUID of the ApiClient in question. -#' @return ApiClient object. -#' @name api_clients.update +#' @param container Container object. +#' @param uuid The UUID of the Container in question. +#' @return Container object. +#' @name containers.update NULL -#' api_clients.delete +#' containers.delete #' -#' api_clients.delete is a method defined in Arvados class. +#' containers.delete is a method defined in Arvados class. #' -#' @usage arv$api_clients.delete(uuid) -#' @param uuid The UUID of the ApiClient in question. -#' @return ApiClient object. -#' @name api_clients.delete +#' @usage arv$containers.delete(uuid) +#' @param uuid The UUID of the Container in question. +#' @return Container object. +#' @name containers.delete NULL -#' api_clients.list +#' containers.auth #' -#' api_clients.list is a method defined in Arvados class. +#' containers.auth is a method defined in Arvados class. #' -#' @usage arv$api_clients.list(filters = NULL, +#' @usage arv$containers.auth(uuid) +#' @param uuid +#' @return Container object. +#' @name containers.auth +NULL + +#' containers.lock +#' +#' containers.lock is a method defined in Arvados class. +#' +#' @usage arv$containers.lock(uuid) +#' @param uuid +#' @return Container object. +#' @name containers.lock +NULL + +#' containers.unlock +#' +#' containers.unlock is a method defined in Arvados class. +#' +#' @usage arv$containers.unlock(uuid) +#' @param uuid +#' @return Container object. +#' @name containers.unlock +NULL + +#' containers.secret_mounts +#' +#' containers.secret_mounts is a method defined in Arvados class. +#' +#' @usage arv$containers.secret_mounts(uuid) +#' @param uuid +#' @return Container object. +#' @name containers.secret_mounts +NULL + +#' containers.current +#' +#' containers.current is a method defined in Arvados class. +#' +#' @usage arv$containers.current(NULL) +#' @return Container object. +#' @name containers.current +NULL + +#' containers.list +#' +#' containers.list is a method defined in Arvados class. +#' +#' @usage arv$containers.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") +#' count = "exact", cluster_id = NULL, bypass_federation = NULL) #' @param filters #' @param where #' @param order @@ -395,8 +444,10 @@ NULL #' @param limit #' @param offset #' @param count -#' @return ApiClientList object. -#' @name api_clients.list +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @return ContainerList object. +#' @name containers.list NULL #' container_requests.get @@ -414,9 +465,10 @@ NULL #' container_requests.create is a method defined in Arvados class. #' #' @usage arv$container_requests.create(containerrequest, -#' ensure_unique_name = "false") +#' ensure_unique_name = "false", cluster_id = NULL) #' @param containerRequest ContainerRequest object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @param cluster_id Create object on a remote federated cluster instead of the current one. #' @return ContainerRequest object. #' @name container_requests.create NULL @@ -450,7 +502,8 @@ NULL #' @usage arv$container_requests.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") +#' count = "exact", cluster_id = NULL, bypass_federation = NULL, +#' include_trash = NULL) #' @param filters #' @param where #' @param order @@ -459,62 +512,96 @@ NULL #' @param limit #' @param offset #' @param count +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @param include_trash Include container requests whose owner project is trashed. #' @return ContainerRequestList object. #' @name container_requests.list NULL -#' authorized_keys.get +#' groups.get #' -#' authorized_keys.get is a method defined in Arvados class. +#' groups.get is a method defined in Arvados class. #' -#' @usage arv$authorized_keys.get(uuid) -#' @param uuid The UUID of the AuthorizedKey in question. -#' @return AuthorizedKey object. -#' @name authorized_keys.get +#' @usage arv$groups.get(uuid) +#' @param uuid The UUID of the Group in question. +#' @return Group object. +#' @name groups.get NULL -#' authorized_keys.create +#' groups.create #' -#' authorized_keys.create is a method defined in Arvados class. +#' groups.create is a method defined in Arvados class. #' -#' @usage arv$authorized_keys.create(authorizedkey, -#' ensure_unique_name = "false") -#' @param authorizedKey AuthorizedKey object. +#' @usage arv$groups.create(group, ensure_unique_name = "false", +#' cluster_id = NULL, async = "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 AuthorizedKey object. -#' @name authorized_keys.create +#' @param cluster_id Create object on a remote federated cluster instead of the current one. +#' @param async defer permissions update +#' @return Group object. +#' @name groups.create NULL -#' authorized_keys.update +#' groups.update #' -#' authorized_keys.update is a method defined in Arvados class. +#' groups.update is a method defined in Arvados class. #' -#' @usage arv$authorized_keys.update(authorizedkey, -#' uuid) -#' @param authorizedKey AuthorizedKey object. -#' @param uuid The UUID of the AuthorizedKey in question. -#' @return AuthorizedKey object. -#' @name authorized_keys.update +#' @usage arv$groups.update(group, uuid, +#' async = "false") +#' @param group Group object. +#' @param uuid The UUID of the Group in question. +#' @param async defer permissions update +#' @return Group object. +#' @name groups.update NULL -#' authorized_keys.delete +#' groups.delete #' -#' authorized_keys.delete is a method defined in Arvados class. +#' groups.delete is a method defined in Arvados class. #' -#' @usage arv$authorized_keys.delete(uuid) -#' @param uuid The UUID of the AuthorizedKey in question. -#' @return AuthorizedKey object. -#' @name authorized_keys.delete +#' @usage arv$groups.delete(uuid) +#' @param uuid The UUID of the Group in question. +#' @return Group object. +#' @name groups.delete NULL -#' authorized_keys.list +#' groups.contents #' -#' authorized_keys.list is a method defined in Arvados class. +#' groups.contents is a method defined in Arvados class. #' -#' @usage arv$authorized_keys.list(filters = NULL, +#' @usage arv$groups.contents(filters = NULL, +#' where = NULL, order = NULL, distinct = NULL, +#' limit = "100", offset = "0", count = "exact", +#' cluster_id = NULL, bypass_federation = NULL, +#' include_trash = NULL, uuid = NULL, recursive = NULL, +#' include = NULL) +#' @param filters +#' @param where +#' @param order +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @param include_trash Include items whose is_trashed attribute is true. +#' @param uuid +#' @param recursive Include contents from child groups recursively. +#' @param include Include objects referred to by listed field in "included" (only owner_uuid) +#' @return Group object. +#' @name groups.contents +NULL + +#' groups.shared +#' +#' groups.shared is a method defined in Arvados class. +#' +#' @usage arv$groups.shared(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") +#' count = "exact", cluster_id = NULL, bypass_federation = NULL, +#' include_trash = NULL, include = NULL) #' @param filters #' @param where #' @param order @@ -523,102 +610,120 @@ NULL #' @param limit #' @param offset #' @param count -#' @return AuthorizedKeyList object. -#' @name authorized_keys.list +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @param include_trash Include items whose is_trashed attribute is true. +#' @param include +#' @return Group object. +#' @name groups.shared NULL -#' collections.get +#' groups.trash #' -#' collections.get is a method defined in Arvados class. +#' groups.trash is a method defined in Arvados class. #' -#' @usage arv$collections.get(uuid) -#' @param uuid The UUID of the Collection in question. -#' @return Collection object. -#' @name collections.get +#' @usage arv$groups.trash(uuid) +#' @param uuid +#' @return Group object. +#' @name groups.trash NULL -#' collections.create +#' groups.untrash #' -#' collections.create is a method defined in Arvados class. +#' groups.untrash is a method defined in Arvados class. #' -#' @usage arv$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 +#' @usage arv$groups.untrash(uuid) +#' @param uuid +#' @return Group object. +#' @name groups.untrash NULL -#' collections.update +#' groups.list #' -#' collections.update is a method defined in Arvados class. +#' groups.list is a method defined in Arvados class. #' -#' @usage arv$collections.update(collection, -#' uuid) -#' @param collection Collection object. -#' @param uuid The UUID of the Collection in question. -#' @return Collection object. -#' @name collections.update +#' @usage arv$groups.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact", cluster_id = NULL, bypass_federation = NULL, +#' include_trash = NULL) +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @param include_trash Include items whose is_trashed attribute is true. +#' @return GroupList object. +#' @name groups.list NULL -#' collections.delete +#' keep_services.get #' -#' collections.delete is a method defined in Arvados class. +#' keep_services.get is a method defined in Arvados class. #' -#' @usage arv$collections.delete(uuid) -#' @param uuid The UUID of the Collection in question. -#' @return Collection object. -#' @name collections.delete +#' @usage arv$keep_services.get(uuid) +#' @param uuid The UUID of the KeepService in question. +#' @return KeepService object. +#' @name keep_services.get NULL -#' collections.provenance +#' keep_services.create #' -#' collections.provenance is a method defined in Arvados class. +#' keep_services.create is a method defined in Arvados class. #' -#' @usage arv$collections.provenance(uuid) -#' @param uuid -#' @return Collection object. -#' @name collections.provenance +#' @usage arv$keep_services.create(keepservice, +#' ensure_unique_name = "false", cluster_id = NULL) +#' @param keepService KeepService object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @param cluster_id Create object on a remote federated cluster instead of the current one. +#' @return KeepService object. +#' @name keep_services.create NULL -#' collections.used_by +#' keep_services.update #' -#' collections.used_by is a method defined in Arvados class. +#' keep_services.update is a method defined in Arvados class. #' -#' @usage arv$collections.used_by(uuid) -#' @param uuid -#' @return Collection object. -#' @name collections.used_by +#' @usage arv$keep_services.update(keepservice, +#' uuid) +#' @param keepService KeepService object. +#' @param uuid The UUID of the KeepService in question. +#' @return KeepService object. +#' @name keep_services.update NULL -#' collections.trash +#' keep_services.delete #' -#' collections.trash is a method defined in Arvados class. +#' keep_services.delete is a method defined in Arvados class. #' -#' @usage arv$collections.trash(uuid) -#' @param uuid -#' @return Collection object. -#' @name collections.trash +#' @usage arv$keep_services.delete(uuid) +#' @param uuid The UUID of the KeepService in question. +#' @return KeepService object. +#' @name keep_services.delete NULL -#' collections.untrash +#' keep_services.accessible #' -#' collections.untrash is a method defined in Arvados class. +#' keep_services.accessible is a method defined in Arvados class. #' -#' @usage arv$collections.untrash(uuid) -#' @param uuid -#' @return Collection object. -#' @name collections.untrash +#' @usage arv$keep_services.accessible(NULL) +#' @return KeepService object. +#' @name keep_services.accessible NULL -#' collections.list +#' keep_services.list #' -#' collections.list is a method defined in Arvados class. +#' keep_services.list is a method defined in Arvados class. #' -#' @usage arv$collections.list(filters = NULL, +#' @usage arv$keep_services.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", -#' count = "exact", include_trash = NULL) +#' count = "exact", cluster_id = NULL, bypass_federation = NULL) #' @param filters #' @param where #' @param order @@ -627,61 +732,64 @@ NULL #' @param limit #' @param offset #' @param count -#' @param include_trash Include collections whose is_trashed attribute is true. -#' @return CollectionList object. -#' @name collections.list +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @return KeepServiceList object. +#' @name keep_services.list NULL -#' humans.get +#' links.get #' -#' humans.get is a method defined in Arvados class. +#' links.get is a method defined in Arvados class. #' -#' @usage arv$humans.get(uuid) -#' @param uuid The UUID of the Human in question. -#' @return Human object. -#' @name humans.get +#' @usage arv$links.get(uuid) +#' @param uuid The UUID of the Link in question. +#' @return Link object. +#' @name links.get NULL -#' humans.create +#' links.create #' -#' humans.create is a method defined in Arvados class. +#' links.create is a method defined in Arvados class. #' -#' @usage arv$humans.create(human, ensure_unique_name = "false") -#' @param human Human object. +#' @usage arv$links.create(link, ensure_unique_name = "false", +#' cluster_id = NULL) +#' @param link Link object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return Human object. -#' @name humans.create +#' @param cluster_id Create object on a remote federated cluster instead of the current one. +#' @return Link object. +#' @name links.create NULL -#' humans.update +#' links.update #' -#' humans.update is a method defined in Arvados class. +#' links.update is a method defined in Arvados class. #' -#' @usage arv$humans.update(human, uuid) -#' @param human Human object. -#' @param uuid The UUID of the Human in question. -#' @return Human object. -#' @name humans.update +#' @usage arv$links.update(link, uuid) +#' @param link Link object. +#' @param uuid The UUID of the Link in question. +#' @return Link object. +#' @name links.update NULL -#' humans.delete +#' links.delete #' -#' humans.delete is a method defined in Arvados class. +#' links.delete is a method defined in Arvados class. #' -#' @usage arv$humans.delete(uuid) -#' @param uuid The UUID of the Human in question. -#' @return Human object. -#' @name humans.delete +#' @usage arv$links.delete(uuid) +#' @param uuid The UUID of the Link in question. +#' @return Link object. +#' @name links.delete NULL -#' humans.list +#' links.list #' -#' humans.list is a method defined in Arvados class. +#' links.list is a method defined in Arvados class. #' -#' @usage arv$humans.list(filters = NULL, +#' @usage arv$links.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") +#' count = "exact", cluster_id = NULL, bypass_federation = NULL) #' @param filters #' @param where #' @param order @@ -690,60 +798,74 @@ NULL #' @param limit #' @param offset #' @param count -#' @return HumanList object. -#' @name humans.list +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @return LinkList object. +#' @name links.list +NULL + +#' links.get_permissions +#' +#' links.get_permissions is a method defined in Arvados class. +#' +#' @usage arv$links.get_permissions(uuid) +#' @param uuid +#' @return Link object. +#' @name links.get_permissions NULL -#' job_tasks.get +#' logs.get #' -#' job_tasks.get is a method defined in Arvados class. +#' logs.get is a method defined in Arvados class. #' -#' @usage arv$job_tasks.get(uuid) -#' @param uuid The UUID of the JobTask in question. -#' @return JobTask object. -#' @name job_tasks.get +#' @usage arv$logs.get(uuid) +#' @param uuid The UUID of the Log in question. +#' @return Log object. +#' @name logs.get NULL -#' job_tasks.create +#' logs.create #' -#' job_tasks.create is a method defined in Arvados class. +#' logs.create is a method defined in Arvados class. #' -#' @usage arv$job_tasks.create(jobtask, ensure_unique_name = "false") -#' @param jobTask JobTask object. +#' @usage arv$logs.create(log, ensure_unique_name = "false", +#' cluster_id = NULL) +#' @param log Log 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 +#' @param cluster_id Create object on a remote federated cluster instead of the current one. +#' @return Log object. +#' @name logs.create NULL -#' job_tasks.update +#' logs.update #' -#' job_tasks.update is a method defined in Arvados class. +#' logs.update is a method defined in Arvados class. #' -#' @usage arv$job_tasks.update(jobtask, uuid) -#' @param jobTask JobTask object. -#' @param uuid The UUID of the JobTask in question. -#' @return JobTask object. -#' @name job_tasks.update +#' @usage arv$logs.update(log, uuid) +#' @param log Log object. +#' @param uuid The UUID of the Log in question. +#' @return Log object. +#' @name logs.update NULL -#' job_tasks.delete +#' logs.delete #' -#' job_tasks.delete is a method defined in Arvados class. +#' logs.delete is a method defined in Arvados class. #' -#' @usage arv$job_tasks.delete(uuid) -#' @param uuid The UUID of the JobTask in question. -#' @return JobTask object. -#' @name job_tasks.delete +#' @usage arv$logs.delete(uuid) +#' @param uuid The UUID of the Log in question. +#' @return Log object. +#' @name logs.delete NULL -#' job_tasks.list +#' logs.list #' -#' job_tasks.list is a method defined in Arvados class. +#' logs.list is a method defined in Arvados class. #' -#' @usage arv$job_tasks.list(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") +#' @usage arv$logs.list(filters = NULL, where = NULL, +#' order = NULL, select = NULL, distinct = NULL, +#' limit = "100", offset = "0", count = "exact", +#' cluster_id = NULL, bypass_federation = NULL) #' @param filters #' @param where #' @param order @@ -752,196 +874,145 @@ NULL #' @param limit #' @param offset #' @param count -#' @return JobTaskList object. -#' @name job_tasks.list +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @return LogList object. +#' @name logs.list NULL -#' jobs.get +#' users.get #' -#' jobs.get is a method defined in Arvados class. +#' users.get is a method defined in Arvados class. #' -#' @usage arv$jobs.get(uuid) -#' @param uuid The UUID of the Job in question. -#' @return Job object. -#' @name jobs.get +#' @usage arv$users.get(uuid) +#' @param uuid The UUID of the User in question. +#' @return User object. +#' @name users.get NULL -#' jobs.create +#' users.create #' -#' jobs.create is a method defined in Arvados class. +#' users.create is a method defined in Arvados class. #' -#' @usage arv$jobs.create(job, ensure_unique_name = "false", -#' find_or_create = "false", filters = NULL, -#' minimum_script_version = NULL, exclude_script_versions = NULL) -#' @param job Job object. +#' @usage arv$users.create(user, ensure_unique_name = "false", +#' cluster_id = NULL) +#' @param user User 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 +#' @param cluster_id Create object on a remote federated cluster instead of the current one. +#' @return User object. +#' @name users.create NULL -#' jobs.update +#' users.update #' -#' jobs.update is a method defined in Arvados class. +#' users.update is a method defined in Arvados class. #' -#' @usage arv$jobs.update(job, uuid) -#' @param job Job object. -#' @param uuid The UUID of the Job in question. -#' @return Job object. -#' @name jobs.update +#' @usage arv$users.update(user, uuid, bypass_federation = NULL) +#' @param user User object. +#' @param uuid The UUID of the User in question. +#' @param bypass_federation +#' @return User object. +#' @name users.update NULL -#' jobs.delete +#' users.delete #' -#' jobs.delete is a method defined in Arvados class. +#' users.delete is a method defined in Arvados class. #' -#' @usage arv$jobs.delete(uuid) -#' @param uuid The UUID of the Job in question. -#' @return Job object. -#' @name jobs.delete +#' @usage arv$users.delete(uuid) +#' @param uuid The UUID of the User in question. +#' @return User object. +#' @name users.delete NULL -#' jobs.queue +#' users.current #' -#' jobs.queue is a method defined in Arvados class. +#' users.current is a method defined in Arvados class. #' -#' @usage arv$jobs.queue(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return Job object. -#' @name jobs.queue +#' @usage arv$users.current(NULL) +#' @return User object. +#' @name users.current NULL -#' jobs.queue_size +#' users.system #' -#' jobs.queue_size is a method defined in Arvados class. +#' users.system is a method defined in Arvados class. #' -#' @usage arv$jobs.queue_size(NULL) -#' @return Job object. -#' @name jobs.queue_size +#' @usage arv$users.system(NULL) +#' @return User object. +#' @name users.system NULL -#' jobs.cancel +#' users.activate #' -#' jobs.cancel is a method defined in Arvados class. +#' users.activate is a method defined in Arvados class. #' -#' @usage arv$jobs.cancel(uuid) +#' @usage arv$users.activate(uuid) #' @param uuid -#' @return Job object. -#' @name jobs.cancel +#' @return User object. +#' @name users.activate NULL -#' jobs.lock +#' users.setup #' -#' jobs.lock is a method defined in Arvados class. +#' users.setup is a method defined in Arvados class. #' -#' @usage arv$jobs.lock(uuid) +#' @usage arv$users.setup(uuid = NULL, user = NULL, +#' repo_name = NULL, vm_uuid = NULL, send_notification_email = "false") #' @param uuid -#' @return Job object. -#' @name jobs.lock +#' @param user +#' @param repo_name +#' @param vm_uuid +#' @param send_notification_email +#' @return User object. +#' @name users.setup NULL -#' jobs.list +#' users.unsetup #' -#' jobs.list is a method defined in Arvados class. +#' users.unsetup is a method defined in Arvados class. #' -#' @usage arv$jobs.list(filters = NULL, where = NULL, -#' order = NULL, select = NULL, distinct = NULL, -#' limit = "100", offset = "0", count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return JobList object. -#' @name jobs.list +#' @usage arv$users.unsetup(uuid) +#' @param uuid +#' @return User object. +#' @name users.unsetup NULL -#' keep_disks.get +#' users.update_uuid #' -#' keep_disks.get is a method defined in Arvados class. +#' users.update_uuid is a method defined in Arvados class. #' -#' @usage arv$keep_disks.get(uuid) -#' @param uuid The UUID of the KeepDisk in question. -#' @return KeepDisk object. -#' @name keep_disks.get +#' @usage arv$users.update_uuid(uuid, new_uuid) +#' @param uuid +#' @param new_uuid +#' @return User object. +#' @name users.update_uuid NULL -#' keep_disks.create +#' users.merge #' -#' keep_disks.create is a method defined in Arvados class. +#' users.merge is a method defined in Arvados class. #' -#' @usage arv$keep_disks.create(keepdisk, -#' ensure_unique_name = "false") -#' @param keepDisk KeepDisk object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return KeepDisk object. -#' @name keep_disks.create -NULL - -#' keep_disks.update -#' -#' keep_disks.update is a method defined in Arvados class. -#' -#' @usage arv$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 -#' -#' keep_disks.delete is a method defined in Arvados class. -#' -#' @usage arv$keep_disks.delete(uuid) -#' @param uuid The UUID of the KeepDisk in question. -#' @return KeepDisk object. -#' @name keep_disks.delete -NULL - -#' keep_disks.ping -#' -#' keep_disks.ping is a method defined in Arvados class. -#' -#' @usage arv$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 +#' @usage arv$users.merge(new_owner_uuid, +#' new_user_token = NULL, redirect_to_new_user = NULL, +#' old_user_uuid = NULL, new_user_uuid = NULL) +#' @param new_owner_uuid +#' @param new_user_token +#' @param redirect_to_new_user +#' @param old_user_uuid +#' @param new_user_uuid +#' @return User object. +#' @name users.merge NULL -#' keep_disks.list +#' users.list #' -#' keep_disks.list is a method defined in Arvados class. +#' users.list is a method defined in Arvados class. #' -#' @usage arv$keep_disks.list(filters = NULL, +#' @usage arv$users.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") +#' count = "exact", cluster_id = NULL, bypass_federation = NULL) #' @param filters #' @param where #' @param order @@ -950,74 +1021,74 @@ NULL #' @param limit #' @param offset #' @param count -#' @return KeepDiskList object. -#' @name keep_disks.list +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @return UserList object. +#' @name users.list NULL -#' nodes.get +#' repositories.get #' -#' nodes.get is a method defined in Arvados class. +#' repositories.get is a method defined in Arvados class. #' -#' @usage arv$nodes.get(uuid) -#' @param uuid The UUID of the Node in question. -#' @return Node object. -#' @name nodes.get +#' @usage arv$repositories.get(uuid) +#' @param uuid The UUID of the Repository in question. +#' @return Repository object. +#' @name repositories.get NULL -#' nodes.create +#' repositories.create #' -#' nodes.create is a method defined in Arvados class. +#' repositories.create is a method defined in Arvados class. #' -#' @usage arv$nodes.create(node, ensure_unique_name = "false", -#' assign_slot = NULL) -#' @param node Node object. +#' @usage arv$repositories.create(repository, +#' ensure_unique_name = "false", cluster_id = NULL) +#' @param repository Repository object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @param assign_slot assign slot and hostname -#' @return Node object. -#' @name nodes.create +#' @param cluster_id Create object on a remote federated cluster instead of the current one. +#' @return Repository object. +#' @name repositories.create NULL -#' nodes.update +#' repositories.update #' -#' nodes.update is a method defined in Arvados class. +#' repositories.update is a method defined in Arvados class. #' -#' @usage arv$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 +#' @usage arv$repositories.update(repository, +#' uuid) +#' @param repository Repository object. +#' @param uuid The UUID of the Repository in question. +#' @return Repository object. +#' @name repositories.update NULL -#' nodes.delete +#' repositories.delete #' -#' nodes.delete is a method defined in Arvados class. +#' repositories.delete is a method defined in Arvados class. #' -#' @usage arv$nodes.delete(uuid) -#' @param uuid The UUID of the Node in question. -#' @return Node object. -#' @name nodes.delete +#' @usage arv$repositories.delete(uuid) +#' @param uuid The UUID of the Repository in question. +#' @return Repository object. +#' @name repositories.delete NULL -#' nodes.ping +#' repositories.get_all_permissions #' -#' nodes.ping is a method defined in Arvados class. +#' repositories.get_all_permissions is a method defined in Arvados class. #' -#' @usage arv$nodes.ping(uuid, ping_secret) -#' @param uuid -#' @param ping_secret -#' @return Node object. -#' @name nodes.ping +#' @usage arv$repositories.get_all_permissions(NULL) +#' @return Repository object. +#' @name repositories.get_all_permissions NULL -#' nodes.list +#' repositories.list #' -#' nodes.list is a method defined in Arvados class. +#' repositories.list is a method defined in Arvados class. #' -#' @usage arv$nodes.list(filters = NULL, +#' @usage arv$repositories.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") +#' count = "exact", cluster_id = NULL, bypass_federation = NULL) #' @param filters #' @param where #' @param order @@ -1026,143 +1097,84 @@ NULL #' @param limit #' @param offset #' @param count -#' @return NodeList object. -#' @name nodes.list +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @return RepositoryList object. +#' @name repositories.list NULL -#' links.get +#' virtual_machines.get #' -#' links.get is a method defined in Arvados class. +#' virtual_machines.get is a method defined in Arvados class. #' -#' @usage arv$links.get(uuid) -#' @param uuid The UUID of the Link in question. -#' @return Link object. -#' @name links.get +#' @usage arv$virtual_machines.get(uuid) +#' @param uuid The UUID of the VirtualMachine in question. +#' @return VirtualMachine object. +#' @name virtual_machines.get NULL -#' links.create +#' virtual_machines.create #' -#' links.create is a method defined in Arvados class. +#' virtual_machines.create is a method defined in Arvados class. #' -#' @usage arv$links.create(link, ensure_unique_name = "false") -#' @param link Link object. +#' @usage arv$virtual_machines.create(virtualmachine, +#' ensure_unique_name = "false", cluster_id = NULL) +#' @param virtualMachine VirtualMachine object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return Link object. -#' @name links.create -NULL - -#' links.update -#' -#' links.update is a method defined in Arvados class. -#' -#' @usage arv$links.update(link, uuid) -#' @param link Link object. -#' @param uuid The UUID of the Link in question. -#' @return Link object. -#' @name links.update +#' @param cluster_id Create object on a remote federated cluster instead of the current one. +#' @return VirtualMachine object. +#' @name virtual_machines.create NULL -#' links.delete +#' virtual_machines.update #' -#' links.delete is a method defined in Arvados class. +#' virtual_machines.update is a method defined in Arvados class. #' -#' @usage arv$links.delete(uuid) -#' @param uuid The UUID of the Link in question. -#' @return Link object. -#' @name links.delete +#' @usage arv$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 -#' links.list +#' virtual_machines.delete #' -#' links.list is a method defined in Arvados class. +#' virtual_machines.delete is a method defined in Arvados class. #' -#' @usage arv$links.list(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return LinkList object. -#' @name links.list +#' @usage arv$virtual_machines.delete(uuid) +#' @param uuid The UUID of the VirtualMachine in question. +#' @return VirtualMachine object. +#' @name virtual_machines.delete NULL -#' links.get_permissions +#' virtual_machines.logins #' -#' links.get_permissions is a method defined in Arvados class. +#' virtual_machines.logins is a method defined in Arvados class. #' -#' @usage arv$links.get_permissions(uuid) +#' @usage arv$virtual_machines.logins(uuid) #' @param uuid -#' @return Link object. -#' @name links.get_permissions -NULL - -#' keep_services.get -#' -#' keep_services.get is a method defined in Arvados class. -#' -#' @usage arv$keep_services.get(uuid) -#' @param uuid The UUID of the KeepService in question. -#' @return KeepService object. -#' @name keep_services.get -NULL - -#' keep_services.create -#' -#' keep_services.create is a method defined in Arvados class. -#' -#' @usage arv$keep_services.create(keepservice, -#' ensure_unique_name = "false") -#' @param keepService KeepService object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return KeepService object. -#' @name keep_services.create -NULL - -#' keep_services.update -#' -#' keep_services.update is a method defined in Arvados class. -#' -#' @usage arv$keep_services.update(keepservice, -#' uuid) -#' @param keepService KeepService object. -#' @param uuid The UUID of the KeepService in question. -#' @return KeepService object. -#' @name keep_services.update -NULL - -#' keep_services.delete -#' -#' keep_services.delete is a method defined in Arvados class. -#' -#' @usage arv$keep_services.delete(uuid) -#' @param uuid The UUID of the KeepService in question. -#' @return KeepService object. -#' @name keep_services.delete +#' @return VirtualMachine object. +#' @name virtual_machines.logins NULL -#' keep_services.accessible +#' virtual_machines.get_all_logins #' -#' keep_services.accessible is a method defined in Arvados class. +#' virtual_machines.get_all_logins is a method defined in Arvados class. #' -#' @usage arv$keep_services.accessible(NULL) -#' @return KeepService object. -#' @name keep_services.accessible +#' @usage arv$virtual_machines.get_all_logins(NULL) +#' @return VirtualMachine object. +#' @name virtual_machines.get_all_logins NULL -#' keep_services.list +#' virtual_machines.list #' -#' keep_services.list is a method defined in Arvados class. +#' virtual_machines.list is a method defined in Arvados class. #' -#' @usage arv$keep_services.list(filters = NULL, +#' @usage arv$virtual_machines.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") +#' count = "exact", cluster_id = NULL, bypass_federation = NULL) #' @param filters #' @param where #' @param order @@ -1171,62 +1183,65 @@ NULL #' @param limit #' @param offset #' @param count -#' @return KeepServiceList object. -#' @name keep_services.list +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @return VirtualMachineList object. +#' @name virtual_machines.list NULL -#' pipeline_templates.get +#' workflows.get #' -#' pipeline_templates.get is a method defined in Arvados class. +#' workflows.get is a method defined in Arvados class. #' -#' @usage arv$pipeline_templates.get(uuid) -#' @param uuid The UUID of the PipelineTemplate in question. -#' @return PipelineTemplate object. -#' @name pipeline_templates.get +#' @usage arv$workflows.get(uuid) +#' @param uuid The UUID of the Workflow in question. +#' @return Workflow object. +#' @name workflows.get NULL -#' pipeline_templates.create +#' workflows.create #' -#' pipeline_templates.create is a method defined in Arvados class. +#' workflows.create is a method defined in Arvados class. #' -#' @usage arv$pipeline_templates.create(pipelinetemplate, -#' ensure_unique_name = "false") -#' @param pipelineTemplate PipelineTemplate object. +#' @usage arv$workflows.create(workflow, +#' ensure_unique_name = "false", cluster_id = NULL) +#' @param workflow Workflow 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 +#' @param cluster_id Create object on a remote federated cluster instead of the current one. +#' @return Workflow object. +#' @name workflows.create NULL -#' pipeline_templates.update +#' workflows.update #' -#' pipeline_templates.update is a method defined in Arvados class. +#' workflows.update is a method defined in Arvados class. #' -#' @usage arv$pipeline_templates.update(pipelinetemplate, +#' @usage arv$workflows.update(workflow, #' uuid) -#' @param pipelineTemplate PipelineTemplate object. -#' @param uuid The UUID of the PipelineTemplate in question. -#' @return PipelineTemplate object. -#' @name pipeline_templates.update +#' @param workflow Workflow object. +#' @param uuid The UUID of the Workflow in question. +#' @return Workflow object. +#' @name workflows.update NULL -#' pipeline_templates.delete +#' workflows.delete #' -#' pipeline_templates.delete is a method defined in Arvados class. +#' workflows.delete is a method defined in Arvados class. #' -#' @usage arv$pipeline_templates.delete(uuid) -#' @param uuid The UUID of the PipelineTemplate in question. -#' @return PipelineTemplate object. -#' @name pipeline_templates.delete +#' @usage arv$workflows.delete(uuid) +#' @param uuid The UUID of the Workflow in question. +#' @return Workflow object. +#' @name workflows.delete NULL -#' pipeline_templates.list +#' workflows.list #' -#' pipeline_templates.list is a method defined in Arvados class. +#' workflows.list is a method defined in Arvados class. #' -#' @usage arv$pipeline_templates.list(filters = NULL, +#' @usage arv$workflows.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") +#' count = "exact", cluster_id = NULL, bypass_federation = NULL) #' @param filters #' @param where #' @param order @@ -1235,209 +1250,83 @@ NULL #' @param limit #' @param offset #' @param count -#' @return PipelineTemplateList object. -#' @name pipeline_templates.list +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @return WorkflowList object. +#' @name workflows.list NULL -#' pipeline_instances.get +#' user_agreements.get #' -#' pipeline_instances.get is a method defined in Arvados class. +#' user_agreements.get is a method defined in Arvados class. #' -#' @usage arv$pipeline_instances.get(uuid) -#' @param uuid The UUID of the PipelineInstance in question. -#' @return PipelineInstance object. -#' @name pipeline_instances.get +#' @usage arv$user_agreements.get(uuid) +#' @param uuid The UUID of the UserAgreement in question. +#' @return UserAgreement object. +#' @name user_agreements.get NULL -#' pipeline_instances.create +#' user_agreements.create #' -#' pipeline_instances.create is a method defined in Arvados class. +#' user_agreements.create is a method defined in Arvados class. #' -#' @usage arv$pipeline_instances.create(pipelineinstance, -#' ensure_unique_name = "false") -#' @param pipelineInstance PipelineInstance object. +#' @usage arv$user_agreements.create(useragreement, +#' ensure_unique_name = "false", cluster_id = NULL) +#' @param userAgreement UserAgreement 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 +#' @param cluster_id Create object on a remote federated cluster instead of the current one. +#' @return UserAgreement object. +#' @name user_agreements.create NULL -#' pipeline_instances.update +#' user_agreements.update #' -#' pipeline_instances.update is a method defined in Arvados class. +#' user_agreements.update is a method defined in Arvados class. #' -#' @usage arv$pipeline_instances.update(pipelineinstance, +#' @usage arv$user_agreements.update(useragreement, #' uuid) -#' @param pipelineInstance PipelineInstance object. -#' @param uuid The UUID of the PipelineInstance in question. -#' @return PipelineInstance object. -#' @name pipeline_instances.update +#' @param userAgreement UserAgreement object. +#' @param uuid The UUID of the UserAgreement in question. +#' @return UserAgreement object. +#' @name user_agreements.update NULL -#' pipeline_instances.delete +#' user_agreements.delete #' -#' pipeline_instances.delete is a method defined in Arvados class. +#' user_agreements.delete is a method defined in Arvados class. #' -#' @usage arv$pipeline_instances.delete(uuid) -#' @param uuid The UUID of the PipelineInstance in question. -#' @return PipelineInstance object. -#' @name pipeline_instances.delete -NULL - -#' pipeline_instances.cancel -#' -#' pipeline_instances.cancel is a method defined in Arvados class. -#' -#' @usage arv$pipeline_instances.cancel(uuid) -#' @param uuid -#' @return PipelineInstance object. -#' @name pipeline_instances.cancel -NULL - -#' pipeline_instances.list -#' -#' pipeline_instances.list is a method defined in Arvados class. -#' -#' @usage arv$pipeline_instances.list(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return PipelineInstanceList object. -#' @name pipeline_instances.list -NULL - -#' repositories.get -#' -#' repositories.get is a method defined in Arvados class. -#' -#' @usage arv$repositories.get(uuid) -#' @param uuid The UUID of the Repository in question. -#' @return Repository object. -#' @name repositories.get -NULL - -#' repositories.create -#' -#' repositories.create is a method defined in Arvados class. -#' -#' @usage arv$repositories.create(repository, -#' ensure_unique_name = "false") -#' @param repository Repository object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return Repository object. -#' @name repositories.create -NULL - -#' repositories.update -#' -#' repositories.update is a method defined in Arvados class. -#' -#' @usage arv$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 -#' -#' repositories.delete is a method defined in Arvados class. -#' -#' @usage arv$repositories.delete(uuid) -#' @param uuid The UUID of the Repository in question. -#' @return Repository object. -#' @name repositories.delete -NULL - -#' repositories.get_all_permissions -#' -#' repositories.get_all_permissions is a method defined in Arvados class. -#' -#' @usage arv$repositories.get_all_permissions(NULL) -#' @return Repository object. -#' @name repositories.get_all_permissions -NULL - -#' repositories.list -#' -#' repositories.list is a method defined in Arvados class. -#' -#' @usage arv$repositories.list(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return RepositoryList object. -#' @name repositories.list -NULL - -#' specimens.get -#' -#' specimens.get is a method defined in Arvados class. -#' -#' @usage arv$specimens.get(uuid) -#' @param uuid The UUID of the Specimen in question. -#' @return Specimen object. -#' @name specimens.get -NULL - -#' specimens.create -#' -#' specimens.create is a method defined in Arvados class. -#' -#' @usage arv$specimens.create(specimen, -#' ensure_unique_name = "false") -#' @param specimen Specimen object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return Specimen object. -#' @name specimens.create +#' @usage arv$user_agreements.delete(uuid) +#' @param uuid The UUID of the UserAgreement in question. +#' @return UserAgreement object. +#' @name user_agreements.delete NULL -#' specimens.update +#' user_agreements.signatures #' -#' specimens.update is a method defined in Arvados class. +#' user_agreements.signatures is a method defined in Arvados class. #' -#' @usage arv$specimens.update(specimen, -#' uuid) -#' @param specimen Specimen object. -#' @param uuid The UUID of the Specimen in question. -#' @return Specimen object. -#' @name specimens.update +#' @usage arv$user_agreements.signatures(NULL) +#' @return UserAgreement object. +#' @name user_agreements.signatures NULL -#' specimens.delete +#' user_agreements.sign #' -#' specimens.delete is a method defined in Arvados class. +#' user_agreements.sign is a method defined in Arvados class. #' -#' @usage arv$specimens.delete(uuid) -#' @param uuid The UUID of the Specimen in question. -#' @return Specimen object. -#' @name specimens.delete +#' @usage arv$user_agreements.sign(NULL) +#' @return UserAgreement object. +#' @name user_agreements.sign NULL -#' specimens.list +#' user_agreements.list #' -#' specimens.list is a method defined in Arvados class. +#' user_agreements.list is a method defined in Arvados class. #' -#' @usage arv$specimens.list(filters = NULL, +#' @usage arv$user_agreements.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") +#' count = "exact", cluster_id = NULL, bypass_federation = NULL) #' @param filters #' @param where #' @param order @@ -1446,1774 +1335,312 @@ NULL #' @param limit #' @param offset #' @param count -#' @return SpecimenList object. -#' @name specimens.list -NULL - -#' logs.get -#' -#' logs.get is a method defined in Arvados class. -#' -#' @usage arv$logs.get(uuid) -#' @param uuid The UUID of the Log in question. -#' @return Log object. -#' @name logs.get -NULL - -#' logs.create -#' -#' logs.create is a method defined in Arvados class. -#' -#' @usage arv$logs.create(log, ensure_unique_name = "false") -#' @param log Log object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return Log object. -#' @name logs.create -NULL - -#' logs.update -#' -#' logs.update is a method defined in Arvados class. -#' -#' @usage arv$logs.update(log, uuid) -#' @param log Log object. -#' @param uuid The UUID of the Log in question. -#' @return Log object. -#' @name logs.update +#' @param cluster_id List objects on a remote federated cluster instead of the current one. +#' @param bypass_federation bypass federation behavior, list items from local instance database only +#' @return UserAgreementList object. +#' @name user_agreements.list NULL -#' logs.delete +#' user_agreements.new #' -#' logs.delete is a method defined in Arvados class. +#' user_agreements.new is a method defined in Arvados class. #' -#' @usage arv$logs.delete(uuid) -#' @param uuid The UUID of the Log in question. -#' @return Log object. -#' @name logs.delete +#' @usage arv$user_agreements.new(NULL) +#' @return UserAgreement object. +#' @name user_agreements.new NULL -#' logs.list +#' configs.get #' -#' logs.list is a method defined in Arvados class. +#' configs.get is a method defined in Arvados class. #' -#' @usage arv$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 +#' @usage arv$configs.get(NULL) +#' @return object. +#' @name configs.get NULL -#' traits.get +#' project.get #' -#' traits.get is a method defined in Arvados class. +#' projects.get is equivalent to groups.get method. #' -#' @usage arv$traits.get(uuid) -#' @param uuid The UUID of the Trait in question. -#' @return Trait object. -#' @name traits.get +#' @usage arv$projects.get(uuid) +#' @param uuid The UUID of the Group in question. +#' @return Group object. +#' @name projects.get NULL -#' traits.create +#' project.create #' -#' traits.create is a method defined in Arvados class. +#' projects.create wrapps groups.create method by setting group_class attribute to "project". #' -#' @usage arv$traits.create(trait, ensure_unique_name = "false") -#' @param trait Trait object. +#' @usage arv$projects.create(group, ensure_unique_name = "false") +#' @param group Group object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return Trait object. -#' @name traits.create +#' @return Group object. +#' @name projects.create NULL -#' traits.update +#' project.update #' -#' traits.update is a method defined in Arvados class. +#' projects.update wrapps groups.update method by setting group_class attribute to "project". #' -#' @usage arv$traits.update(trait, uuid) -#' @param trait Trait object. -#' @param uuid The UUID of the Trait in question. -#' @return Trait object. -#' @name traits.update +#' @usage arv$projects.update(group, uuid) +#' @param group Group object. +#' @param uuid The UUID of the Group in question. +#' @return Group object. +#' @name projects.update NULL -#' traits.delete +#' project.delete #' -#' traits.delete is a method defined in Arvados class. +#' projects.delete is equivalent to groups.delete method. #' -#' @usage arv$traits.delete(uuid) -#' @param uuid The UUID of the Trait in question. -#' @return Trait object. -#' @name traits.delete +#' @usage arv$project.delete(uuid) +#' @param uuid The UUID of the Group in question. +#' @return Group object. +#' @name projects.delete NULL -#' traits.list +#' project.list #' -#' traits.list is a method defined in Arvados class. +#' projects.list wrapps groups.list method by setting group_class attribute to "project". #' -#' @usage arv$traits.list(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") +#' @usage arv$projects.list(filters = NULL, +#' where = NULL, order = NULL, distinct = NULL, +#' limit = "100", offset = "0", count = "exact", +#' include_trash = NULL, uuid = NULL, recursive = NULL) #' @param filters #' @param where #' @param order -#' @param select #' @param distinct #' @param limit #' @param offset #' @param count -#' @return TraitList object. -#' @name traits.list -NULL - -#' virtual_machines.get -#' -#' virtual_machines.get is a method defined in Arvados class. -#' -#' @usage arv$virtual_machines.get(uuid) -#' @param uuid The UUID of the VirtualMachine in question. -#' @return VirtualMachine object. -#' @name virtual_machines.get -NULL - -#' virtual_machines.create -#' -#' virtual_machines.create is a method defined in Arvados class. -#' -#' @usage arv$virtual_machines.create(virtualmachine, -#' ensure_unique_name = "false") -#' @param virtualMachine VirtualMachine object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return VirtualMachine object. -#' @name virtual_machines.create -NULL - -#' virtual_machines.update -#' -#' virtual_machines.update is a method defined in Arvados class. -#' -#' @usage arv$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 +#' @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 projects.list NULL -#' virtual_machines.delete -#' -#' virtual_machines.delete is a method defined in Arvados class. -#' -#' @usage arv$virtual_machines.delete(uuid) -#' @param uuid The UUID of the VirtualMachine in question. -#' @return VirtualMachine object. -#' @name virtual_machines.delete -NULL - -#' virtual_machines.logins -#' -#' virtual_machines.logins is a method defined in Arvados class. -#' -#' @usage arv$virtual_machines.logins(uuid) -#' @param uuid -#' @return VirtualMachine object. -#' @name virtual_machines.logins -NULL - -#' virtual_machines.get_all_logins -#' -#' virtual_machines.get_all_logins is a method defined in Arvados class. -#' -#' @usage arv$virtual_machines.get_all_logins(NULL) -#' @return VirtualMachine object. -#' @name virtual_machines.get_all_logins -NULL - -#' virtual_machines.list -#' -#' virtual_machines.list is a method defined in Arvados class. -#' -#' @usage arv$virtual_machines.list(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return VirtualMachineList object. -#' @name virtual_machines.list -NULL - -#' workflows.get -#' -#' workflows.get is a method defined in Arvados class. -#' -#' @usage arv$workflows.get(uuid) -#' @param uuid The UUID of the Workflow in question. -#' @return Workflow object. -#' @name workflows.get -NULL - -#' workflows.create -#' -#' workflows.create is a method defined in Arvados class. -#' -#' @usage arv$workflows.create(workflow, -#' ensure_unique_name = "false") -#' @param workflow Workflow object. -#' @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 -#' -#' workflows.update is a method defined in Arvados class. -#' -#' @usage arv$workflows.update(workflow, -#' uuid) -#' @param workflow Workflow object. -#' @param uuid The UUID of the Workflow in question. -#' @return Workflow object. -#' @name workflows.update -NULL - -#' workflows.delete -#' -#' workflows.delete is a method defined in Arvados class. -#' -#' @usage arv$workflows.delete(uuid) -#' @param uuid The UUID of the Workflow in question. -#' @return Workflow object. -#' @name workflows.delete -NULL - -#' workflows.list -#' -#' workflows.list is a method defined in Arvados class. -#' -#' @usage arv$workflows.list(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return WorkflowList object. -#' @name workflows.list -NULL - -#' groups.get -#' -#' groups.get is a method defined in Arvados class. -#' -#' @usage arv$groups.get(uuid) -#' @param uuid The UUID of the Group in question. -#' @return Group object. -#' @name groups.get -NULL - -#' groups.create -#' -#' groups.create is a method defined in Arvados class. -#' -#' @usage arv$groups.create(group, ensure_unique_name = "false") -#' @param group Group object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return Group object. -#' @name groups.create -NULL - -#' groups.update -#' -#' groups.update is a method defined in Arvados class. -#' -#' @usage arv$groups.update(group, uuid) -#' @param group Group object. -#' @param uuid The UUID of the Group in question. -#' @return Group object. -#' @name groups.update -NULL - -#' groups.delete -#' -#' groups.delete is a method defined in Arvados class. -#' -#' @usage arv$groups.delete(uuid) -#' @param uuid The UUID of the Group in question. -#' @return Group object. -#' @name groups.delete -NULL - -#' groups.contents -#' -#' groups.contents is a method defined in Arvados class. -#' -#' @usage arv$groups.contents(filters = NULL, -#' where = NULL, order = NULL, distinct = NULL, -#' limit = "100", offset = "0", count = "exact", -#' include_trash = NULL, uuid = NULL, recursive = NULL) -#' @param filters -#' @param where -#' @param order -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @param 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 -#' -#' groups.trash is a method defined in Arvados class. -#' -#' @usage arv$groups.trash(uuid) -#' @param uuid -#' @return Group object. -#' @name groups.trash -NULL - -#' groups.untrash -#' -#' groups.untrash is a method defined in Arvados class. -#' -#' @usage arv$groups.untrash(uuid) -#' @param uuid -#' @return Group object. -#' @name groups.untrash -NULL - -#' groups.list -#' -#' groups.list is a method defined in Arvados class. -#' -#' @usage arv$groups.list(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact", include_trash = NULL) -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @param include_trash Include items whose is_trashed attribute is true. -#' @return GroupList object. -#' @name groups.list -NULL - -#' user_agreements.get -#' -#' user_agreements.get is a method defined in Arvados class. -#' -#' @usage arv$user_agreements.get(uuid) -#' @param uuid The UUID of the UserAgreement in question. -#' @return UserAgreement object. -#' @name user_agreements.get -NULL - -#' user_agreements.create -#' -#' user_agreements.create is a method defined in Arvados class. -#' -#' @usage arv$user_agreements.create(useragreement, -#' ensure_unique_name = "false") -#' @param userAgreement UserAgreement object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return UserAgreement object. -#' @name user_agreements.create -NULL - -#' user_agreements.update -#' -#' user_agreements.update is a method defined in Arvados class. -#' -#' @usage arv$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 -#' -#' user_agreements.delete is a method defined in Arvados class. -#' -#' @usage arv$user_agreements.delete(uuid) -#' @param uuid The UUID of the UserAgreement in question. -#' @return UserAgreement object. -#' @name user_agreements.delete -NULL - -#' user_agreements.signatures -#' -#' user_agreements.signatures is a method defined in Arvados class. -#' -#' @usage arv$user_agreements.signatures(NULL) -#' @return UserAgreement object. -#' @name user_agreements.signatures -NULL - -#' user_agreements.sign -#' -#' user_agreements.sign is a method defined in Arvados class. -#' -#' @usage arv$user_agreements.sign(NULL) -#' @return UserAgreement object. -#' @name user_agreements.sign -NULL - -#' user_agreements.list -#' -#' user_agreements.list is a method defined in Arvados class. -#' -#' @usage arv$user_agreements.list(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return UserAgreementList object. -#' @name user_agreements.list -NULL - -#' user_agreements.new -#' -#' user_agreements.new is a method defined in Arvados class. -#' -#' @usage arv$user_agreements.new(NULL) -#' @return UserAgreement object. -#' @name user_agreements.new -NULL - -#' project.get -#' -#' projects.get is equivalent to groups.get method. -#' -#' @usage arv$projects.get(uuid) -#' @param uuid The UUID of the Group in question. -#' @return Group object. -#' @name projects.get -NULL - -#' project.create -#' -#' projects.create wrapps groups.create method by setting group_class attribute to "project". -#' -#' @usage arv$projects.create(group, ensure_unique_name = "false") -#' @param group Group object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return Group object. -#' @name projects.create -NULL - -#' project.update -#' -#' projects.update wrapps groups.update method by setting group_class attribute to "project". -#' -#' @usage arv$projects.update(group, uuid) -#' @param group Group object. -#' @param uuid The UUID of the Group in question. -#' @return Group object. -#' @name projects.update -NULL - -#' project.delete -#' -#' projects.delete is equivalent to groups.delete method. -#' -#' @usage arv$project.delete(uuid) -#' @param uuid The UUID of the Group in question. -#' @return Group object. -#' @name projects.delete -NULL - -#' project.list -#' -#' projects.list wrapps groups.list method by setting group_class attribute to "project". -#' -#' @usage arv$projects.list(filters = NULL, -#' where = NULL, order = NULL, distinct = NULL, -#' limit = "100", offset = "0", count = "exact", -#' include_trash = NULL, uuid = NULL, recursive = NULL) -#' @param filters -#' @param where -#' @param order -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @param include_trash Include items whose is_trashed attribute is true. -#' @param uuid -#' @param recursive Include contents from child groups recursively. -#' @return Group object. -#' @name projects.list -NULL - -#' Arvados -#' -#' Arvados class gives users ability to access Arvados REST API. -#' -#' @section Usage: -#' \preformatted{arv = Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)} -#' -#' @section Arguments: -#' \describe{ -#' \item{authToken}{Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.} -#' \item{hostName}{Host name. If not specified ARVADOS_API_HOST environment variable will be used.} -#' \item{numRetries}{Number which specifies how many times to retry failed service requests.} -#' } -#' -#' @section Methods: -#' \describe{ -#' \item{}{\code{\link{api_client_authorizations.create}}} -#' \item{}{\code{\link{api_client_authorizations.create_system_auth}}} -#' \item{}{\code{\link{api_client_authorizations.current}}} -#' \item{}{\code{\link{api_client_authorizations.delete}}} -#' \item{}{\code{\link{api_client_authorizations.get}}} -#' \item{}{\code{\link{api_client_authorizations.list}}} -#' \item{}{\code{\link{api_client_authorizations.update}}} -#' \item{}{\code{\link{api_clients.create}}} -#' \item{}{\code{\link{api_clients.delete}}} -#' \item{}{\code{\link{api_clients.get}}} -#' \item{}{\code{\link{api_clients.list}}} -#' \item{}{\code{\link{api_clients.update}}} -#' \item{}{\code{\link{authorized_keys.create}}} -#' \item{}{\code{\link{authorized_keys.delete}}} -#' \item{}{\code{\link{authorized_keys.get}}} -#' \item{}{\code{\link{authorized_keys.list}}} -#' \item{}{\code{\link{authorized_keys.update}}} -#' \item{}{\code{\link{collections.create}}} -#' \item{}{\code{\link{collections.delete}}} -#' \item{}{\code{\link{collections.get}}} -#' \item{}{\code{\link{collections.list}}} -#' \item{}{\code{\link{collections.provenance}}} -#' \item{}{\code{\link{collections.trash}}} -#' \item{}{\code{\link{collections.untrash}}} -#' \item{}{\code{\link{collections.update}}} -#' \item{}{\code{\link{collections.used_by}}} -#' \item{}{\code{\link{container_requests.create}}} -#' \item{}{\code{\link{container_requests.delete}}} -#' \item{}{\code{\link{container_requests.get}}} -#' \item{}{\code{\link{container_requests.list}}} -#' \item{}{\code{\link{container_requests.update}}} -#' \item{}{\code{\link{containers.auth}}} -#' \item{}{\code{\link{containers.create}}} -#' \item{}{\code{\link{containers.current}}} -#' \item{}{\code{\link{containers.delete}}} -#' \item{}{\code{\link{containers.get}}} -#' \item{}{\code{\link{containers.list}}} -#' \item{}{\code{\link{containers.lock}}} -#' \item{}{\code{\link{containers.secret_mounts}}} -#' \item{}{\code{\link{containers.unlock}}} -#' \item{}{\code{\link{containers.update}}} -#' \item{}{\code{\link{groups.contents}}} -#' \item{}{\code{\link{groups.create}}} -#' \item{}{\code{\link{groups.delete}}} -#' \item{}{\code{\link{groups.get}}} -#' \item{}{\code{\link{groups.list}}} -#' \item{}{\code{\link{groups.trash}}} -#' \item{}{\code{\link{groups.untrash}}} -#' \item{}{\code{\link{groups.update}}} -#' \item{}{\code{\link{humans.create}}} -#' \item{}{\code{\link{humans.delete}}} -#' \item{}{\code{\link{humans.get}}} -#' \item{}{\code{\link{humans.list}}} -#' \item{}{\code{\link{humans.update}}} -#' \item{}{\code{\link{jobs.cancel}}} -#' \item{}{\code{\link{jobs.create}}} -#' \item{}{\code{\link{jobs.delete}}} -#' \item{}{\code{\link{jobs.get}}} -#' \item{}{\code{\link{jobs.list}}} -#' \item{}{\code{\link{jobs.lock}}} -#' \item{}{\code{\link{jobs.queue}}} -#' \item{}{\code{\link{jobs.queue_size}}} -#' \item{}{\code{\link{jobs.update}}} -#' \item{}{\code{\link{job_tasks.create}}} -#' \item{}{\code{\link{job_tasks.delete}}} -#' \item{}{\code{\link{job_tasks.get}}} -#' \item{}{\code{\link{job_tasks.list}}} -#' \item{}{\code{\link{job_tasks.update}}} -#' \item{}{\code{\link{keep_disks.create}}} -#' \item{}{\code{\link{keep_disks.delete}}} -#' \item{}{\code{\link{keep_disks.get}}} -#' \item{}{\code{\link{keep_disks.list}}} -#' \item{}{\code{\link{keep_disks.ping}}} -#' \item{}{\code{\link{keep_disks.update}}} -#' \item{}{\code{\link{keep_services.accessible}}} -#' \item{}{\code{\link{keep_services.create}}} -#' \item{}{\code{\link{keep_services.delete}}} -#' \item{}{\code{\link{keep_services.get}}} -#' \item{}{\code{\link{keep_services.list}}} -#' \item{}{\code{\link{keep_services.update}}} -#' \item{}{\code{\link{links.create}}} -#' \item{}{\code{\link{links.delete}}} -#' \item{}{\code{\link{links.get}}} -#' \item{}{\code{\link{links.get_permissions}}} -#' \item{}{\code{\link{links.list}}} -#' \item{}{\code{\link{links.update}}} -#' \item{}{\code{\link{logs.create}}} -#' \item{}{\code{\link{logs.delete}}} -#' \item{}{\code{\link{logs.get}}} -#' \item{}{\code{\link{logs.list}}} -#' \item{}{\code{\link{logs.update}}} -#' \item{}{\code{\link{nodes.create}}} -#' \item{}{\code{\link{nodes.delete}}} -#' \item{}{\code{\link{nodes.get}}} -#' \item{}{\code{\link{nodes.list}}} -#' \item{}{\code{\link{nodes.ping}}} -#' \item{}{\code{\link{nodes.update}}} -#' \item{}{\code{\link{pipeline_instances.cancel}}} -#' \item{}{\code{\link{pipeline_instances.create}}} -#' \item{}{\code{\link{pipeline_instances.delete}}} -#' \item{}{\code{\link{pipeline_instances.get}}} -#' \item{}{\code{\link{pipeline_instances.list}}} -#' \item{}{\code{\link{pipeline_instances.update}}} -#' \item{}{\code{\link{pipeline_templates.create}}} -#' \item{}{\code{\link{pipeline_templates.delete}}} -#' \item{}{\code{\link{pipeline_templates.get}}} -#' \item{}{\code{\link{pipeline_templates.list}}} -#' \item{}{\code{\link{pipeline_templates.update}}} -#' \item{}{\code{\link{projects.create}}} -#' \item{}{\code{\link{projects.delete}}} -#' \item{}{\code{\link{projects.get}}} -#' \item{}{\code{\link{projects.list}}} -#' \item{}{\code{\link{projects.update}}} -#' \item{}{\code{\link{repositories.create}}} -#' \item{}{\code{\link{repositories.delete}}} -#' \item{}{\code{\link{repositories.get}}} -#' \item{}{\code{\link{repositories.get_all_permissions}}} -#' \item{}{\code{\link{repositories.list}}} -#' \item{}{\code{\link{repositories.update}}} -#' \item{}{\code{\link{specimens.create}}} -#' \item{}{\code{\link{specimens.delete}}} -#' \item{}{\code{\link{specimens.get}}} -#' \item{}{\code{\link{specimens.list}}} -#' \item{}{\code{\link{specimens.update}}} -#' \item{}{\code{\link{traits.create}}} -#' \item{}{\code{\link{traits.delete}}} -#' \item{}{\code{\link{traits.get}}} -#' \item{}{\code{\link{traits.list}}} -#' \item{}{\code{\link{traits.update}}} -#' \item{}{\code{\link{user_agreements.create}}} -#' \item{}{\code{\link{user_agreements.delete}}} -#' \item{}{\code{\link{user_agreements.get}}} -#' \item{}{\code{\link{user_agreements.list}}} -#' \item{}{\code{\link{user_agreements.new}}} -#' \item{}{\code{\link{user_agreements.sign}}} -#' \item{}{\code{\link{user_agreements.signatures}}} -#' \item{}{\code{\link{user_agreements.update}}} -#' \item{}{\code{\link{users.activate}}} -#' \item{}{\code{\link{users.create}}} -#' \item{}{\code{\link{users.current}}} -#' \item{}{\code{\link{users.delete}}} -#' \item{}{\code{\link{users.get}}} -#' \item{}{\code{\link{users.list}}} -#' \item{}{\code{\link{users.merge}}} -#' \item{}{\code{\link{users.setup}}} -#' \item{}{\code{\link{users.system}}} -#' \item{}{\code{\link{users.unsetup}}} -#' \item{}{\code{\link{users.update}}} -#' \item{}{\code{\link{users.update_uuid}}} -#' \item{}{\code{\link{virtual_machines.create}}} -#' \item{}{\code{\link{virtual_machines.delete}}} -#' \item{}{\code{\link{virtual_machines.get}}} -#' \item{}{\code{\link{virtual_machines.get_all_logins}}} -#' \item{}{\code{\link{virtual_machines.list}}} -#' \item{}{\code{\link{virtual_machines.logins}}} -#' \item{}{\code{\link{virtual_machines.update}}} -#' \item{}{\code{\link{workflows.create}}} -#' \item{}{\code{\link{workflows.delete}}} -#' \item{}{\code{\link{workflows.get}}} -#' \item{}{\code{\link{workflows.list}}} -#' \item{}{\code{\link{workflows.update}}} -#' } -#' -#' @name Arvados -#' @examples -#' \dontrun{ -#' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com") -#' -#' collection <- arv$collections.get("uuid") -#' -#' collectionList <- arv$collections.list(list(list("name", "like", "Test%"))) -#' collectionList <- listAll(arv$collections.list, list(list("name", "like", "Test%"))) -#' -#' deletedCollection <- arv$collections.delete("uuid") -#' -#' updatedCollection <- arv$collections.update(list(name = "New name", description = "New description"), -#' "uuid") -#' -#' createdCollection <- arv$collections.create(list(name = "Example", -#' description = "This is a test collection")) -#' } -NULL - -#' @export -Arvados <- R6::R6Class( - - "Arvados", - - public = list( - - initialize = function(authToken = NULL, hostName = NULL, numRetries = 0) - { - if(!is.null(hostName)) - Sys.setenv(ARVADOS_API_HOST = hostName) - - if(!is.null(authToken)) - Sys.setenv(ARVADOS_API_TOKEN = authToken) - - hostName <- Sys.getenv("ARVADOS_API_HOST") - token <- Sys.getenv("ARVADOS_API_TOKEN") - - if(hostName == "" | token == "") - stop(paste("Please provide host name and authentification token", - "or set ARVADOS_API_HOST and ARVADOS_API_TOKEN", - "environment variables.")) - - private$token <- token - private$host <- paste0("https://", hostName, "/arvados/v1/") - private$numRetries <- numRetries - private$REST <- RESTService$new(token, hostName, - HttpRequest$new(), HttpParser$new(), - numRetries) - - }, - - projects.get = function(uuid) - { - self$groups.get(uuid) - }, - - projects.create = function(group, ensure_unique_name = "false") - { - group <- c("group_class" = "project", group) - self$groups.create(group, ensure_unique_name) - }, - - projects.update = function(group, uuid) - { - group <- c("group_class" = "project", group) - self$groups.update(group, uuid) - }, - - projects.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$groups.list(filters, where, order, select, distinct, - limit, offset, count, include_trash) - }, - - projects.delete = function(uuid) - { - self$groups.delete(uuid) - }, - - users.get = function(uuid) - { - endPoint <- stringr::str_interp("users/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.create = function(user, ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("users") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(user) > 0) - body <- jsonlite::toJSON(list(user = user), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.update = function(user, uuid) - { - endPoint <- stringr::str_interp("users/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(user) > 0) - body <- jsonlite::toJSON(list(user = user), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$REST$http$exec("PUT", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.delete = function(uuid) - { - endPoint <- stringr::str_interp("users/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.current = function() - { - endPoint <- stringr::str_interp("users/current") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.system = function() - { - endPoint <- stringr::str_interp("users/system") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.activate = function(uuid) - { - endPoint <- stringr::str_interp("users/${uuid}/activate") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.setup = function(user = NULL, openid_prefix = NULL, - repo_name = NULL, vm_uuid = NULL, send_notification_email = "false") - { - endPoint <- stringr::str_interp("users/setup") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(user = user, openid_prefix = openid_prefix, - repo_name = repo_name, vm_uuid = vm_uuid, - send_notification_email = send_notification_email) - - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.unsetup = function(uuid) - { - endPoint <- stringr::str_interp("users/${uuid}/unsetup") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.update_uuid = function(uuid, new_uuid) - { - endPoint <- stringr::str_interp("users/${uuid}/update_uuid") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(new_uuid = new_uuid) - - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.merge = function(new_owner_uuid, new_user_token, - redirect_to_new_user = NULL) - { - endPoint <- stringr::str_interp("users/merge") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(new_owner_uuid = new_owner_uuid, - new_user_token = new_user_token, redirect_to_new_user = redirect_to_new_user) - - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.list = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("users") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_client_authorizations.get = function(uuid) - { - endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_client_authorizations.create = function(apiclientauthorization, - ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("api_client_authorizations") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(apiclientauthorization) > 0) - body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_client_authorizations.update = function(apiclientauthorization, uuid) - { - endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(apiclientauthorization) > 0) - body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$REST$http$exec("PUT", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_client_authorizations.delete = function(uuid) - { - endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_client_authorizations.create_system_auth = function(api_client_id = NULL, scopes = NULL) - { - endPoint <- stringr::str_interp("api_client_authorizations/create_system_auth") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(api_client_id = api_client_id, - scopes = scopes) - - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_client_authorizations.current = function() - { - endPoint <- stringr::str_interp("api_client_authorizations/current") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_client_authorizations.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - endPoint <- stringr::str_interp("api_client_authorizations") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - containers.get = function(uuid) - { - endPoint <- stringr::str_interp("containers/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - containers.create = function(container, ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("containers") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(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) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - containers.update = function(container, uuid) - { - endPoint <- stringr::str_interp("containers/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(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) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - containers.delete = function(uuid) - { - endPoint <- stringr::str_interp("containers/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - containers.auth = function(uuid) - { - endPoint <- stringr::str_interp("containers/${uuid}/auth") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - containers.lock = function(uuid) - { - endPoint <- stringr::str_interp("containers/${uuid}/lock") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - containers.unlock = function(uuid) - { - endPoint <- stringr::str_interp("containers/${uuid}/unlock") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - containers.secret_mounts = function(uuid) - { - endPoint <- stringr::str_interp("containers/${uuid}/secret_mounts") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - containers.current = function() - { - endPoint <- stringr::str_interp("containers/current") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - containers.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - 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) - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_clients.get = function(uuid) - { - endPoint <- stringr::str_interp("api_clients/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_clients.create = function(apiclient, ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("api_clients") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(apiclient) > 0) - body <- jsonlite::toJSON(list(apiclient = apiclient), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_clients.update = function(apiclient, uuid) - { - endPoint <- stringr::str_interp("api_clients/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(apiclient) > 0) - body <- jsonlite::toJSON(list(apiclient = apiclient), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$REST$http$exec("PUT", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_clients.delete = function(uuid) - { - endPoint <- stringr::str_interp("api_clients/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, +#' Arvados +#' +#' Arvados class gives users ability to access Arvados REST API. +#' +#' @section Usage: +#' \preformatted{arv = Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)} +#' +#' @section Arguments: +#' \describe{ +#' \item{authToken}{Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.} +#' \item{hostName}{Host name. If not specified ARVADOS_API_HOST environment variable will be used.} +#' \item{numRetries}{Number which specifies how many times to retry failed service requests.} +#' } +#' +#' @section Methods: +#' \describe{ +#' \item{}{\code{\link{api_client_authorizations.create}}} +#' \item{}{\code{\link{api_client_authorizations.create_system_auth}}} +#' \item{}{\code{\link{api_client_authorizations.current}}} +#' \item{}{\code{\link{api_client_authorizations.delete}}} +#' \item{}{\code{\link{api_client_authorizations.get}}} +#' \item{}{\code{\link{api_client_authorizations.list}}} +#' \item{}{\code{\link{api_client_authorizations.update}}} +#' \item{}{\code{\link{api_clients.create}}} +#' \item{}{\code{\link{api_clients.delete}}} +#' \item{}{\code{\link{api_clients.get}}} +#' \item{}{\code{\link{api_clients.list}}} +#' \item{}{\code{\link{api_clients.update}}} +#' \item{}{\code{\link{authorized_keys.create}}} +#' \item{}{\code{\link{authorized_keys.delete}}} +#' \item{}{\code{\link{authorized_keys.get}}} +#' \item{}{\code{\link{authorized_keys.list}}} +#' \item{}{\code{\link{authorized_keys.update}}} +#' \item{}{\code{\link{collections.create}}} +#' \item{}{\code{\link{collections.delete}}} +#' \item{}{\code{\link{collections.get}}} +#' \item{}{\code{\link{collections.list}}} +#' \item{}{\code{\link{collections.provenance}}} +#' \item{}{\code{\link{collections.trash}}} +#' \item{}{\code{\link{collections.untrash}}} +#' \item{}{\code{\link{collections.update}}} +#' \item{}{\code{\link{collections.used_by}}} +#' \item{}{\code{\link{configs.get}}} +#' \item{}{\code{\link{container_requests.create}}} +#' \item{}{\code{\link{container_requests.delete}}} +#' \item{}{\code{\link{container_requests.get}}} +#' \item{}{\code{\link{container_requests.list}}} +#' \item{}{\code{\link{container_requests.update}}} +#' \item{}{\code{\link{containers.auth}}} +#' \item{}{\code{\link{containers.create}}} +#' \item{}{\code{\link{containers.current}}} +#' \item{}{\code{\link{containers.delete}}} +#' \item{}{\code{\link{containers.get}}} +#' \item{}{\code{\link{containers.list}}} +#' \item{}{\code{\link{containers.lock}}} +#' \item{}{\code{\link{containers.secret_mounts}}} +#' \item{}{\code{\link{containers.unlock}}} +#' \item{}{\code{\link{containers.update}}} +#' \item{}{\code{\link{groups.contents}}} +#' \item{}{\code{\link{groups.create}}} +#' \item{}{\code{\link{groups.delete}}} +#' \item{}{\code{\link{groups.get}}} +#' \item{}{\code{\link{groups.list}}} +#' \item{}{\code{\link{groups.shared}}} +#' \item{}{\code{\link{groups.trash}}} +#' \item{}{\code{\link{groups.untrash}}} +#' \item{}{\code{\link{groups.update}}} +#' \item{}{\code{\link{keep_services.accessible}}} +#' \item{}{\code{\link{keep_services.create}}} +#' \item{}{\code{\link{keep_services.delete}}} +#' \item{}{\code{\link{keep_services.get}}} +#' \item{}{\code{\link{keep_services.list}}} +#' \item{}{\code{\link{keep_services.update}}} +#' \item{}{\code{\link{links.create}}} +#' \item{}{\code{\link{links.delete}}} +#' \item{}{\code{\link{links.get}}} +#' \item{}{\code{\link{links.get_permissions}}} +#' \item{}{\code{\link{links.list}}} +#' \item{}{\code{\link{links.update}}} +#' \item{}{\code{\link{logs.create}}} +#' \item{}{\code{\link{logs.delete}}} +#' \item{}{\code{\link{logs.get}}} +#' \item{}{\code{\link{logs.list}}} +#' \item{}{\code{\link{logs.update}}} +#' \item{}{\code{\link{projects.create}}} +#' \item{}{\code{\link{projects.delete}}} +#' \item{}{\code{\link{projects.get}}} +#' \item{}{\code{\link{projects.list}}} +#' \item{}{\code{\link{projects.update}}} +#' \item{}{\code{\link{repositories.create}}} +#' \item{}{\code{\link{repositories.delete}}} +#' \item{}{\code{\link{repositories.get}}} +#' \item{}{\code{\link{repositories.get_all_permissions}}} +#' \item{}{\code{\link{repositories.list}}} +#' \item{}{\code{\link{repositories.update}}} +#' \item{}{\code{\link{user_agreements.create}}} +#' \item{}{\code{\link{user_agreements.delete}}} +#' \item{}{\code{\link{user_agreements.get}}} +#' \item{}{\code{\link{user_agreements.list}}} +#' \item{}{\code{\link{user_agreements.new}}} +#' \item{}{\code{\link{user_agreements.sign}}} +#' \item{}{\code{\link{user_agreements.signatures}}} +#' \item{}{\code{\link{user_agreements.update}}} +#' \item{}{\code{\link{users.activate}}} +#' \item{}{\code{\link{users.create}}} +#' \item{}{\code{\link{users.current}}} +#' \item{}{\code{\link{users.delete}}} +#' \item{}{\code{\link{users.get}}} +#' \item{}{\code{\link{users.list}}} +#' \item{}{\code{\link{users.merge}}} +#' \item{}{\code{\link{users.setup}}} +#' \item{}{\code{\link{users.system}}} +#' \item{}{\code{\link{users.unsetup}}} +#' \item{}{\code{\link{users.update}}} +#' \item{}{\code{\link{users.update_uuid}}} +#' \item{}{\code{\link{virtual_machines.create}}} +#' \item{}{\code{\link{virtual_machines.delete}}} +#' \item{}{\code{\link{virtual_machines.get}}} +#' \item{}{\code{\link{virtual_machines.get_all_logins}}} +#' \item{}{\code{\link{virtual_machines.list}}} +#' \item{}{\code{\link{virtual_machines.logins}}} +#' \item{}{\code{\link{virtual_machines.update}}} +#' \item{}{\code{\link{workflows.create}}} +#' \item{}{\code{\link{workflows.delete}}} +#' \item{}{\code{\link{workflows.get}}} +#' \item{}{\code{\link{workflows.list}}} +#' \item{}{\code{\link{workflows.update}}} +#' } +#' +#' @name Arvados +#' @examples +#' \dontrun{ +#' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com") +#' +#' collection <- arv$collections.get("uuid") +#' +#' collectionList <- arv$collections.list(list(list("name", "like", "Test%"))) +#' collectionList <- listAll(arv$collections.list, list(list("name", "like", "Test%"))) +#' +#' deletedCollection <- arv$collections.delete("uuid") +#' +#' updatedCollection <- arv$collections.update(list(name = "New name", description = "New description"), +#' "uuid") +#' +#' createdCollection <- arv$collections.create(list(name = "Example", +#' description = "This is a test collection")) +#' } +NULL - api_clients.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - endPoint <- stringr::str_interp("api_clients") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, +#' @export +Arvados <- R6::R6Class( - container_requests.get = function(uuid) - { - endPoint <- stringr::str_interp("container_requests/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, + "Arvados", - container_requests.create = function(containerrequest, - ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("container_requests") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(containerrequest) > 0) - body <- jsonlite::toJSON(list(containerrequest = containerrequest), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, + public = list( - container_requests.update = function(containerrequest, uuid) + initialize = function(authToken = NULL, hostName = NULL, numRetries = 0) { - endPoint <- stringr::str_interp("container_requests/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(containerrequest) > 0) - body <- jsonlite::toJSON(list(containerrequest = containerrequest), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$REST$http$exec("PUT", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, + if(!is.null(hostName)) + Sys.setenv(ARVADOS_API_HOST = hostName) - container_requests.delete = function(uuid) - { - endPoint <- stringr::str_interp("container_requests/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, + if(!is.null(authToken)) + Sys.setenv(ARVADOS_API_TOKEN = authToken) + + hostName <- Sys.getenv("ARVADOS_API_HOST") + token <- Sys.getenv("ARVADOS_API_TOKEN") + + if(hostName == "" | token == "") + stop(paste("Please provide host name and authentification token", + "or set ARVADOS_API_HOST and ARVADOS_API_TOKEN", + "environment variables.")) + + private$token <- token + private$host <- paste0("https://", hostName, "/arvados/v1/") + private$numRetries <- numRetries + private$REST <- RESTService$new(token, hostName, + HttpRequest$new(), HttpParser$new(), + numRetries) - container_requests.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - endPoint <- stringr::str_interp("container_requests") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource }, - authorized_keys.get = function(uuid) + projects.get = function(uuid) { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource + self$groups.get(uuid) }, - authorized_keys.create = function(authorizedkey, - ensure_unique_name = "false") + projects.create = function(group, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("authorized_keys") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(authorizedkey) > 0) - body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource + group <- c("group_class" = "project", group) + self$groups.create(group, ensure_unique_name) }, - authorized_keys.update = function(authorizedkey, uuid) + projects.update = function(group, uuid) { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(authorizedkey) > 0) - body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$REST$http$exec("PUT", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource + group <- c("group_class" = "project", group) + self$groups.update(group, uuid) }, - authorized_keys.delete = function(uuid) + projects.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact", + include_trash = NULL) { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource + filters[[length(filters) + 1]] <- list("group_class", "=", "project") + self$groups.list(filters, where, order, select, distinct, + limit, offset, count, include_trash) }, - authorized_keys.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - endPoint <- stringr::str_interp("authorized_keys") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource + projects.delete = function(uuid) + { + self$groups.delete(uuid) }, - collections.get = function(uuid) + api_clients.get = function(uuid) { - endPoint <- stringr::str_interp("collections/${uuid}") + endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -3229,16 +1656,18 @@ Arvados <- R6::R6Class( resource }, - collections.create = function(collection, ensure_unique_name = "false") + api_clients.create = function(apiclient, + ensure_unique_name = "false", cluster_id = NULL) { - endPoint <- stringr::str_interp("collections") + endPoint <- stringr::str_interp("api_clients") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- list(ensure_unique_name = ensure_unique_name, + cluster_id = cluster_id) - if(length(collection) > 0) - body <- jsonlite::toJSON(list(collection = collection), + if(length(apiclient) > 0) + body <- jsonlite::toJSON(list(apiclient = apiclient), auto_unbox = TRUE) else body <- NULL @@ -3253,16 +1682,16 @@ Arvados <- R6::R6Class( resource }, - collections.update = function(collection, uuid) + api_clients.update = function(apiclient, uuid) { - endPoint <- stringr::str_interp("collections/${uuid}") + endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(collection) > 0) - body <- jsonlite::toJSON(list(collection = collection), + if(length(apiclient) > 0) + body <- jsonlite::toJSON(list(apiclient = apiclient), auto_unbox = TRUE) else body <- NULL @@ -3277,11 +1706,11 @@ Arvados <- R6::R6Class( resource }, - collections.delete = function(uuid) + api_clients.delete = function(uuid) { - endPoint <- stringr::str_interp("collections/${uuid}") + endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -3297,13 +1726,19 @@ Arvados <- R6::R6Class( resource }, - collections.provenance = function(uuid) + api_clients.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact", cluster_id = NULL, bypass_federation = NULL) { - endPoint <- stringr::str_interp("collections/${uuid}/provenance") + endPoint <- stringr::str_interp("api_clients") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count, + cluster_id = cluster_id, bypass_federation = bypass_federation) body <- NULL @@ -3317,11 +1752,11 @@ Arvados <- R6::R6Class( resource }, - collections.used_by = function(uuid) + api_client_authorizations.get = function(uuid) { - endPoint <- stringr::str_interp("collections/${uuid}/used_by") + endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -3337,15 +1772,21 @@ Arvados <- R6::R6Class( resource }, - collections.trash = function(uuid) + api_client_authorizations.create = function(apiclientauthorization, + ensure_unique_name = "false", cluster_id = NULL) { - endPoint <- stringr::str_interp("collections/${uuid}/trash") + endPoint <- stringr::str_interp("api_client_authorizations") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name, + cluster_id = cluster_id) - body <- NULL + 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) @@ -3357,43 +1798,21 @@ Arvados <- R6::R6Class( resource }, - collections.untrash = function(uuid) + api_client_authorizations.update = function(apiclientauthorization, uuid) { - endPoint <- stringr::str_interp("collections/${uuid}/untrash") + endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - collections.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact", include_trash = NULL) - { - endPoint <- stringr::str_interp("collections") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count, - include_trash = include_trash) - - body <- NULL + if(length(apiclientauthorization) > 0) + body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -3403,17 +1822,17 @@ Arvados <- R6::R6Class( resource }, - humans.get = function(uuid) + api_client_authorizations.delete = function(uuid) { - endPoint <- stringr::str_interp("humans/${uuid}") + endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -3423,19 +1842,16 @@ Arvados <- R6::R6Class( resource }, - humans.create = function(human, ensure_unique_name = "false") + api_client_authorizations.create_system_auth = function(api_client_id = NULL, scopes = NULL) { - endPoint <- stringr::str_interp("humans") + endPoint <- stringr::str_interp("api_client_authorizations/create_system_auth") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- list(api_client_id = api_client_id, + scopes = scopes) - if(length(human) > 0) - body <- jsonlite::toJSON(list(human = human), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -3447,41 +1863,17 @@ Arvados <- R6::R6Class( resource }, - humans.update = function(human, uuid) - { - endPoint <- stringr::str_interp("humans/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(human) > 0) - body <- jsonlite::toJSON(list(human = human), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$REST$http$exec("PUT", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - humans.delete = function(uuid) + api_client_authorizations.current = function() { - endPoint <- stringr::str_interp("humans/${uuid}") + endPoint <- stringr::str_interp("api_client_authorizations/current") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -3491,17 +1883,19 @@ Arvados <- R6::R6Class( resource }, - humans.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", cluster_id = NULL, bypass_federation = NULL) { - endPoint <- stringr::str_interp("humans") + endPoint <- stringr::str_interp("api_client_authorizations") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + limit = limit, offset = offset, count = count, + cluster_id = cluster_id, bypass_federation = bypass_federation) body <- NULL @@ -3515,11 +1909,11 @@ Arvados <- R6::R6Class( resource }, - job_tasks.get = function(uuid) + authorized_keys.get = function(uuid) { - endPoint <- stringr::str_interp("job_tasks/${uuid}") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -3535,16 +1929,18 @@ Arvados <- R6::R6Class( resource }, - job_tasks.create = function(jobtask, ensure_unique_name = "false") + authorized_keys.create = function(authorizedkey, + ensure_unique_name = "false", cluster_id = NULL) { - endPoint <- stringr::str_interp("job_tasks") + endPoint <- stringr::str_interp("authorized_keys") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- list(ensure_unique_name = ensure_unique_name, + cluster_id = cluster_id) - if(length(jobtask) > 0) - body <- jsonlite::toJSON(list(jobtask = jobtask), + if(length(authorizedkey) > 0) + body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), auto_unbox = TRUE) else body <- NULL @@ -3559,16 +1955,16 @@ Arvados <- R6::R6Class( resource }, - job_tasks.update = function(jobtask, uuid) + authorized_keys.update = function(authorizedkey, uuid) { - endPoint <- stringr::str_interp("job_tasks/${uuid}") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(jobtask) > 0) - body <- jsonlite::toJSON(list(jobtask = jobtask), + if(length(authorizedkey) > 0) + body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), auto_unbox = TRUE) else body <- NULL @@ -3583,11 +1979,11 @@ Arvados <- R6::R6Class( resource }, - job_tasks.delete = function(uuid) + authorized_keys.delete = function(uuid) { - endPoint <- stringr::str_interp("job_tasks/${uuid}") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -3603,18 +1999,19 @@ Arvados <- R6::R6Class( resource }, - job_tasks.list = function(filters = NULL, + authorized_keys.list = function(filters = NULL, where = NULL, order = NULL, select = NULL, distinct = NULL, limit = "100", offset = "0", - count = "exact") + count = "exact", cluster_id = NULL, bypass_federation = NULL) { - endPoint <- stringr::str_interp("job_tasks") + endPoint <- stringr::str_interp("authorized_keys") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + limit = limit, offset = offset, count = count, + cluster_id = cluster_id, bypass_federation = bypass_federation) body <- NULL @@ -3628,11 +2025,11 @@ Arvados <- R6::R6Class( resource }, - jobs.get = function(uuid) + collections.get = function(uuid) { - endPoint <- stringr::str_interp("jobs/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -3648,21 +2045,18 @@ Arvados <- R6::R6Class( resource }, - jobs.create = function(job, ensure_unique_name = "false", - find_or_create = "false", filters = NULL, - minimum_script_version = NULL, exclude_script_versions = NULL) + collections.create = function(collection, + ensure_unique_name = "false", cluster_id = NULL) { - endPoint <- stringr::str_interp("jobs") + endPoint <- stringr::str_interp("collections") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$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) + cluster_id = cluster_id) - if(length(job) > 0) - body <- jsonlite::toJSON(list(job = job), + if(length(collection) > 0) + body <- jsonlite::toJSON(list(collection = collection), auto_unbox = TRUE) else body <- NULL @@ -3677,16 +2071,16 @@ Arvados <- R6::R6Class( resource }, - jobs.update = function(job, uuid) + collections.update = function(collection, uuid) { - endPoint <- stringr::str_interp("jobs/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(job) > 0) - body <- jsonlite::toJSON(list(job = job), + if(length(collection) > 0) + body <- jsonlite::toJSON(list(collection = collection), auto_unbox = TRUE) else body <- NULL @@ -3701,11 +2095,11 @@ Arvados <- R6::R6Class( resource }, - jobs.delete = function(uuid) + collections.delete = function(uuid) { - endPoint <- stringr::str_interp("jobs/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -3721,17 +2115,13 @@ Arvados <- R6::R6Class( resource }, - jobs.queue = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + collections.provenance = function(uuid) { - endPoint <- stringr::str_interp("jobs/queue") + endPoint <- stringr::str_interp("collections/${uuid}/provenance") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$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 @@ -3745,11 +2135,11 @@ Arvados <- R6::R6Class( resource }, - jobs.queue_size = function() + collections.used_by = function(uuid) { - endPoint <- stringr::str_interp("jobs/queue_size") + endPoint <- stringr::str_interp("collections/${uuid}/used_by") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -3765,11 +2155,11 @@ Arvados <- R6::R6Class( resource }, - jobs.cancel = function(uuid) + collections.trash = function(uuid) { - endPoint <- stringr::str_interp("jobs/${uuid}/cancel") + endPoint <- stringr::str_interp("collections/${uuid}/trash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -3785,11 +2175,11 @@ Arvados <- R6::R6Class( resource }, - jobs.lock = function(uuid) + collections.untrash = function(uuid) { - endPoint <- stringr::str_interp("jobs/${uuid}/lock") + endPoint <- stringr::str_interp("collections/${uuid}/untrash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -3805,17 +2195,21 @@ Arvados <- R6::R6Class( resource }, - jobs.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", cluster_id = NULL, bypass_federation = NULL, + include_trash = NULL, include_old_versions = NULL) { - endPoint <- stringr::str_interp("jobs") + endPoint <- stringr::str_interp("collections") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + limit = limit, offset = offset, count = count, + cluster_id = cluster_id, bypass_federation = bypass_federation, + include_trash = include_trash, include_old_versions = include_old_versions) body <- NULL @@ -3829,11 +2223,11 @@ Arvados <- R6::R6Class( resource }, - keep_disks.get = function(uuid) + containers.get = function(uuid) { - endPoint <- stringr::str_interp("keep_disks/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -3849,16 +2243,18 @@ Arvados <- R6::R6Class( resource }, - keep_disks.create = function(keepdisk, ensure_unique_name = "false") + containers.create = function(container, ensure_unique_name = "false", + cluster_id = NULL) { - endPoint <- stringr::str_interp("keep_disks") + endPoint <- stringr::str_interp("containers") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- list(ensure_unique_name = ensure_unique_name, + cluster_id = cluster_id) - if(length(keepdisk) > 0) - body <- jsonlite::toJSON(list(keepdisk = keepdisk), + if(length(container) > 0) + body <- jsonlite::toJSON(list(container = container), auto_unbox = TRUE) else body <- NULL @@ -3873,16 +2269,16 @@ Arvados <- R6::R6Class( resource }, - keep_disks.update = function(keepdisk, uuid) + containers.update = function(container, uuid) { - endPoint <- stringr::str_interp("keep_disks/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(keepdisk) > 0) - body <- jsonlite::toJSON(list(keepdisk = keepdisk), + if(length(container) > 0) + body <- jsonlite::toJSON(list(container = container), auto_unbox = TRUE) else body <- NULL @@ -3897,11 +2293,11 @@ Arvados <- R6::R6Class( resource }, - keep_disks.delete = function(uuid) + containers.delete = function(uuid) { - endPoint <- stringr::str_interp("keep_disks/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -3917,43 +2313,13 @@ Arvados <- R6::R6Class( resource }, - keep_disks.ping = function(uuid = NULL, ping_secret, - node_uuid = NULL, filesystem_uuid = NULL, - service_host = NULL, service_port, service_ssl_flag) - { - endPoint <- stringr::str_interp("keep_disks/ping") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid, ping_secret = ping_secret, - node_uuid = node_uuid, filesystem_uuid = filesystem_uuid, - service_host = service_host, service_port = service_port, - service_ssl_flag = service_ssl_flag) - - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - keep_disks.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("keep_disks") + endPoint <- stringr::str_interp("containers/${uuid}/auth") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$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 @@ -3967,42 +2333,16 @@ Arvados <- R6::R6Class( resource }, - nodes.get = function(uuid) + containers.lock = function(uuid) { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}/lock") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - nodes.create = function(node, ensure_unique_name = "false", - assign_slot = NULL) - { - endPoint <- stringr::str_interp("nodes") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name, - assign_slot = assign_slot) - - if(length(node) > 0) - body <- jsonlite::toJSON(list(node = node), - auto_unbox = TRUE) - else - body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4013,21 +2353,17 @@ Arvados <- R6::R6Class( resource }, - nodes.update = function(node, uuid, assign_slot = NULL) + containers.unlock = function(uuid) { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}/unlock") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(assign_slot = assign_slot) + queryArgs <- NULL - if(length(node) > 0) - body <- jsonlite::toJSON(list(node = node), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4037,17 +2373,17 @@ Arvados <- R6::R6Class( resource }, - nodes.delete = function(uuid) + containers.secret_mounts = function(uuid) { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}/secret_mounts") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4057,17 +2393,17 @@ Arvados <- R6::R6Class( resource }, - nodes.ping = function(uuid, ping_secret) + containers.current = function() { - endPoint <- stringr::str_interp("nodes/${uuid}/ping") + endPoint <- stringr::str_interp("containers/current") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(ping_secret = ping_secret) + queryArgs <- NULL body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4077,17 +2413,19 @@ Arvados <- R6::R6Class( resource }, - nodes.list = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + containers.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact", cluster_id = NULL, bypass_federation = NULL) { - endPoint <- stringr::str_interp("nodes") + endPoint <- stringr::str_interp("containers") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + limit = limit, offset = offset, count = count, + cluster_id = cluster_id, bypass_federation = bypass_federation) body <- NULL @@ -4101,11 +2439,11 @@ Arvados <- R6::R6Class( resource }, - links.get = function(uuid) + container_requests.get = function(uuid) { - endPoint <- stringr::str_interp("links/${uuid}") + endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -4121,16 +2459,18 @@ Arvados <- R6::R6Class( resource }, - links.create = function(link, ensure_unique_name = "false") + container_requests.create = function(containerrequest, + ensure_unique_name = "false", cluster_id = NULL) { - endPoint <- stringr::str_interp("links") + endPoint <- stringr::str_interp("container_requests") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- list(ensure_unique_name = ensure_unique_name, + cluster_id = cluster_id) - if(length(link) > 0) - body <- jsonlite::toJSON(list(link = link), + if(length(containerrequest) > 0) + body <- jsonlite::toJSON(list(containerrequest = containerrequest), auto_unbox = TRUE) else body <- NULL @@ -4145,16 +2485,16 @@ Arvados <- R6::R6Class( resource }, - links.update = function(link, uuid) + container_requests.update = function(containerrequest, uuid) { - endPoint <- stringr::str_interp("links/${uuid}") + endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(link) > 0) - body <- jsonlite::toJSON(list(link = link), + if(length(containerrequest) > 0) + body <- jsonlite::toJSON(list(containerrequest = containerrequest), auto_unbox = TRUE) else body <- NULL @@ -4169,11 +2509,11 @@ Arvados <- R6::R6Class( resource }, - links.delete = function(uuid) + container_requests.delete = function(uuid) { - endPoint <- stringr::str_interp("links/${uuid}") + endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -4189,37 +2529,21 @@ Arvados <- R6::R6Class( resource }, - links.list = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + container_requests.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact", cluster_id = NULL, bypass_federation = NULL, + include_trash = NULL) { - endPoint <- stringr::str_interp("links") + endPoint <- stringr::str_interp("container_requests") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - links.get_permissions = function(uuid) - { - endPoint <- stringr::str_interp("permissions/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL + limit = limit, offset = offset, count = count, + cluster_id = cluster_id, bypass_federation = bypass_federation, + include_trash = include_trash) body <- NULL @@ -4233,11 +2557,11 @@ Arvados <- R6::R6Class( resource }, - keep_services.get = function(uuid) + groups.get = function(uuid) { - endPoint <- stringr::str_interp("keep_services/${uuid}") + endPoint <- stringr::str_interp("groups/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -4253,17 +2577,18 @@ Arvados <- R6::R6Class( resource }, - keep_services.create = function(keepservice, - ensure_unique_name = "false") + groups.create = function(group, ensure_unique_name = "false", + cluster_id = NULL, async = "false") { - endPoint <- stringr::str_interp("keep_services") + endPoint <- stringr::str_interp("groups") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- list(ensure_unique_name = ensure_unique_name, + cluster_id = cluster_id, async = async) - if(length(keepservice) > 0) - body <- jsonlite::toJSON(list(keepservice = keepservice), + if(length(group) > 0) + body <- jsonlite::toJSON(list(group = group), auto_unbox = TRUE) else body <- NULL @@ -4278,16 +2603,16 @@ Arvados <- R6::R6Class( resource }, - keep_services.update = function(keepservice, uuid) + groups.update = function(group, uuid, async = "false") { - endPoint <- stringr::str_interp("keep_services/${uuid}") + endPoint <- stringr::str_interp("groups/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(async = async) - if(length(keepservice) > 0) - body <- jsonlite::toJSON(list(keepservice = keepservice), + if(length(group) > 0) + body <- jsonlite::toJSON(list(group = group), auto_unbox = TRUE) else body <- NULL @@ -4302,11 +2627,11 @@ Arvados <- R6::R6Class( resource }, - keep_services.delete = function(uuid) + groups.delete = function(uuid) { - endPoint <- stringr::str_interp("keep_services/${uuid}") + endPoint <- stringr::str_interp("groups/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -4322,13 +2647,22 @@ Arvados <- R6::R6Class( resource }, - keep_services.accessible = function() + groups.contents = function(filters = NULL, + where = NULL, order = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact", + cluster_id = NULL, bypass_federation = NULL, + include_trash = NULL, uuid = NULL, recursive = NULL, + include = NULL) { - endPoint <- stringr::str_interp("keep_services/accessible") + endPoint <- stringr::str_interp("groups/contents") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, distinct = distinct, limit = limit, + offset = offset, count = count, cluster_id = cluster_id, + bypass_federation = bypass_federation, include_trash = include_trash, + uuid = uuid, recursive = recursive, include = include) body <- NULL @@ -4342,18 +2676,21 @@ Arvados <- R6::R6Class( resource }, - keep_services.list = function(filters = NULL, + groups.shared = function(filters = NULL, where = NULL, order = NULL, select = NULL, distinct = NULL, limit = "100", offset = "0", - count = "exact") + count = "exact", cluster_id = NULL, bypass_federation = NULL, + include_trash = NULL, include = NULL) { - endPoint <- stringr::str_interp("keep_services") + endPoint <- stringr::str_interp("groups/shared") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + limit = limit, offset = offset, count = count, + cluster_id = cluster_id, bypass_federation = bypass_federation, + include_trash = include_trash, include = include) body <- NULL @@ -4367,41 +2704,16 @@ Arvados <- R6::R6Class( resource }, - pipeline_templates.get = function(uuid) + groups.trash = function(uuid) { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") + endPoint <- stringr::str_interp("groups/${uuid}/trash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - pipeline_templates.create = function(pipelinetemplate, - ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("pipeline_templates") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(pipelinetemplate) > 0) - body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), - auto_unbox = TRUE) - else - body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4412,41 +2724,17 @@ Arvados <- R6::R6Class( resource }, - pipeline_templates.update = function(pipelinetemplate, uuid) - { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(pipelinetemplate) > 0) - body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$REST$http$exec("PUT", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - pipeline_templates.delete = function(uuid) + groups.untrash = function(uuid) { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") + endPoint <- stringr::str_interp("groups/${uuid}/untrash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4456,18 +2744,21 @@ Arvados <- R6::R6Class( resource }, - pipeline_templates.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + groups.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact", + cluster_id = NULL, bypass_federation = NULL, + include_trash = NULL) { - endPoint <- stringr::str_interp("pipeline_templates") + endPoint <- stringr::str_interp("groups") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + limit = limit, offset = offset, count = count, + cluster_id = cluster_id, bypass_federation = bypass_federation, + include_trash = include_trash) body <- NULL @@ -4481,11 +2772,11 @@ Arvados <- R6::R6Class( resource }, - pipeline_instances.get = function(uuid) + keep_services.get = function(uuid) { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") + endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -4501,17 +2792,18 @@ Arvados <- R6::R6Class( resource }, - pipeline_instances.create = function(pipelineinstance, - ensure_unique_name = "false") + keep_services.create = function(keepservice, + ensure_unique_name = "false", cluster_id = NULL) { - endPoint <- stringr::str_interp("pipeline_instances") + endPoint <- stringr::str_interp("keep_services") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- list(ensure_unique_name = ensure_unique_name, + cluster_id = cluster_id) - if(length(pipelineinstance) > 0) - body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), + if(length(keepservice) > 0) + body <- jsonlite::toJSON(list(keepservice = keepservice), auto_unbox = TRUE) else body <- NULL @@ -4526,16 +2818,16 @@ Arvados <- R6::R6Class( resource }, - pipeline_instances.update = function(pipelineinstance, uuid) + keep_services.update = function(keepservice, uuid) { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") + endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(pipelineinstance) > 0) - body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), + if(length(keepservice) > 0) + body <- jsonlite::toJSON(list(keepservice = keepservice), auto_unbox = TRUE) else body <- NULL @@ -4550,11 +2842,11 @@ Arvados <- R6::R6Class( resource }, - pipeline_instances.delete = function(uuid) + keep_services.delete = function(uuid) { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") + endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -4570,17 +2862,17 @@ Arvados <- R6::R6Class( resource }, - pipeline_instances.cancel = function(uuid) + keep_services.accessible = function() { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}/cancel") + endPoint <- stringr::str_interp("keep_services/accessible") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") 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) @@ -4590,18 +2882,19 @@ Arvados <- R6::R6Class( resource }, - pipeline_instances.list = function(filters = NULL, + keep_services.list = function(filters = NULL, where = NULL, order = NULL, select = NULL, distinct = NULL, limit = "100", offset = "0", - count = "exact") + count = "exact", cluster_id = NULL, bypass_federation = NULL) { - endPoint <- stringr::str_interp("pipeline_instances") + endPoint <- stringr::str_interp("keep_services") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + limit = limit, offset = offset, count = count, + cluster_id = cluster_id, bypass_federation = bypass_federation) body <- NULL @@ -4615,11 +2908,11 @@ Arvados <- R6::R6Class( resource }, - repositories.get = function(uuid) + links.get = function(uuid) { - endPoint <- stringr::str_interp("repositories/${uuid}") + endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -4635,16 +2928,18 @@ Arvados <- R6::R6Class( resource }, - repositories.create = function(repository, ensure_unique_name = "false") + links.create = function(link, ensure_unique_name = "false", + cluster_id = NULL) { - endPoint <- stringr::str_interp("repositories") + endPoint <- stringr::str_interp("links") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- list(ensure_unique_name = ensure_unique_name, + cluster_id = cluster_id) - if(length(repository) > 0) - body <- jsonlite::toJSON(list(repository = repository), + if(length(link) > 0) + body <- jsonlite::toJSON(list(link = link), auto_unbox = TRUE) else body <- NULL @@ -4659,16 +2954,16 @@ Arvados <- R6::R6Class( resource }, - repositories.update = function(repository, uuid) + links.update = function(link, uuid) { - endPoint <- stringr::str_interp("repositories/${uuid}") + endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(repository) > 0) - body <- jsonlite::toJSON(list(repository = repository), + if(length(link) > 0) + body <- jsonlite::toJSON(list(link = link), auto_unbox = TRUE) else body <- NULL @@ -4683,11 +2978,11 @@ Arvados <- R6::R6Class( resource }, - repositories.delete = function(uuid) + links.delete = function(uuid) { - endPoint <- stringr::str_interp("repositories/${uuid}") + endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -4703,13 +2998,19 @@ Arvados <- R6::R6Class( resource }, - repositories.get_all_permissions = function() + links.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact", + cluster_id = NULL, bypass_federation = NULL) { - endPoint <- stringr::str_interp("repositories/get_all_permissions") + endPoint <- stringr::str_interp("links") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count, + cluster_id = cluster_id, bypass_federation = bypass_federation) body <- NULL @@ -4723,18 +3024,13 @@ Arvados <- R6::R6Class( resource }, - repositories.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + links.get_permissions = function(uuid) { - endPoint <- stringr::str_interp("repositories") + endPoint <- stringr::str_interp("permissions/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$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 @@ -4748,11 +3044,11 @@ Arvados <- R6::R6Class( resource }, - specimens.get = function(uuid) + logs.get = function(uuid) { - endPoint <- stringr::str_interp("specimens/${uuid}") + endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -4768,16 +3064,18 @@ Arvados <- R6::R6Class( resource }, - specimens.create = function(specimen, ensure_unique_name = "false") + logs.create = function(log, ensure_unique_name = "false", + cluster_id = NULL) { - endPoint <- stringr::str_interp("specimens") + endPoint <- stringr::str_interp("logs") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- list(ensure_unique_name = ensure_unique_name, + cluster_id = cluster_id) - if(length(specimen) > 0) - body <- jsonlite::toJSON(list(specimen = specimen), + if(length(log) > 0) + body <- jsonlite::toJSON(list(log = log), auto_unbox = TRUE) else body <- NULL @@ -4792,16 +3090,16 @@ Arvados <- R6::R6Class( resource }, - specimens.update = function(specimen, uuid) + logs.update = function(log, uuid) { - endPoint <- stringr::str_interp("specimens/${uuid}") + endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(specimen) > 0) - body <- jsonlite::toJSON(list(specimen = specimen), + if(length(log) > 0) + body <- jsonlite::toJSON(list(log = log), auto_unbox = TRUE) else body <- NULL @@ -4816,11 +3114,11 @@ Arvados <- R6::R6Class( resource }, - specimens.delete = function(uuid) + logs.delete = function(uuid) { - endPoint <- stringr::str_interp("specimens/${uuid}") + endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -4836,18 +3134,19 @@ Arvados <- R6::R6Class( resource }, - specimens.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", + cluster_id = NULL, bypass_federation = NULL) { - endPoint <- stringr::str_interp("specimens") + endPoint <- stringr::str_interp("logs") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + limit = limit, offset = offset, count = count, + cluster_id = cluster_id, bypass_federation = bypass_federation) body <- NULL @@ -4861,11 +3160,11 @@ Arvados <- R6::R6Class( resource }, - logs.get = function(uuid) + users.get = function(uuid) { - endPoint <- stringr::str_interp("logs/${uuid}") + endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -4881,16 +3180,18 @@ Arvados <- R6::R6Class( resource }, - logs.create = function(log, ensure_unique_name = "false") + users.create = function(user, ensure_unique_name = "false", + cluster_id = NULL) { - endPoint <- stringr::str_interp("logs") + endPoint <- stringr::str_interp("users") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- list(ensure_unique_name = ensure_unique_name, + cluster_id = cluster_id) - if(length(log) > 0) - body <- jsonlite::toJSON(list(log = log), + if(length(user) > 0) + body <- jsonlite::toJSON(list(user = user), auto_unbox = TRUE) else body <- NULL @@ -4905,21 +3206,41 @@ Arvados <- R6::R6Class( resource }, - logs.update = function(log, uuid) + users.update = function(user, uuid, bypass_federation = NULL) { - endPoint <- stringr::str_interp("logs/${uuid}") + endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(bypass_federation = bypass_federation) - if(length(log) > 0) - body <- jsonlite::toJSON(list(log = log), + if(length(user) > 0) + body <- jsonlite::toJSON(list(user = user), auto_unbox = TRUE) else body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, + queryArgs, private$numRetries) + resource <- private$REST$httpParser$parseJSONResponse(response) + + if(!is.null(resource$errors)) + stop(resource$errors) + + resource + }, + + users.delete = function(uuid) + { + endPoint <- stringr::str_interp("users/${uuid}") + url <- paste0(private$host, endPoint) + headers <- list(Authorization = paste("Bearer", private$token), + "Content-Type" = "application/json") + queryArgs <- NULL + + body <- NULL + + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4929,17 +3250,17 @@ Arvados <- R6::R6Class( resource }, - logs.delete = function(uuid) + users.current = function() { - endPoint <- stringr::str_interp("logs/${uuid}") + endPoint <- stringr::str_interp("users/current") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4949,17 +3270,13 @@ Arvados <- R6::R6Class( resource }, - logs.list = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + users.system = function() { - endPoint <- stringr::str_interp("logs") + endPoint <- stringr::str_interp("users/system") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL body <- NULL @@ -4973,17 +3290,17 @@ Arvados <- R6::R6Class( resource }, - traits.get = function(uuid) + users.activate = function(uuid) { - endPoint <- stringr::str_interp("traits/${uuid}") + endPoint <- stringr::str_interp("users/${uuid}/activate") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$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) @@ -4993,19 +3310,18 @@ Arvados <- R6::R6Class( resource }, - traits.create = function(trait, ensure_unique_name = "false") + users.setup = function(uuid = NULL, user = NULL, + repo_name = NULL, vm_uuid = NULL, send_notification_email = "false") { - endPoint <- stringr::str_interp("traits") + endPoint <- stringr::str_interp("users/setup") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- list(uuid = uuid, user = user, + repo_name = repo_name, vm_uuid = vm_uuid, + send_notification_email = send_notification_email) - if(length(trait) > 0) - body <- jsonlite::toJSON(list(trait = trait), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -5017,21 +3333,17 @@ Arvados <- R6::R6Class( resource }, - traits.update = function(trait, uuid) + users.unsetup = function(uuid) { - endPoint <- stringr::str_interp("traits/${uuid}") + endPoint <- stringr::str_interp("users/${uuid}/unsetup") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(trait) > 0) - body <- jsonlite::toJSON(list(trait = trait), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5041,17 +3353,17 @@ Arvados <- R6::R6Class( resource }, - traits.delete = function(uuid) + users.update_uuid = function(uuid, new_uuid) { - endPoint <- stringr::str_interp("traits/${uuid}") + endPoint <- stringr::str_interp("users/${uuid}/update_uuid") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(new_uuid = new_uuid) body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5061,21 +3373,21 @@ Arvados <- R6::R6Class( resource }, - traits.list = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + users.merge = function(new_owner_uuid, new_user_token = NULL, + redirect_to_new_user = NULL, old_user_uuid = NULL, + new_user_uuid = NULL) { - endPoint <- stringr::str_interp("traits") + endPoint <- stringr::str_interp("users/merge") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$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(new_owner_uuid = new_owner_uuid, + new_user_token = new_user_token, redirect_to_new_user = redirect_to_new_user, + old_user_uuid = old_user_uuid, new_user_uuid = new_user_uuid) body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5085,13 +3397,19 @@ Arvados <- R6::R6Class( resource }, - virtual_machines.get = function(uuid) + users.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact", + cluster_id = NULL, bypass_federation = NULL) { - endPoint <- stringr::str_interp("virtual_machines/${uuid}") + endPoint <- stringr::str_interp("users") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count, + cluster_id = cluster_id, bypass_federation = bypass_federation) body <- NULL @@ -5105,22 +3423,17 @@ Arvados <- R6::R6Class( resource }, - virtual_machines.create = function(virtualmachine, - ensure_unique_name = "false") + repositories.get = function(uuid) { - endPoint <- stringr::str_interp("virtual_machines") + endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- NULL - if(length(virtualmachine) > 0) - body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5130,21 +3443,23 @@ Arvados <- R6::R6Class( resource }, - virtual_machines.update = function(virtualmachine, uuid) + repositories.create = function(repository, + ensure_unique_name = "false", cluster_id = NULL) { - endPoint <- stringr::str_interp("virtual_machines/${uuid}") + endPoint <- stringr::str_interp("repositories") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name, + cluster_id = cluster_id) - if(length(virtualmachine) > 0) - body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), + if(length(repository) > 0) + body <- jsonlite::toJSON(list(repository = repository), auto_unbox = TRUE) else body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5154,17 +3469,21 @@ Arvados <- R6::R6Class( resource }, - virtual_machines.delete = function(uuid) + repositories.update = function(repository, uuid) { - endPoint <- stringr::str_interp("virtual_machines/${uuid}") + endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL + if(length(repository) > 0) + body <- jsonlite::toJSON(list(repository = repository), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5174,17 +3493,17 @@ Arvados <- R6::R6Class( resource }, - virtual_machines.logins = function(uuid) + repositories.delete = function(uuid) { - endPoint <- stringr::str_interp("virtual_machines/${uuid}/logins") + endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") 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) @@ -5194,11 +3513,11 @@ Arvados <- R6::R6Class( resource }, - virtual_machines.get_all_logins = function() + repositories.get_all_permissions = function() { - endPoint <- stringr::str_interp("virtual_machines/get_all_logins") + endPoint <- stringr::str_interp("repositories/get_all_permissions") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -5214,18 +3533,19 @@ Arvados <- R6::R6Class( resource }, - virtual_machines.list = function(filters = NULL, + repositories.list = function(filters = NULL, where = NULL, order = NULL, select = NULL, distinct = NULL, limit = "100", offset = "0", - count = "exact") + count = "exact", cluster_id = NULL, bypass_federation = NULL) { - endPoint <- stringr::str_interp("virtual_machines") + endPoint <- stringr::str_interp("repositories") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + limit = limit, offset = offset, count = count, + cluster_id = cluster_id, bypass_federation = bypass_federation) body <- NULL @@ -5239,11 +3559,11 @@ Arvados <- R6::R6Class( resource }, - workflows.get = function(uuid) + virtual_machines.get = function(uuid) { - endPoint <- stringr::str_interp("workflows/${uuid}") + endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -5259,16 +3579,18 @@ Arvados <- R6::R6Class( resource }, - workflows.create = function(workflow, ensure_unique_name = "false") + virtual_machines.create = function(virtualmachine, + ensure_unique_name = "false", cluster_id = NULL) { - endPoint <- stringr::str_interp("workflows") + endPoint <- stringr::str_interp("virtual_machines") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- list(ensure_unique_name = ensure_unique_name, + cluster_id = cluster_id) - if(length(workflow) > 0) - body <- jsonlite::toJSON(list(workflow = workflow), + if(length(virtualmachine) > 0) + body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), auto_unbox = TRUE) else body <- NULL @@ -5283,16 +3605,16 @@ Arvados <- R6::R6Class( resource }, - workflows.update = function(workflow, uuid) + virtual_machines.update = function(virtualmachine, uuid) { - endPoint <- stringr::str_interp("workflows/${uuid}") + endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(workflow) > 0) - body <- jsonlite::toJSON(list(workflow = workflow), + if(length(virtualmachine) > 0) + body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), auto_unbox = TRUE) else body <- NULL @@ -5307,11 +3629,11 @@ Arvados <- R6::R6Class( resource }, - workflows.delete = function(uuid) + virtual_machines.delete = function(uuid) { - endPoint <- stringr::str_interp("workflows/${uuid}") + endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -5327,18 +3649,13 @@ Arvados <- R6::R6Class( resource }, - workflows.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + virtual_machines.logins = function(uuid) { - endPoint <- stringr::str_interp("workflows") + endPoint <- stringr::str_interp("virtual_machines/${uuid}/logins") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$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 @@ -5352,11 +3669,11 @@ Arvados <- R6::R6Class( resource }, - groups.get = function(uuid) + virtual_machines.get_all_logins = function() { - endPoint <- stringr::str_interp("groups/${uuid}") + endPoint <- stringr::str_interp("virtual_machines/get_all_logins") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -5372,45 +3689,23 @@ Arvados <- R6::R6Class( resource }, - groups.create = function(group, ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("groups") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(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) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - groups.update = function(group, uuid) + virtual_machines.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact", cluster_id = NULL, bypass_federation = NULL) { - endPoint <- stringr::str_interp("groups/${uuid}") + endPoint <- stringr::str_interp("virtual_machines") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count, + cluster_id = cluster_id, bypass_federation = bypass_federation) - if(length(group) > 0) - body <- jsonlite::toJSON(list(group = group), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5420,17 +3715,17 @@ Arvados <- R6::R6Class( resource }, - groups.delete = function(uuid) + workflows.get = function(uuid) { - endPoint <- stringr::str_interp("groups/${uuid}") + endPoint <- stringr::str_interp("workflows/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5440,23 +3735,23 @@ Arvados <- R6::R6Class( 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) + workflows.create = function(workflow, ensure_unique_name = "false", + cluster_id = NULL) { - endPoint <- stringr::str_interp("groups/contents") + endPoint <- stringr::str_interp("workflows") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, distinct = distinct, limit = limit, - offset = offset, count = count, include_trash = include_trash, - uuid = uuid, recursive = recursive) + queryArgs <- list(ensure_unique_name = ensure_unique_name, + cluster_id = cluster_id) - body <- NULL + if(length(workflow) > 0) + body <- jsonlite::toJSON(list(workflow = workflow), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5466,17 +3761,21 @@ Arvados <- R6::R6Class( resource }, - groups.trash = function(uuid) + workflows.update = function(workflow, uuid) { - endPoint <- stringr::str_interp("groups/${uuid}/trash") + endPoint <- stringr::str_interp("workflows/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL + if(length(workflow) > 0) + body <- jsonlite::toJSON(list(workflow = workflow), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5486,17 +3785,17 @@ Arvados <- R6::R6Class( resource }, - groups.untrash = function(uuid) + workflows.delete = function(uuid) { - endPoint <- stringr::str_interp("groups/${uuid}/untrash") + endPoint <- stringr::str_interp("workflows/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5506,19 +3805,19 @@ Arvados <- R6::R6Class( resource }, - groups.list = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact", - include_trash = NULL) + workflows.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact", cluster_id = NULL, bypass_federation = NULL) { - endPoint <- stringr::str_interp("groups") + endPoint <- stringr::str_interp("workflows") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$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) + cluster_id = cluster_id, bypass_federation = bypass_federation) body <- NULL @@ -5536,7 +3835,7 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -5553,13 +3852,14 @@ Arvados <- R6::R6Class( }, user_agreements.create = function(useragreement, - ensure_unique_name = "false") + ensure_unique_name = "false", cluster_id = NULL) { endPoint <- stringr::str_interp("user_agreements") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- list(ensure_unique_name = ensure_unique_name, + cluster_id = cluster_id) if(length(useragreement) > 0) body <- jsonlite::toJSON(list(useragreement = useragreement), @@ -5581,7 +3881,7 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -5605,7 +3905,7 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -5625,7 +3925,7 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/signatures") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -5645,7 +3945,7 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/sign") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL @@ -5664,15 +3964,16 @@ Arvados <- R6::R6Class( user_agreements.list = function(filters = NULL, where = NULL, order = NULL, select = NULL, distinct = NULL, limit = "100", offset = "0", - count = "exact") + count = "exact", cluster_id = NULL, bypass_federation = NULL) { endPoint <- stringr::str_interp("user_agreements") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + limit = limit, offset = offset, count = count, + cluster_id = cluster_id, bypass_federation = bypass_federation) body <- NULL @@ -5690,7 +3991,27 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/new") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("Bearer", private$token), + "Content-Type" = "application/json") + queryArgs <- NULL + + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, + queryArgs, private$numRetries) + resource <- private$REST$httpParser$parseJSONResponse(response) + + if(!is.null(resource$errors)) + stop(resource$errors) + + resource + }, + + configs.get = function() + { + endPoint <- stringr::str_interp("config") + url <- paste0(private$host, endPoint) + headers <- list(Authorization = paste("Bearer", private$token), "Content-Type" = "application/json") queryArgs <- NULL diff --git a/sdk/R/R/autoGenAPI.R b/sdk/R/R/autoGenAPI.R index aea64323b5..c86684f8b0 100644 --- a/sdk/R/R/autoGenAPI.R +++ b/sdk/R/R/autoGenAPI.R @@ -3,7 +3,7 @@ # SPDX-License-Identifier: Apache-2.0 getAPIDocument <- function(){ - url <- "https://ce8i5.arvadosapi.com/discovery/v1/apis/arvados/v1/rest" + url <- "https://jutro.arvadosapi.com/discovery/v1/apis/arvados/v1/rest" serverResponse <- httr::RETRY("GET", url = url) httr::content(serverResponse, as = "parsed", type = "application/json") @@ -17,6 +17,10 @@ generateAPI <- function() discoveryDocument <- getAPIDocument() methodResources <- discoveryDocument$resources + + # Don't emit deprecated APIs + methodResources <- methodResources[!(names(methodResources) %in% c("jobs", "job_tasks", "pipeline_templates", "pipeline_instances", + "keep_disks", "nodes", "humans", "traits", "specimens"))] resourceNames <- names(methodResources) methodDoc <- genMethodsDoc(methodResources, resourceNames) @@ -34,6 +38,10 @@ generateAPI <- function() arvadosAPIFooter) fileConn <- file("./R/Arvados.R", "w") + writeLines(c( + "# Copyright (C) The Arvados Authors. All rights reserved.", + "#", + "# SPDX-License-Identifier: Apache-2.0", ""), fileConn) writeLines(unlist(arvadosClass), fileConn) close(fileConn) NULL @@ -252,7 +260,7 @@ getRequestURL <- function(methodMetaData) getRequestHeaders <- function() { - c("headers <- list(Authorization = paste(\"OAuth2\", private$token), ", + c("headers <- list(Authorization = paste(\"Bearer\", private$token), ", " \"Content-Type\" = \"application/json\")") } -- 2.30.2