From: Fuad Muhic Date: Thu, 26 Jul 2018 15:18:24 +0000 (+0200) Subject: Merge branch 'master' of git.curoverse.com:arvados into 13609-r-sdk-copy X-Git-Tag: 1.2.0~46^2~4 X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/c9bfa91e3c3ec90778795969fdd3787578a76ed4?hp=8fdac0b6f954b6265798390b95e61f8192b85630 Merge branch 'master' of git.curoverse.com:arvados into 13609-r-sdk-copy Arvados-DCO-1.1-Signed-off-by: Fuad Muhic --- diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R index 4b65546912..744cb3c296 100644 --- a/sdk/R/R/Arvados.R +++ b/sdk/R/R/Arvados.R @@ -1,11 +1,7 @@ -# Copyright (C) The Arvados Authors. All rights reserved. -# -# SPDX-License-Identifier: Apache-2.0 - #' users.get -#' +#' #' users.get is a method defined in Arvados class. -#' +#' #' @usage arv$users.get(uuid) #' @param uuid The UUID of the User in question. #' @return User object. @@ -13,9 +9,9 @@ NULL #' users.create -#' +#' #' users.create is a method defined in Arvados class. -#' +#' #' @usage arv$users.create(user, ensure_unique_name = "false") #' @param user User object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -24,9 +20,9 @@ NULL NULL #' users.update -#' +#' #' users.update is a method defined in Arvados class. -#' +#' #' @usage arv$users.update(user, uuid) #' @param user User object. #' @param uuid The UUID of the User in question. @@ -35,9 +31,9 @@ NULL NULL #' users.delete -#' +#' #' users.delete is a method defined in Arvados class. -#' +#' #' @usage arv$users.delete(uuid) #' @param uuid The UUID of the User in question. #' @return User object. @@ -45,93 +41,106 @@ NULL NULL #' users.current -#' +#' #' users.current is a method defined in Arvados class. -#' +#' #' @usage arv$users.current(NULL) #' @return User object. #' @name users.current NULL #' users.system -#' +#' #' users.system is a method defined in Arvados class. -#' +#' #' @usage arv$users.system(NULL) #' @return User object. #' @name users.system NULL #' users.activate -#' +#' #' users.activate is a method defined in Arvados class. -#' +#' #' @usage arv$users.activate(uuid) -#' @param uuid +#' @param uuid #' @return User object. #' @name users.activate NULL #' users.setup -#' +#' #' users.setup is a method defined in Arvados class. -#' +#' #' @usage arv$users.setup(user = NULL, openid_prefix = NULL, #' repo_name = NULL, vm_uuid = NULL, send_notification_email = "false") -#' @param user -#' @param openid_prefix -#' @param repo_name -#' @param vm_uuid -#' @param send_notification_email +#' @param user +#' @param openid_prefix +#' @param repo_name +#' @param vm_uuid +#' @param send_notification_email #' @return User object. #' @name users.setup NULL #' users.unsetup -#' +#' #' users.unsetup is a method defined in Arvados class. -#' +#' #' @usage arv$users.unsetup(uuid) -#' @param uuid +#' @param uuid #' @return User object. #' @name users.unsetup NULL #' users.update_uuid -#' +#' #' users.update_uuid is a method defined in Arvados class. -#' +#' #' @usage arv$users.update_uuid(uuid, new_uuid) -#' @param uuid -#' @param new_uuid +#' @param uuid +#' @param new_uuid #' @return User object. #' @name users.update_uuid NULL +#' users.merge +#' +#' users.merge is a method defined in Arvados class. +#' +#' @usage arv$users.merge(new_owner_uuid, +#' new_user_token, redirect_to_new_user = NULL) +#' @param new_owner_uuid +#' @param new_user_token +#' @param redirect_to_new_user +#' @return User object. +#' @name users.merge +NULL + #' users.list -#' +#' #' users.list is a method defined in Arvados class. -#' +#' #' @usage arv$users.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return UserList object. #' @name users.list NULL #' api_client_authorizations.get -#' +#' #' api_client_authorizations.get is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.get(uuid) #' @param uuid The UUID of the ApiClientAuthorization in question. #' @return ApiClientAuthorization object. @@ -139,9 +148,9 @@ NULL NULL #' api_client_authorizations.create -#' +#' #' api_client_authorizations.create is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.create(apiclientauthorization, #' ensure_unique_name = "false") #' @param apiClientAuthorization ApiClientAuthorization object. @@ -151,9 +160,9 @@ NULL NULL #' api_client_authorizations.update -#' +#' #' api_client_authorizations.update is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.update(apiclientauthorization, #' uuid) #' @param apiClientAuthorization ApiClientAuthorization object. @@ -163,9 +172,9 @@ NULL NULL #' api_client_authorizations.delete -#' +#' #' api_client_authorizations.delete is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.delete(uuid) #' @param uuid The UUID of the ApiClientAuthorization in question. #' @return ApiClientAuthorization object. @@ -173,50 +182,50 @@ NULL NULL #' api_client_authorizations.create_system_auth -#' +#' #' api_client_authorizations.create_system_auth is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.create_system_auth(api_client_id = NULL, #' scopes = NULL) -#' @param api_client_id -#' @param scopes +#' @param api_client_id +#' @param scopes #' @return ApiClientAuthorization object. #' @name api_client_authorizations.create_system_auth NULL #' api_client_authorizations.current -#' +#' #' api_client_authorizations.current is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.current(NULL) #' @return ApiClientAuthorization object. #' @name api_client_authorizations.current NULL #' api_client_authorizations.list -#' +#' #' api_client_authorizations.list is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return ApiClientAuthorizationList object. #' @name api_client_authorizations.list NULL #' containers.get -#' +#' #' containers.get is a method defined in Arvados class. -#' +#' #' @usage arv$containers.get(uuid) #' @param uuid The UUID of the Container in question. #' @return Container object. @@ -224,9 +233,9 @@ NULL NULL #' containers.create -#' +#' #' containers.create is a method defined in Arvados class. -#' +#' #' @usage arv$containers.create(container, #' ensure_unique_name = "false") #' @param container Container object. @@ -236,9 +245,9 @@ NULL NULL #' containers.update -#' +#' #' containers.update is a method defined in Arvados class. -#' +#' #' @usage arv$containers.update(container, #' uuid) #' @param container Container object. @@ -248,9 +257,9 @@ NULL NULL #' containers.delete -#' +#' #' containers.delete is a method defined in Arvados class. -#' +#' #' @usage arv$containers.delete(uuid) #' @param uuid The UUID of the Container in question. #' @return Container object. @@ -258,78 +267,78 @@ NULL NULL #' containers.auth -#' +#' #' containers.auth is a method defined in Arvados class. -#' +#' #' @usage arv$containers.auth(uuid) -#' @param uuid +#' @param uuid #' @return Container object. #' @name containers.auth NULL #' containers.lock -#' +#' #' containers.lock is a method defined in Arvados class. -#' +#' #' @usage arv$containers.lock(uuid) -#' @param uuid +#' @param uuid #' @return Container object. #' @name containers.lock NULL #' containers.unlock -#' +#' #' containers.unlock is a method defined in Arvados class. -#' +#' #' @usage arv$containers.unlock(uuid) -#' @param uuid +#' @param uuid #' @return Container object. #' @name containers.unlock NULL #' containers.secret_mounts -#' +#' #' containers.secret_mounts is a method defined in Arvados class. -#' +#' #' @usage arv$containers.secret_mounts(uuid) -#' @param uuid +#' @param uuid #' @return Container object. #' @name containers.secret_mounts NULL #' containers.current -#' +#' #' containers.current is a method defined in Arvados class. -#' +#' #' @usage arv$containers.current(NULL) #' @return Container object. #' @name containers.current NULL #' containers.list -#' +#' #' containers.list is a method defined in Arvados class. -#' +#' #' @usage arv$containers.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return ContainerList object. #' @name containers.list NULL #' api_clients.get -#' +#' #' api_clients.get is a method defined in Arvados class. -#' +#' #' @usage arv$api_clients.get(uuid) #' @param uuid The UUID of the ApiClient in question. #' @return ApiClient object. @@ -337,9 +346,9 @@ NULL NULL #' api_clients.create -#' +#' #' api_clients.create is a method defined in Arvados class. -#' +#' #' @usage arv$api_clients.create(apiclient, #' ensure_unique_name = "false") #' @param apiClient ApiClient object. @@ -349,9 +358,9 @@ NULL NULL #' api_clients.update -#' +#' #' api_clients.update is a method defined in Arvados class. -#' +#' #' @usage arv$api_clients.update(apiclient, #' uuid) #' @param apiClient ApiClient object. @@ -361,9 +370,9 @@ NULL NULL #' api_clients.delete -#' +#' #' api_clients.delete is a method defined in Arvados class. -#' +#' #' @usage arv$api_clients.delete(uuid) #' @param uuid The UUID of the ApiClient in question. #' @return ApiClient object. @@ -371,93 +380,29 @@ NULL NULL #' api_clients.list -#' +#' #' api_clients.list is a method defined in Arvados class. -#' +#' #' @usage arv$api_clients.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return ApiClientList object. #' @name api_clients.list NULL -#' authorized_keys.get -#' -#' authorized_keys.get is a method defined in Arvados class. -#' -#' @usage arv$authorized_keys.get(uuid) -#' @param uuid The UUID of the AuthorizedKey in question. -#' @return AuthorizedKey object. -#' @name authorized_keys.get -NULL - -#' authorized_keys.create -#' -#' authorized_keys.create is a method defined in Arvados class. -#' -#' @usage arv$authorized_keys.create(authorizedkey, -#' ensure_unique_name = "false") -#' @param authorizedKey AuthorizedKey object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return AuthorizedKey object. -#' @name authorized_keys.create -NULL - -#' authorized_keys.update -#' -#' authorized_keys.update is a method defined in Arvados class. -#' -#' @usage arv$authorized_keys.update(authorizedkey, -#' uuid) -#' @param authorizedKey AuthorizedKey object. -#' @param uuid The UUID of the AuthorizedKey in question. -#' @return AuthorizedKey object. -#' @name authorized_keys.update -NULL - -#' authorized_keys.delete -#' -#' authorized_keys.delete is a method defined in Arvados class. -#' -#' @usage arv$authorized_keys.delete(uuid) -#' @param uuid The UUID of the AuthorizedKey in question. -#' @return AuthorizedKey object. -#' @name authorized_keys.delete -NULL - -#' authorized_keys.list -#' -#' authorized_keys.list is a method defined in Arvados class. -#' -#' @usage arv$authorized_keys.list(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return AuthorizedKeyList object. -#' @name authorized_keys.list -NULL - #' container_requests.get -#' +#' #' container_requests.get is a method defined in Arvados class. -#' +#' #' @usage arv$container_requests.get(uuid) #' @param uuid The UUID of the ContainerRequest in question. #' @return ContainerRequest object. @@ -465,9 +410,9 @@ NULL NULL #' container_requests.create -#' +#' #' container_requests.create is a method defined in Arvados class. -#' +#' #' @usage arv$container_requests.create(containerrequest, #' ensure_unique_name = "false") #' @param containerRequest ContainerRequest object. @@ -477,9 +422,9 @@ NULL NULL #' container_requests.update -#' +#' #' container_requests.update is a method defined in Arvados class. -#' +#' #' @usage arv$container_requests.update(containerrequest, #' uuid) #' @param containerRequest ContainerRequest object. @@ -489,9 +434,9 @@ NULL NULL #' container_requests.delete -#' +#' #' container_requests.delete is a method defined in Arvados class. -#' +#' #' @usage arv$container_requests.delete(uuid) #' @param uuid The UUID of the ContainerRequest in question. #' @return ContainerRequest object. @@ -499,29 +444,93 @@ NULL NULL #' container_requests.list -#' +#' #' container_requests.list is a method defined in Arvados class. -#' +#' #' @usage arv$container_requests.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return ContainerRequestList object. #' @name container_requests.list NULL +#' authorized_keys.get +#' +#' authorized_keys.get is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.get(uuid) +#' @param uuid The UUID of the AuthorizedKey in question. +#' @return AuthorizedKey object. +#' @name authorized_keys.get +NULL + +#' authorized_keys.create +#' +#' authorized_keys.create is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.create(authorizedkey, +#' ensure_unique_name = "false") +#' @param authorizedKey AuthorizedKey object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return AuthorizedKey object. +#' @name authorized_keys.create +NULL + +#' authorized_keys.update +#' +#' authorized_keys.update is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.update(authorizedkey, +#' uuid) +#' @param authorizedKey AuthorizedKey object. +#' @param uuid The UUID of the AuthorizedKey in question. +#' @return AuthorizedKey object. +#' @name authorized_keys.update +NULL + +#' authorized_keys.delete +#' +#' authorized_keys.delete is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.delete(uuid) +#' @param uuid The UUID of the AuthorizedKey in question. +#' @return AuthorizedKey object. +#' @name authorized_keys.delete +NULL + +#' authorized_keys.list +#' +#' authorized_keys.list is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return AuthorizedKeyList object. +#' @name authorized_keys.list +NULL + #' collections.get -#' +#' #' collections.get is a method defined in Arvados class. -#' +#' #' @usage arv$collections.get(uuid) #' @param uuid The UUID of the Collection in question. #' @return Collection object. @@ -529,9 +538,9 @@ NULL NULL #' collections.create -#' +#' #' collections.create is a method defined in Arvados class. -#' +#' #' @usage arv$collections.create(collection, #' ensure_unique_name = "false") #' @param collection Collection object. @@ -541,9 +550,9 @@ NULL NULL #' collections.update -#' +#' #' collections.update is a method defined in Arvados class. -#' +#' #' @usage arv$collections.update(collection, #' uuid) #' @param collection Collection object. @@ -553,9 +562,9 @@ NULL NULL #' collections.delete -#' +#' #' collections.delete is a method defined in Arvados class. -#' +#' #' @usage arv$collections.delete(uuid) #' @param uuid The UUID of the Collection in question. #' @return Collection object. @@ -563,70 +572,70 @@ NULL NULL #' collections.provenance -#' +#' #' collections.provenance is a method defined in Arvados class. -#' +#' #' @usage arv$collections.provenance(uuid) -#' @param uuid +#' @param uuid #' @return Collection object. #' @name collections.provenance NULL #' collections.used_by -#' +#' #' collections.used_by is a method defined in Arvados class. -#' +#' #' @usage arv$collections.used_by(uuid) -#' @param uuid +#' @param uuid #' @return Collection object. #' @name collections.used_by NULL #' collections.trash -#' +#' #' collections.trash is a method defined in Arvados class. -#' +#' #' @usage arv$collections.trash(uuid) -#' @param uuid +#' @param uuid #' @return Collection object. #' @name collections.trash NULL #' collections.untrash -#' +#' #' collections.untrash is a method defined in Arvados class. -#' +#' #' @usage arv$collections.untrash(uuid) -#' @param uuid +#' @param uuid #' @return Collection object. #' @name collections.untrash NULL #' collections.list -#' +#' #' collections.list is a method defined in Arvados class. -#' +#' #' @usage arv$collections.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact", include_trash = NULL) -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @param include_trash Include collections whose is_trashed attribute is true. #' @return CollectionList object. #' @name collections.list NULL #' humans.get -#' +#' #' humans.get is a method defined in Arvados class. -#' +#' #' @usage arv$humans.get(uuid) #' @param uuid The UUID of the Human in question. #' @return Human object. @@ -634,9 +643,9 @@ NULL NULL #' humans.create -#' +#' #' humans.create is a method defined in Arvados class. -#' +#' #' @usage arv$humans.create(human, ensure_unique_name = "false") #' @param human Human object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -645,9 +654,9 @@ NULL NULL #' humans.update -#' +#' #' humans.update is a method defined in Arvados class. -#' +#' #' @usage arv$humans.update(human, uuid) #' @param human Human object. #' @param uuid The UUID of the Human in question. @@ -656,9 +665,9 @@ NULL NULL #' humans.delete -#' +#' #' humans.delete is a method defined in Arvados class. -#' +#' #' @usage arv$humans.delete(uuid) #' @param uuid The UUID of the Human in question. #' @return Human object. @@ -666,29 +675,29 @@ NULL NULL #' humans.list -#' +#' #' humans.list is a method defined in Arvados class. -#' +#' #' @usage arv$humans.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return HumanList object. #' @name humans.list NULL #' job_tasks.get -#' +#' #' job_tasks.get is a method defined in Arvados class. -#' +#' #' @usage arv$job_tasks.get(uuid) #' @param uuid The UUID of the JobTask in question. #' @return JobTask object. @@ -696,9 +705,9 @@ NULL NULL #' job_tasks.create -#' +#' #' job_tasks.create is a method defined in Arvados class. -#' +#' #' @usage arv$job_tasks.create(jobtask, ensure_unique_name = "false") #' @param jobTask JobTask object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -707,9 +716,9 @@ NULL NULL #' job_tasks.update -#' +#' #' job_tasks.update is a method defined in Arvados class. -#' +#' #' @usage arv$job_tasks.update(jobtask, uuid) #' @param jobTask JobTask object. #' @param uuid The UUID of the JobTask in question. @@ -718,9 +727,9 @@ NULL NULL #' job_tasks.delete -#' +#' #' job_tasks.delete is a method defined in Arvados class. -#' +#' #' @usage arv$job_tasks.delete(uuid) #' @param uuid The UUID of the JobTask in question. #' @return JobTask object. @@ -728,128 +737,56 @@ NULL NULL #' job_tasks.list -#' +#' #' job_tasks.list is a method defined in Arvados class. -#' +#' #' @usage arv$job_tasks.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return JobTaskList object. #' @name job_tasks.list NULL -#' links.get -#' -#' links.get is a method defined in Arvados class. -#' -#' @usage arv$links.get(uuid) -#' @param uuid The UUID of the Link in question. -#' @return Link object. -#' @name links.get +#' jobs.get +#' +#' jobs.get is a method defined in Arvados class. +#' +#' @usage arv$jobs.get(uuid) +#' @param uuid The UUID of the Job in question. +#' @return Job object. +#' @name jobs.get NULL -#' links.create -#' -#' links.create is a method defined in Arvados class. -#' -#' @usage arv$links.create(link, ensure_unique_name = "false") -#' @param link Link object. +#' jobs.create +#' +#' jobs.create is a method defined in Arvados class. +#' +#' @usage arv$jobs.create(job, ensure_unique_name = "false", +#' find_or_create = "false", filters = NULL, +#' minimum_script_version = NULL, exclude_script_versions = NULL) +#' @param job Job object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return Link object. -#' @name links.create -NULL - -#' links.update -#' -#' links.update is a method defined in Arvados class. -#' -#' @usage arv$links.update(link, uuid) -#' @param link Link object. -#' @param uuid The UUID of the Link in question. -#' @return Link object. -#' @name links.update -NULL - -#' links.delete -#' -#' links.delete is a method defined in Arvados class. -#' -#' @usage arv$links.delete(uuid) -#' @param uuid The UUID of the Link in question. -#' @return Link object. -#' @name links.delete -NULL - -#' links.list -#' -#' links.list is a method defined in Arvados class. -#' -#' @usage arv$links.list(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return LinkList object. -#' @name links.list -NULL - -#' links.get_permissions -#' -#' links.get_permissions is a method defined in Arvados class. -#' -#' @usage arv$links.get_permissions(uuid) -#' @param uuid -#' @return Link object. -#' @name links.get_permissions -NULL - -#' jobs.get -#' -#' jobs.get is a method defined in Arvados class. -#' -#' @usage arv$jobs.get(uuid) -#' @param uuid The UUID of the Job in question. -#' @return Job object. -#' @name jobs.get -NULL - -#' jobs.create -#' -#' jobs.create is a method defined in Arvados class. -#' -#' @usage arv$jobs.create(job, ensure_unique_name = "false", -#' find_or_create = "false", filters = NULL, -#' minimum_script_version = NULL, exclude_script_versions = NULL) -#' @param job Job object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @param find_or_create -#' @param filters -#' @param minimum_script_version -#' @param exclude_script_versions -#' @return Job object. -#' @name jobs.create +#' @param find_or_create +#' @param filters +#' @param minimum_script_version +#' @param exclude_script_versions +#' @return Job object. +#' @name jobs.create NULL #' jobs.update -#' +#' #' jobs.update is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.update(job, uuid) #' @param job Job object. #' @param uuid The UUID of the Job in question. @@ -858,9 +795,9 @@ NULL NULL #' jobs.delete -#' +#' #' jobs.delete is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.delete(uuid) #' @param uuid The UUID of the Job in question. #' @return Job object. @@ -868,77 +805,77 @@ NULL NULL #' jobs.queue -#' +#' #' jobs.queue is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.queue(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return Job object. #' @name jobs.queue NULL #' jobs.queue_size -#' +#' #' jobs.queue_size is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.queue_size(NULL) #' @return Job object. #' @name jobs.queue_size NULL #' jobs.cancel -#' +#' #' jobs.cancel is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.cancel(uuid) -#' @param uuid +#' @param uuid #' @return Job object. #' @name jobs.cancel NULL #' jobs.lock -#' +#' #' jobs.lock is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.lock(uuid) -#' @param uuid +#' @param uuid #' @return Job object. #' @name jobs.lock NULL #' jobs.list -#' +#' #' jobs.list is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.list(filters = NULL, where = NULL, #' order = NULL, select = NULL, distinct = NULL, #' limit = "100", offset = "0", count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return JobList object. #' @name jobs.list NULL #' keep_disks.get -#' +#' #' keep_disks.get is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.get(uuid) #' @param uuid The UUID of the KeepDisk in question. #' @return KeepDisk object. @@ -946,9 +883,9 @@ NULL NULL #' keep_disks.create -#' +#' #' keep_disks.create is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.create(keepdisk, #' ensure_unique_name = "false") #' @param keepDisk KeepDisk object. @@ -958,9 +895,9 @@ NULL NULL #' keep_disks.update -#' +#' #' keep_disks.update is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.update(keepdisk, #' uuid) #' @param keepDisk KeepDisk object. @@ -970,9 +907,9 @@ NULL NULL #' keep_disks.delete -#' +#' #' keep_disks.delete is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.delete(uuid) #' @param uuid The UUID of the KeepDisk in question. #' @return KeepDisk object. @@ -980,47 +917,195 @@ NULL NULL #' keep_disks.ping -#' +#' #' keep_disks.ping is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.ping(uuid = NULL, #' ping_secret, node_uuid = NULL, filesystem_uuid = NULL, #' service_host = NULL, service_port, service_ssl_flag) -#' @param uuid -#' @param ping_secret -#' @param node_uuid -#' @param filesystem_uuid -#' @param service_host -#' @param service_port -#' @param service_ssl_flag +#' @param uuid +#' @param ping_secret +#' @param node_uuid +#' @param filesystem_uuid +#' @param service_host +#' @param service_port +#' @param service_ssl_flag #' @return KeepDisk object. #' @name keep_disks.ping NULL #' keep_disks.list -#' +#' #' keep_disks.list is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return KeepDiskList object. #' @name keep_disks.list NULL +#' nodes.get +#' +#' nodes.get is a method defined in Arvados class. +#' +#' @usage arv$nodes.get(uuid) +#' @param uuid The UUID of the Node in question. +#' @return Node object. +#' @name nodes.get +NULL + +#' nodes.create +#' +#' nodes.create is a method defined in Arvados class. +#' +#' @usage arv$nodes.create(node, ensure_unique_name = "false", +#' assign_slot = NULL) +#' @param node Node object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @param assign_slot assign slot and hostname +#' @return Node object. +#' @name nodes.create +NULL + +#' nodes.update +#' +#' nodes.update is a method defined in Arvados class. +#' +#' @usage arv$nodes.update(node, uuid, assign_slot = NULL) +#' @param node Node object. +#' @param uuid The UUID of the Node in question. +#' @param assign_slot assign slot and hostname +#' @return Node object. +#' @name nodes.update +NULL + +#' nodes.delete +#' +#' nodes.delete is a method defined in Arvados class. +#' +#' @usage arv$nodes.delete(uuid) +#' @param uuid The UUID of the Node in question. +#' @return Node object. +#' @name nodes.delete +NULL + +#' nodes.ping +#' +#' nodes.ping is a method defined in Arvados class. +#' +#' @usage arv$nodes.ping(uuid, ping_secret) +#' @param uuid +#' @param ping_secret +#' @return Node object. +#' @name nodes.ping +NULL + +#' nodes.list +#' +#' nodes.list is a method defined in Arvados class. +#' +#' @usage arv$nodes.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return NodeList object. +#' @name nodes.list +NULL + +#' links.get +#' +#' links.get is a method defined in Arvados class. +#' +#' @usage arv$links.get(uuid) +#' @param uuid The UUID of the Link in question. +#' @return Link object. +#' @name links.get +NULL + +#' links.create +#' +#' links.create is a method defined in Arvados class. +#' +#' @usage arv$links.create(link, ensure_unique_name = "false") +#' @param link Link object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Link object. +#' @name links.create +NULL + +#' links.update +#' +#' links.update is a method defined in Arvados class. +#' +#' @usage arv$links.update(link, uuid) +#' @param link Link object. +#' @param uuid The UUID of the Link in question. +#' @return Link object. +#' @name links.update +NULL + +#' links.delete +#' +#' links.delete is a method defined in Arvados class. +#' +#' @usage arv$links.delete(uuid) +#' @param uuid The UUID of the Link in question. +#' @return Link object. +#' @name links.delete +NULL + +#' links.list +#' +#' links.list is a method defined in Arvados class. +#' +#' @usage arv$links.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return LinkList object. +#' @name links.list +NULL + +#' links.get_permissions +#' +#' links.get_permissions is a method defined in Arvados class. +#' +#' @usage arv$links.get_permissions(uuid) +#' @param uuid +#' @return Link object. +#' @name links.get_permissions +NULL + #' keep_services.get -#' +#' #' keep_services.get is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.get(uuid) #' @param uuid The UUID of the KeepService in question. #' @return KeepService object. @@ -1028,9 +1113,9 @@ NULL NULL #' keep_services.create -#' +#' #' keep_services.create is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.create(keepservice, #' ensure_unique_name = "false") #' @param keepService KeepService object. @@ -1040,9 +1125,9 @@ NULL NULL #' keep_services.update -#' +#' #' keep_services.update is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.update(keepservice, #' uuid) #' @param keepService KeepService object. @@ -1052,9 +1137,9 @@ NULL NULL #' keep_services.delete -#' +#' #' keep_services.delete is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.delete(uuid) #' @param uuid The UUID of the KeepService in question. #' @return KeepService object. @@ -1062,38 +1147,38 @@ NULL NULL #' keep_services.accessible -#' +#' #' keep_services.accessible is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.accessible(NULL) #' @return KeepService object. #' @name keep_services.accessible NULL #' keep_services.list -#' +#' #' keep_services.list is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return KeepServiceList object. #' @name keep_services.list NULL #' pipeline_templates.get -#' +#' #' pipeline_templates.get is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_templates.get(uuid) #' @param uuid The UUID of the PipelineTemplate in question. #' @return PipelineTemplate object. @@ -1101,9 +1186,9 @@ NULL NULL #' pipeline_templates.create -#' +#' #' pipeline_templates.create is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_templates.create(pipelinetemplate, #' ensure_unique_name = "false") #' @param pipelineTemplate PipelineTemplate object. @@ -1113,9 +1198,9 @@ NULL NULL #' pipeline_templates.update -#' +#' #' pipeline_templates.update is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_templates.update(pipelinetemplate, #' uuid) #' @param pipelineTemplate PipelineTemplate object. @@ -1125,9 +1210,9 @@ NULL NULL #' pipeline_templates.delete -#' +#' #' pipeline_templates.delete is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_templates.delete(uuid) #' @param uuid The UUID of the PipelineTemplate in question. #' @return PipelineTemplate object. @@ -1135,29 +1220,29 @@ NULL NULL #' pipeline_templates.list -#' +#' #' pipeline_templates.list is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_templates.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return PipelineTemplateList object. #' @name pipeline_templates.list NULL #' pipeline_instances.get -#' +#' #' pipeline_instances.get is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.get(uuid) #' @param uuid The UUID of the PipelineInstance in question. #' @return PipelineInstance object. @@ -1165,9 +1250,9 @@ NULL NULL #' pipeline_instances.create -#' +#' #' pipeline_instances.create is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.create(pipelineinstance, #' ensure_unique_name = "false") #' @param pipelineInstance PipelineInstance object. @@ -1177,9 +1262,9 @@ NULL NULL #' pipeline_instances.update -#' +#' #' pipeline_instances.update is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.update(pipelineinstance, #' uuid) #' @param pipelineInstance PipelineInstance object. @@ -1189,9 +1274,9 @@ NULL NULL #' pipeline_instances.delete -#' +#' #' pipeline_instances.delete is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.delete(uuid) #' @param uuid The UUID of the PipelineInstance in question. #' @return PipelineInstance object. @@ -1199,115 +1284,39 @@ NULL NULL #' pipeline_instances.cancel -#' +#' #' pipeline_instances.cancel is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.cancel(uuid) -#' @param uuid +#' @param uuid #' @return PipelineInstance object. #' @name pipeline_instances.cancel NULL #' pipeline_instances.list -#' +#' #' pipeline_instances.list is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return PipelineInstanceList object. #' @name pipeline_instances.list NULL -#' nodes.get -#' -#' nodes.get is a method defined in Arvados class. -#' -#' @usage arv$nodes.get(uuid) -#' @param uuid The UUID of the Node in question. -#' @return Node object. -#' @name nodes.get -NULL - -#' nodes.create -#' -#' nodes.create is a method defined in Arvados class. -#' -#' @usage arv$nodes.create(node, ensure_unique_name = "false", -#' assign_slot = NULL) -#' @param node Node object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @param assign_slot assign slot and hostname -#' @return Node object. -#' @name nodes.create -NULL - -#' nodes.update -#' -#' nodes.update is a method defined in Arvados class. -#' -#' @usage arv$nodes.update(node, uuid, assign_slot = NULL) -#' @param node Node object. -#' @param uuid The UUID of the Node in question. -#' @param assign_slot assign slot and hostname -#' @return Node object. -#' @name nodes.update -NULL - -#' nodes.delete -#' -#' nodes.delete is a method defined in Arvados class. -#' -#' @usage arv$nodes.delete(uuid) -#' @param uuid The UUID of the Node in question. -#' @return Node object. -#' @name nodes.delete -NULL - -#' nodes.ping -#' -#' nodes.ping is a method defined in Arvados class. -#' -#' @usage arv$nodes.ping(uuid, ping_secret) -#' @param uuid -#' @param ping_secret -#' @return Node object. -#' @name nodes.ping -NULL - -#' nodes.list -#' -#' nodes.list is a method defined in Arvados class. -#' -#' @usage arv$nodes.list(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return NodeList object. -#' @name nodes.list -NULL - #' repositories.get -#' +#' #' repositories.get is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.get(uuid) #' @param uuid The UUID of the Repository in question. #' @return Repository object. @@ -1315,9 +1324,9 @@ NULL NULL #' repositories.create -#' +#' #' repositories.create is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.create(repository, #' ensure_unique_name = "false") #' @param repository Repository object. @@ -1327,9 +1336,9 @@ NULL NULL #' repositories.update -#' +#' #' repositories.update is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.update(repository, #' uuid) #' @param repository Repository object. @@ -1339,9 +1348,9 @@ NULL NULL #' repositories.delete -#' +#' #' repositories.delete is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.delete(uuid) #' @param uuid The UUID of the Repository in question. #' @return Repository object. @@ -1349,38 +1358,38 @@ NULL NULL #' repositories.get_all_permissions -#' +#' #' repositories.get_all_permissions is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.get_all_permissions(NULL) #' @return Repository object. #' @name repositories.get_all_permissions NULL #' repositories.list -#' +#' #' repositories.list is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return RepositoryList object. #' @name repositories.list NULL #' specimens.get -#' +#' #' specimens.get is a method defined in Arvados class. -#' +#' #' @usage arv$specimens.get(uuid) #' @param uuid The UUID of the Specimen in question. #' @return Specimen object. @@ -1388,9 +1397,9 @@ NULL NULL #' specimens.create -#' +#' #' specimens.create is a method defined in Arvados class. -#' +#' #' @usage arv$specimens.create(specimen, #' ensure_unique_name = "false") #' @param specimen Specimen object. @@ -1400,9 +1409,9 @@ NULL NULL #' specimens.update -#' +#' #' specimens.update is a method defined in Arvados class. -#' +#' #' @usage arv$specimens.update(specimen, #' uuid) #' @param specimen Specimen object. @@ -1412,9 +1421,9 @@ NULL NULL #' specimens.delete -#' +#' #' specimens.delete is a method defined in Arvados class. -#' +#' #' @usage arv$specimens.delete(uuid) #' @param uuid The UUID of the Specimen in question. #' @return Specimen object. @@ -1422,29 +1431,29 @@ NULL NULL #' specimens.list -#' +#' #' specimens.list is a method defined in Arvados class. -#' +#' #' @usage arv$specimens.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return SpecimenList object. #' @name specimens.list NULL #' logs.get -#' +#' #' logs.get is a method defined in Arvados class. -#' +#' #' @usage arv$logs.get(uuid) #' @param uuid The UUID of the Log in question. #' @return Log object. @@ -1452,9 +1461,9 @@ NULL NULL #' logs.create -#' +#' #' logs.create is a method defined in Arvados class. -#' +#' #' @usage arv$logs.create(log, ensure_unique_name = "false") #' @param log Log object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -1463,9 +1472,9 @@ NULL NULL #' logs.update -#' +#' #' logs.update is a method defined in Arvados class. -#' +#' #' @usage arv$logs.update(log, uuid) #' @param log Log object. #' @param uuid The UUID of the Log in question. @@ -1474,9 +1483,9 @@ NULL NULL #' logs.delete -#' +#' #' logs.delete is a method defined in Arvados class. -#' +#' #' @usage arv$logs.delete(uuid) #' @param uuid The UUID of the Log in question. #' @return Log object. @@ -1484,28 +1493,28 @@ NULL NULL #' logs.list -#' +#' #' logs.list is a method defined in Arvados class. -#' +#' #' @usage arv$logs.list(filters = NULL, where = NULL, #' order = NULL, select = NULL, distinct = NULL, #' limit = "100", offset = "0", count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return LogList object. #' @name logs.list NULL #' traits.get -#' +#' #' traits.get is a method defined in Arvados class. -#' +#' #' @usage arv$traits.get(uuid) #' @param uuid The UUID of the Trait in question. #' @return Trait object. @@ -1513,9 +1522,9 @@ NULL NULL #' traits.create -#' +#' #' traits.create is a method defined in Arvados class. -#' +#' #' @usage arv$traits.create(trait, ensure_unique_name = "false") #' @param trait Trait object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -1524,9 +1533,9 @@ NULL NULL #' traits.update -#' +#' #' traits.update is a method defined in Arvados class. -#' +#' #' @usage arv$traits.update(trait, uuid) #' @param trait Trait object. #' @param uuid The UUID of the Trait in question. @@ -1535,9 +1544,9 @@ NULL NULL #' traits.delete -#' +#' #' traits.delete is a method defined in Arvados class. -#' +#' #' @usage arv$traits.delete(uuid) #' @param uuid The UUID of the Trait in question. #' @return Trait object. @@ -1545,29 +1554,29 @@ NULL NULL #' traits.list -#' +#' #' traits.list is a method defined in Arvados class. -#' +#' #' @usage arv$traits.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return TraitList object. #' @name traits.list NULL #' virtual_machines.get -#' +#' #' virtual_machines.get is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.get(uuid) #' @param uuid The UUID of the VirtualMachine in question. #' @return VirtualMachine object. @@ -1575,9 +1584,9 @@ NULL NULL #' virtual_machines.create -#' +#' #' virtual_machines.create is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.create(virtualmachine, #' ensure_unique_name = "false") #' @param virtualMachine VirtualMachine object. @@ -1587,9 +1596,9 @@ NULL NULL #' virtual_machines.update -#' +#' #' virtual_machines.update is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.update(virtualmachine, #' uuid) #' @param virtualMachine VirtualMachine object. @@ -1599,9 +1608,9 @@ NULL NULL #' virtual_machines.delete -#' +#' #' virtual_machines.delete is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.delete(uuid) #' @param uuid The UUID of the VirtualMachine in question. #' @return VirtualMachine object. @@ -1609,48 +1618,48 @@ NULL NULL #' virtual_machines.logins -#' +#' #' virtual_machines.logins is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.logins(uuid) -#' @param uuid +#' @param uuid #' @return VirtualMachine object. #' @name virtual_machines.logins NULL #' virtual_machines.get_all_logins -#' +#' #' virtual_machines.get_all_logins is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.get_all_logins(NULL) #' @return VirtualMachine object. #' @name virtual_machines.get_all_logins NULL #' virtual_machines.list -#' +#' #' virtual_machines.list is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return VirtualMachineList object. #' @name virtual_machines.list NULL #' workflows.get -#' +#' #' workflows.get is a method defined in Arvados class. -#' +#' #' @usage arv$workflows.get(uuid) #' @param uuid The UUID of the Workflow in question. #' @return Workflow object. @@ -1658,9 +1667,9 @@ NULL NULL #' workflows.create -#' +#' #' workflows.create is a method defined in Arvados class. -#' +#' #' @usage arv$workflows.create(workflow, #' ensure_unique_name = "false") #' @param workflow Workflow object. @@ -1670,9 +1679,9 @@ NULL NULL #' workflows.update -#' +#' #' workflows.update is a method defined in Arvados class. -#' +#' #' @usage arv$workflows.update(workflow, #' uuid) #' @param workflow Workflow object. @@ -1682,9 +1691,9 @@ NULL NULL #' workflows.delete -#' +#' #' workflows.delete is a method defined in Arvados class. -#' +#' #' @usage arv$workflows.delete(uuid) #' @param uuid The UUID of the Workflow in question. #' @return Workflow object. @@ -1692,29 +1701,29 @@ NULL NULL #' workflows.list -#' +#' #' workflows.list is a method defined in Arvados class. -#' +#' #' @usage arv$workflows.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return WorkflowList object. #' @name workflows.list NULL #' groups.get -#' +#' #' groups.get is a method defined in Arvados class. -#' +#' #' @usage arv$groups.get(uuid) #' @param uuid The UUID of the Group in question. #' @return Group object. @@ -1722,9 +1731,9 @@ NULL NULL #' groups.create -#' +#' #' groups.create is a method defined in Arvados class. -#' +#' #' @usage arv$groups.create(group, ensure_unique_name = "false") #' @param group Group object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -1733,9 +1742,9 @@ NULL NULL #' groups.update -#' +#' #' groups.update is a method defined in Arvados class. -#' +#' #' @usage arv$groups.update(group, uuid) #' @param group Group object. #' @param uuid The UUID of the Group in question. @@ -1744,9 +1753,9 @@ NULL NULL #' groups.delete -#' +#' #' groups.delete is a method defined in Arvados class. -#' +#' #' @usage arv$groups.delete(uuid) #' @param uuid The UUID of the Group in question. #' @return Group object. @@ -1754,72 +1763,72 @@ NULL NULL #' groups.contents -#' +#' #' groups.contents is a method defined in Arvados class. -#' +#' #' @usage arv$groups.contents(filters = NULL, #' where = NULL, order = NULL, distinct = NULL, #' limit = "100", offset = "0", count = "exact", #' include_trash = NULL, uuid = NULL, recursive = NULL) -#' @param filters -#' @param where -#' @param order -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @param include_trash Include items whose is_trashed attribute is true. -#' @param uuid +#' @param uuid #' @param recursive Include contents from child groups recursively. #' @return Group object. #' @name groups.contents NULL #' groups.trash -#' +#' #' groups.trash is a method defined in Arvados class. -#' +#' #' @usage arv$groups.trash(uuid) -#' @param uuid +#' @param uuid #' @return Group object. #' @name groups.trash NULL #' groups.untrash -#' +#' #' groups.untrash is a method defined in Arvados class. -#' +#' #' @usage arv$groups.untrash(uuid) -#' @param uuid +#' @param uuid #' @return Group object. #' @name groups.untrash NULL #' groups.list -#' +#' #' groups.list is a method defined in Arvados class. -#' +#' #' @usage arv$groups.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact", include_trash = NULL) -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @param include_trash Include items whose is_trashed attribute is true. #' @return GroupList object. #' @name groups.list NULL #' user_agreements.get -#' +#' #' user_agreements.get is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.get(uuid) #' @param uuid The UUID of the UserAgreement in question. #' @return UserAgreement object. @@ -1827,9 +1836,9 @@ NULL NULL #' user_agreements.create -#' +#' #' user_agreements.create is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.create(useragreement, #' ensure_unique_name = "false") #' @param userAgreement UserAgreement object. @@ -1839,9 +1848,9 @@ NULL NULL #' user_agreements.update -#' +#' #' user_agreements.update is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.update(useragreement, #' uuid) #' @param userAgreement UserAgreement object. @@ -1851,9 +1860,9 @@ NULL NULL #' user_agreements.delete -#' +#' #' user_agreements.delete is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.delete(uuid) #' @param uuid The UUID of the UserAgreement in question. #' @return UserAgreement object. @@ -1861,56 +1870,56 @@ NULL NULL #' user_agreements.signatures -#' +#' #' user_agreements.signatures is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.signatures(NULL) #' @return UserAgreement object. #' @name user_agreements.signatures NULL #' user_agreements.sign -#' +#' #' user_agreements.sign is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.sign(NULL) #' @return UserAgreement object. #' @name user_agreements.sign NULL #' user_agreements.list -#' +#' #' user_agreements.list is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return UserAgreementList object. #' @name user_agreements.list NULL #' user_agreements.new -#' +#' #' user_agreements.new is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.new(NULL) #' @return UserAgreement object. #' @name user_agreements.new NULL #' project.get -#' +#' #' projects.get is equivalent to groups.get method. -#' +#' #' @usage arv$projects.get(uuid) #' @param uuid The UUID of the Group in question. #' @return Group object. @@ -1918,9 +1927,9 @@ NULL NULL #' project.create -#' +#' #' projects.create wrapps groups.create method by setting group_class attribute to "project". -#' +#' #' @usage arv$projects.create(group, ensure_unique_name = "false") #' @param group Group object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -1929,9 +1938,9 @@ NULL NULL #' project.update -#' +#' #' projects.update wrapps groups.update method by setting group_class attribute to "project". -#' +#' #' @usage arv$projects.update(group, uuid) #' @param group Group object. #' @param uuid The UUID of the Group in question. @@ -1940,9 +1949,9 @@ NULL NULL #' project.delete -#' +#' #' projects.delete is equivalent to groups.delete method. -#' +#' #' @usage arv$project.delete(uuid) #' @param uuid The UUID of the Group in question. #' @return Group object. @@ -1950,22 +1959,22 @@ NULL NULL #' project.list -#' +#' #' projects.list wrapps groups.list method by setting group_class attribute to "project". -#' +#' #' @usage arv$projects.list(filters = NULL, #' where = NULL, order = NULL, distinct = NULL, #' limit = "100", offset = "0", count = "exact", #' include_trash = NULL, uuid = NULL, recursive = NULL) -#' @param filters -#' @param where -#' @param order -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @param include_trash Include items whose is_trashed attribute is true. -#' @param uuid +#' @param uuid #' @param recursive Include contents from child groups recursively. #' @return Group object. #' @name projects.list @@ -2130,6 +2139,7 @@ NULL #' \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}}} @@ -2237,19 +2247,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2257,23 +2267,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(user) > 0) - body <- jsonlite::toJSON(list(user = user), + body <- jsonlite::toJSON(list(user = user), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2281,23 +2291,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(user) > 0) - body <- jsonlite::toJSON(list(user = user), + body <- jsonlite::toJSON(list(user = user), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2305,19 +2315,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2325,19 +2335,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/current") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2345,19 +2355,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/system") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2365,19 +2375,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}/activate") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2386,21 +2396,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/setup") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(user = user, openid_prefix = openid_prefix, repo_name = repo_name, vm_uuid = vm_uuid, send_notification_email = send_notification_email) - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2408,19 +2418,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}/unsetup") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2428,19 +2438,41 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}/update_uuid") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(new_uuid = new_uuid) - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) + + resource + }, + 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$errors) + resource }, @@ -2450,21 +2482,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2472,19 +2504,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2493,23 +2525,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(apiclientauthorization) > 0) - body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), + body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2517,23 +2549,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(apiclientauthorization) > 0) - body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), + body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2541,19 +2573,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2561,20 +2593,20 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations/create_system_auth") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(api_client_id = api_client_id, scopes = scopes) - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2582,19 +2614,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations/current") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2605,21 +2637,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2627,19 +2659,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2647,23 +2679,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(container) > 0) - body <- jsonlite::toJSON(list(container = container), + body <- jsonlite::toJSON(list(container = container), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2671,23 +2703,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(container) > 0) - body <- jsonlite::toJSON(list(container = container), + body <- jsonlite::toJSON(list(container = container), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2695,19 +2727,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2715,19 +2747,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}/auth") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2735,19 +2767,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}/lock") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2755,19 +2787,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}/unlock") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2775,19 +2807,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}/secret_mounts") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2795,19 +2827,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/current") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2818,21 +2850,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2840,19 +2872,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2860,23 +2892,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_clients") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(apiclient) > 0) - body <- jsonlite::toJSON(list(apiclient = apiclient), + body <- jsonlite::toJSON(list(apiclient = apiclient), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2884,23 +2916,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(apiclient) > 0) - body <- jsonlite::toJSON(list(apiclient = apiclient), + body <- jsonlite::toJSON(list(apiclient = apiclient), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2908,19 +2940,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2931,249 +2963,249 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_clients") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - authorized_keys.get = function(uuid) + container_requests.get = function(uuid) { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") + endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - authorized_keys.create = function(authorizedkey, + container_requests.create = function(containerrequest, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("authorized_keys") + endPoint <- stringr::str_interp("container_requests") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(authorizedkey) > 0) - body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), + + if(length(containerrequest) > 0) + body <- jsonlite::toJSON(list(containerrequest = containerrequest), auto_unbox = TRUE) else body <- NULL - + response <- private$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 }, - authorized_keys.update = function(authorizedkey, uuid) + container_requests.update = function(containerrequest, uuid) { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") + endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - - if(length(authorizedkey) > 0) - body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), + + if(length(containerrequest) > 0) + body <- jsonlite::toJSON(list(containerrequest = containerrequest), auto_unbox = TRUE) else body <- NULL - + response <- private$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 }, - authorized_keys.delete = function(uuid) + container_requests.delete = function(uuid) { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") + endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - authorized_keys.list = function(filters = NULL, + container_requests.list = function(filters = NULL, where = NULL, order = NULL, select = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("authorized_keys") + endPoint <- stringr::str_interp("container_requests") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - container_requests.get = function(uuid) + authorized_keys.get = function(uuid) { - endPoint <- stringr::str_interp("container_requests/${uuid}") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - container_requests.create = function(containerrequest, + authorized_keys.create = function(authorizedkey, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("container_requests") + endPoint <- stringr::str_interp("authorized_keys") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(containerrequest) > 0) - body <- jsonlite::toJSON(list(containerrequest = containerrequest), + + if(length(authorizedkey) > 0) + body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), auto_unbox = TRUE) else body <- NULL - + response <- private$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 }, - container_requests.update = function(containerrequest, uuid) + authorized_keys.update = function(authorizedkey, uuid) { - endPoint <- stringr::str_interp("container_requests/${uuid}") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - - if(length(containerrequest) > 0) - body <- jsonlite::toJSON(list(containerrequest = containerrequest), + + if(length(authorizedkey) > 0) + body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), auto_unbox = TRUE) else body <- NULL - + response <- private$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 }, - container_requests.delete = function(uuid) + authorized_keys.delete = function(uuid) { - endPoint <- stringr::str_interp("container_requests/${uuid}") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - container_requests.list = function(filters = NULL, + authorized_keys.list = function(filters = NULL, where = NULL, order = NULL, select = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("container_requests") + endPoint <- stringr::str_interp("authorized_keys") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3181,19 +3213,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3201,23 +3233,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(collection) > 0) - body <- jsonlite::toJSON(list(collection = collection), + body <- jsonlite::toJSON(list(collection = collection), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3225,23 +3257,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(collection) > 0) - body <- jsonlite::toJSON(list(collection = collection), + body <- jsonlite::toJSON(list(collection = collection), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3249,19 +3281,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3269,19 +3301,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}/provenance") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3289,19 +3321,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}/used_by") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3309,19 +3341,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}/trash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3329,19 +3361,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}/untrash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3352,22 +3384,22 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count, include_trash = include_trash) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3375,19 +3407,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("humans/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3395,23 +3427,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("humans") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(human) > 0) - body <- jsonlite::toJSON(list(human = human), + body <- jsonlite::toJSON(list(human = human), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3419,23 +3451,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("humans/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(human) > 0) - body <- jsonlite::toJSON(list(human = human), + body <- jsonlite::toJSON(list(human = human), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3443,19 +3475,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("humans/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3465,21 +3497,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("humans") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3487,19 +3519,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3507,23 +3539,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("job_tasks") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(jobtask) > 0) - body <- jsonlite::toJSON(list(jobtask = jobtask), + body <- jsonlite::toJSON(list(jobtask = jobtask), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3531,23 +3563,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(jobtask) > 0) - body <- jsonlite::toJSON(list(jobtask = jobtask), + body <- jsonlite::toJSON(list(jobtask = jobtask), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3555,19 +3587,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3578,1008 +3610,1008 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("job_tasks") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - links.get = function(uuid) + jobs.get = function(uuid) { - endPoint <- stringr::str_interp("links/${uuid}") + endPoint <- stringr::str_interp("jobs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - links.create = function(link, ensure_unique_name = "false") + jobs.create = function(job, ensure_unique_name = "false", + find_or_create = "false", filters = NULL, + minimum_script_version = NULL, exclude_script_versions = NULL) { - endPoint <- stringr::str_interp("links") + endPoint <- stringr::str_interp("jobs") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(link) > 0) - body <- jsonlite::toJSON(list(link = link), + queryArgs <- list(ensure_unique_name = ensure_unique_name, + find_or_create = find_or_create, filters = filters, + minimum_script_version = minimum_script_version, + exclude_script_versions = exclude_script_versions) + + if(length(job) > 0) + body <- jsonlite::toJSON(list(job = job), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - links.update = function(link, uuid) + jobs.update = function(job, uuid) { - endPoint <- stringr::str_interp("links/${uuid}") + endPoint <- stringr::str_interp("jobs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - - if(length(link) > 0) - body <- jsonlite::toJSON(list(link = link), + + if(length(job) > 0) + body <- jsonlite::toJSON(list(job = job), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - links.delete = function(uuid) + jobs.delete = function(uuid) { - endPoint <- stringr::str_interp("links/${uuid}") + endPoint <- stringr::str_interp("jobs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - links.list = function(filters = NULL, where = NULL, + jobs.queue = function(filters = NULL, where = NULL, order = NULL, select = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("links") + endPoint <- stringr::str_interp("jobs/queue") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - links.get_permissions = function(uuid) + jobs.queue_size = function() { - endPoint <- stringr::str_interp("permissions/${uuid}") + endPoint <- stringr::str_interp("jobs/queue_size") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - jobs.get = function(uuid) + jobs.cancel = function(uuid) { - endPoint <- stringr::str_interp("jobs/${uuid}") + endPoint <- stringr::str_interp("jobs/${uuid}/cancel") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, + + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - jobs.create = function(job, ensure_unique_name = "false", - find_or_create = "false", filters = NULL, - minimum_script_version = NULL, exclude_script_versions = NULL) + jobs.lock = function(uuid) { - endPoint <- stringr::str_interp("jobs") + endPoint <- stringr::str_interp("jobs/${uuid}/lock") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name, - find_or_create = find_or_create, filters = filters, - minimum_script_version = minimum_script_version, - exclude_script_versions = exclude_script_versions) - - if(length(job) > 0) - body <- jsonlite::toJSON(list(job = job), - auto_unbox = TRUE) - else - body <- NULL - + queryArgs <- NULL + + body <- NULL + response <- private$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 }, - jobs.update = function(job, uuid) + jobs.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("jobs/${uuid}") + endPoint <- stringr::str_interp("jobs") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(job) > 0) - body <- jsonlite::toJSON(list(job = job), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$REST$http$exec("PUT", url, headers, body, + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + + body <- NULL + + response <- private$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 }, - jobs.delete = function(uuid) + keep_disks.get = function(uuid) { - endPoint <- stringr::str_interp("jobs/${uuid}") + endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, + + 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$errors) - + resource }, - jobs.queue = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + keep_disks.create = function(keepdisk, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("jobs/queue") + endPoint <- stringr::str_interp("keep_disks") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, + queryArgs <- list(ensure_unique_name = ensure_unique_name) + + if(length(keepdisk) > 0) + body <- jsonlite::toJSON(list(keepdisk = keepdisk), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - jobs.queue_size = function() + keep_disks.update = function(keepdisk, uuid) { - endPoint <- stringr::str_interp("jobs/queue_size") + endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, + + if(length(keepdisk) > 0) + body <- jsonlite::toJSON(list(keepdisk = keepdisk), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - jobs.cancel = function(uuid) + keep_disks.delete = function(uuid) { - endPoint <- stringr::str_interp("jobs/${uuid}/cancel") + endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, + + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - jobs.lock = function(uuid) + keep_disks.ping = function(uuid = NULL, ping_secret, + node_uuid = NULL, filesystem_uuid = NULL, + service_host = NULL, service_port, service_ssl_flag) { - endPoint <- stringr::str_interp("jobs/${uuid}/lock") + endPoint <- stringr::str_interp("keep_disks/ping") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL - + queryArgs <- list(uuid = uuid, ping_secret = ping_secret, + node_uuid = node_uuid, filesystem_uuid = filesystem_uuid, + service_host = service_host, service_port = service_port, + service_ssl_flag = service_ssl_flag) + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - jobs.list = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + keep_disks.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("jobs") + endPoint <- stringr::str_interp("keep_disks") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - keep_disks.get = function(uuid) + nodes.get = function(uuid) { - endPoint <- stringr::str_interp("keep_disks/${uuid}") + endPoint <- stringr::str_interp("nodes/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - keep_disks.create = function(keepdisk, ensure_unique_name = "false") + nodes.create = function(node, ensure_unique_name = "false", + assign_slot = NULL) { - endPoint <- stringr::str_interp("keep_disks") + endPoint <- stringr::str_interp("nodes") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(keepdisk) > 0) - body <- jsonlite::toJSON(list(keepdisk = keepdisk), + queryArgs <- list(ensure_unique_name = ensure_unique_name, + assign_slot = assign_slot) + + if(length(node) > 0) + body <- jsonlite::toJSON(list(node = node), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - keep_disks.update = function(keepdisk, uuid) + nodes.update = function(node, uuid, assign_slot = NULL) { - endPoint <- stringr::str_interp("keep_disks/${uuid}") + endPoint <- stringr::str_interp("nodes/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(keepdisk) > 0) - body <- jsonlite::toJSON(list(keepdisk = keepdisk), + queryArgs <- list(assign_slot = assign_slot) + + if(length(node) > 0) + body <- jsonlite::toJSON(list(node = node), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - keep_disks.delete = function(uuid) + nodes.delete = function(uuid) { - endPoint <- stringr::str_interp("keep_disks/${uuid}") + endPoint <- stringr::str_interp("nodes/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - keep_disks.ping = function(uuid = NULL, ping_secret, - node_uuid = NULL, filesystem_uuid = NULL, - service_host = NULL, service_port, service_ssl_flag) + nodes.ping = function(uuid, ping_secret) { - endPoint <- stringr::str_interp("keep_disks/ping") + endPoint <- stringr::str_interp("nodes/${uuid}/ping") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid, ping_secret = ping_secret, - node_uuid = node_uuid, filesystem_uuid = filesystem_uuid, - service_host = service_host, service_port = service_port, - service_ssl_flag = service_ssl_flag) - + queryArgs <- list(ping_secret = ping_secret) + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - keep_disks.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + nodes.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("keep_disks") + endPoint <- stringr::str_interp("nodes") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - keep_services.get = function(uuid) + links.get = function(uuid) { - endPoint <- stringr::str_interp("keep_services/${uuid}") + endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - keep_services.create = function(keepservice, - ensure_unique_name = "false") + links.create = function(link, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("keep_services") + endPoint <- stringr::str_interp("links") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(keepservice) > 0) - body <- jsonlite::toJSON(list(keepservice = keepservice), + + if(length(link) > 0) + body <- jsonlite::toJSON(list(link = link), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - keep_services.update = function(keepservice, uuid) + links.update = function(link, uuid) { - endPoint <- stringr::str_interp("keep_services/${uuid}") + endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - - if(length(keepservice) > 0) - body <- jsonlite::toJSON(list(keepservice = keepservice), + + if(length(link) > 0) + body <- jsonlite::toJSON(list(link = link), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - keep_services.delete = function(uuid) + links.delete = function(uuid) { - endPoint <- stringr::str_interp("keep_services/${uuid}") + endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - keep_services.accessible = function() + links.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("keep_services/accessible") + endPoint <- stringr::str_interp("links") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL - + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - keep_services.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + links.get_permissions = function(uuid) { - endPoint <- stringr::str_interp("keep_services") + endPoint <- stringr::str_interp("permissions/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - + queryArgs <- NULL + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - pipeline_templates.get = function(uuid) + keep_services.get = function(uuid) { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") + endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - pipeline_templates.create = function(pipelinetemplate, + keep_services.create = function(keepservice, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("pipeline_templates") + endPoint <- stringr::str_interp("keep_services") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(pipelinetemplate) > 0) - body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), + + if(length(keepservice) > 0) + body <- jsonlite::toJSON(list(keepservice = keepservice), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - pipeline_templates.update = function(pipelinetemplate, uuid) + keep_services.update = function(keepservice, uuid) { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") + endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - - if(length(pipelinetemplate) > 0) - body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), + + if(length(keepservice) > 0) + body <- jsonlite::toJSON(list(keepservice = keepservice), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - pipeline_templates.delete = function(uuid) + keep_services.delete = function(uuid) { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") + endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) + + resource + }, + keep_services.accessible = function() + { + endPoint <- stringr::str_interp("keep_services/accessible") + 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$errors) + resource }, - pipeline_templates.list = function(filters = NULL, + keep_services.list = function(filters = NULL, where = NULL, order = NULL, select = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("pipeline_templates") + endPoint <- stringr::str_interp("keep_services") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - pipeline_instances.get = function(uuid) + pipeline_templates.get = function(uuid) { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") + endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - pipeline_instances.create = function(pipelineinstance, + pipeline_templates.create = function(pipelinetemplate, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("pipeline_instances") + endPoint <- stringr::str_interp("pipeline_templates") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(pipelineinstance) > 0) - body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), + + 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$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - pipeline_instances.update = function(pipelineinstance, uuid) + pipeline_templates.update = function(pipelinetemplate, uuid) { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") + endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - - if(length(pipelineinstance) > 0) - body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), + + 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$errors) - + resource }, - pipeline_instances.delete = function(uuid) + pipeline_templates.delete = function(uuid) { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") + endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - pipeline_instances.cancel = function(uuid) - { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}/cancel") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- 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$errors) - + resource }, - pipeline_instances.list = function(filters = NULL, + pipeline_templates.list = function(filters = NULL, where = NULL, order = NULL, select = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("pipeline_instances") + endPoint <- stringr::str_interp("pipeline_templates") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - nodes.get = function(uuid) + pipeline_instances.get = function(uuid) { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - nodes.create = function(node, ensure_unique_name = "false", - assign_slot = NULL) + pipeline_instances.create = function(pipelineinstance, + ensure_unique_name = "false") { - endPoint <- stringr::str_interp("nodes") + endPoint <- stringr::str_interp("pipeline_instances") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name, - assign_slot = assign_slot) - - if(length(node) > 0) - body <- jsonlite::toJSON(list(node = node), + queryArgs <- list(ensure_unique_name = ensure_unique_name) + + if(length(pipelineinstance) > 0) + body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - nodes.update = function(node, uuid, assign_slot = NULL) + pipeline_instances.update = function(pipelineinstance, uuid) { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(assign_slot = assign_slot) - - if(length(node) > 0) - body <- jsonlite::toJSON(list(node = node), + queryArgs <- NULL + + if(length(pipelineinstance) > 0) + body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - nodes.delete = function(uuid) + pipeline_instances.delete = function(uuid) { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, - nodes.ping = function(uuid, ping_secret) + pipeline_instances.cancel = function(uuid) { - endPoint <- stringr::str_interp("nodes/${uuid}/ping") + endPoint <- stringr::str_interp("pipeline_instances/${uuid}/cancel") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ping_secret = ping_secret) - + 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$errors) - + resource }, - nodes.list = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + pipeline_instances.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("nodes") + endPoint <- stringr::str_interp("pipeline_instances") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4587,19 +4619,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4607,23 +4639,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(repository) > 0) - body <- jsonlite::toJSON(list(repository = repository), + body <- jsonlite::toJSON(list(repository = repository), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4631,23 +4663,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(repository) > 0) - body <- jsonlite::toJSON(list(repository = repository), + body <- jsonlite::toJSON(list(repository = repository), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4655,19 +4687,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4675,19 +4707,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories/get_all_permissions") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4698,21 +4730,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4720,19 +4752,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("specimens/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4740,23 +4772,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("specimens") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(specimen) > 0) - body <- jsonlite::toJSON(list(specimen = specimen), + body <- jsonlite::toJSON(list(specimen = specimen), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4764,23 +4796,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("specimens/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(specimen) > 0) - body <- jsonlite::toJSON(list(specimen = specimen), + body <- jsonlite::toJSON(list(specimen = specimen), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4788,19 +4820,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("specimens/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4811,21 +4843,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("specimens") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4833,19 +4865,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4853,23 +4885,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("logs") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(log) > 0) - body <- jsonlite::toJSON(list(log = log), + body <- jsonlite::toJSON(list(log = log), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4877,23 +4909,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(log) > 0) - body <- jsonlite::toJSON(list(log = log), + body <- jsonlite::toJSON(list(log = log), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4901,19 +4933,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4923,21 +4955,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("logs") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4945,19 +4977,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("traits/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4965,23 +4997,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("traits") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(trait) > 0) - body <- jsonlite::toJSON(list(trait = trait), + body <- jsonlite::toJSON(list(trait = trait), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4989,23 +5021,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("traits/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(trait) > 0) - body <- jsonlite::toJSON(list(trait = trait), + body <- jsonlite::toJSON(list(trait = trait), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5013,19 +5045,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("traits/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5035,21 +5067,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("traits") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5057,19 +5089,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5078,23 +5110,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(virtualmachine) > 0) - body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), + body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5102,23 +5134,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(virtualmachine) > 0) - body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), + body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5126,19 +5158,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5146,19 +5178,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines/${uuid}/logins") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5166,19 +5198,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines/get_all_logins") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5189,21 +5221,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5211,19 +5243,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("workflows/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5231,23 +5263,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("workflows") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(workflow) > 0) - body <- jsonlite::toJSON(list(workflow = workflow), + body <- jsonlite::toJSON(list(workflow = workflow), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5255,23 +5287,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("workflows/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(workflow) > 0) - body <- jsonlite::toJSON(list(workflow = workflow), + body <- jsonlite::toJSON(list(workflow = workflow), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5279,19 +5311,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("workflows/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5302,21 +5334,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("workflows") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5324,19 +5356,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5344,23 +5376,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(group) > 0) - body <- jsonlite::toJSON(list(group = group), + body <- jsonlite::toJSON(list(group = group), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5368,23 +5400,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(group) > 0) - body <- jsonlite::toJSON(list(group = group), + body <- jsonlite::toJSON(list(group = group), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5392,19 +5424,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5415,22 +5447,22 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/contents") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, distinct = distinct, limit = limit, offset = offset, count = count, include_trash = include_trash, uuid = uuid, recursive = recursive) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5438,19 +5470,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/${uuid}/trash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5458,19 +5490,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/${uuid}/untrash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5481,22 +5513,22 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count, include_trash = include_trash) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5504,19 +5536,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5525,23 +5557,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(useragreement) > 0) - body <- jsonlite::toJSON(list(useragreement = useragreement), + body <- jsonlite::toJSON(list(useragreement = useragreement), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5549,23 +5581,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(useragreement) > 0) - body <- jsonlite::toJSON(list(useragreement = useragreement), + body <- jsonlite::toJSON(list(useragreement = useragreement), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5573,19 +5605,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5593,19 +5625,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/signatures") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5613,19 +5645,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/sign") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5636,21 +5668,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5658,19 +5690,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/new") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, diff --git a/sdk/R/R/ArvadosFile.R b/sdk/R/R/ArvadosFile.R index 1071302892..70bb4450ec 100644 --- a/sdk/R/R/ArvadosFile.R +++ b/sdk/R/R/ArvadosFile.R @@ -26,7 +26,8 @@ source("./R/util.R") #' \item{flush()}{Write connections content to a file (override current content of the file).} #' \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.} #' \item{getSizeInBytes()}{Returns file size in bytes.} -#' \item{move(newLocation)}{Moves file to a new location inside collection.} +#' \item{move(destination)}{Moves file to a new location inside collection.} +#' \item{copy(destination)}{Copies file to a new location inside collection.} #' } #' #' @name ArvadosFile @@ -49,6 +50,7 @@ source("./R/util.R") #' mytable <- read.table(arvConnection) #' #' myFile$move("newFolder/myFile") +#' myFile$copy("newFolder/myFile") #' } NULL @@ -83,7 +85,6 @@ ArvadosFile <- R6::R6Class( fileSize <- REST$getResourceSize(self$getRelativePath(), private$collection$uuid) - fileSize }, @@ -99,7 +100,7 @@ ArvadosFile <- R6::R6Class( getCollection = function() private$collection, - setCollection = function(collection) + setCollection = function(collection, setRecursively = TRUE) { private$collection <- collection }, @@ -176,20 +177,18 @@ ArvadosFile <- R6::R6Class( writeResult }, - move = function(newLocation) + move = function(destination) { if(is.null(private$collection)) - stop("ArvadosFile doesn't belong to any collection") + stop("ArvadosFile doesn't belong to any collection.") - newLocation <- trimFromEnd(newLocation, "/") - nameAndPath <- splitToPathAndName(newLocation) + destination <- trimFromEnd(destination, "/") + nameAndPath <- splitToPathAndName(destination) newParent <- private$collection$get(nameAndPath$path) if(is.null(newParent)) - { - stop("Unable to get destination subcollection") - } + stop("Unable to get destination subcollection.") childWithSameName <- newParent$get(nameAndPath$name) @@ -202,11 +201,50 @@ ArvadosFile <- R6::R6Class( private$collection$uuid) private$dettachFromCurrentParent() - private$attachToNewParent(newParent) + private$attachToNewParent(self, newParent) + private$parent <- newParent private$name <- nameAndPath$name - "Content moved successfully." + self + }, + + copy = function(destination) + { + if(is.null(private$collection)) + stop("ArvadosFile doesn't belong to any collection.") + + destination <- trimFromEnd(destination, "/") + nameAndPath <- splitToPathAndName(destination) + + newParent <- private$collection$get(nameAndPath$path) + + if(is.null(newParent)) + stop("Unable to get destination subcollection.") + + childWithSameName <- newParent$get(nameAndPath$name) + + if(!is.null(childWithSameName)) + stop("Destination already contains content with same name.") + + REST <- private$collection$getRESTService() + REST$copy(self$getRelativePath(), + paste0(newParent$getRelativePath(), "/", nameAndPath$name), + private$collection$uuid) + + newFile <- self$duplicate(nameAndPath$name) + newFile$setCollection(self$getCollection()) + private$attachToNewParent(newFile, newParent) + newFile$setParent(newParent) + + newFile + }, + + duplicate = function(newName = NULL) + { + name <- if(!is.null(newName)) newName else private$name + newFile <- ArvadosFile$new(name) + newFile } ), @@ -218,30 +256,29 @@ ArvadosFile <- R6::R6Class( collection = NULL, buffer = NULL, - attachToNewParent = function(newParent) + attachToNewParent = function(content, newParent) { - #Note: We temporary set parents collection to NULL. This will ensure that - # add method doesn't post file on REST. + # We temporary set parents collection to NULL. This will ensure that + # add method doesn't post this file on REST. + # We also need to set content's collection to NULL because + # add method throws exception if we try to add content that already + # belongs to a collection. parentsCollection <- newParent$getCollection() + content$setCollection(NULL, setRecursively = FALSE) newParent$setCollection(NULL, setRecursively = FALSE) - - newParent$add(self) - + newParent$add(content) + content$setCollection(parentsCollection, setRecursively = FALSE) newParent$setCollection(parentsCollection, setRecursively = FALSE) - - private$parent <- newParent }, dettachFromCurrentParent = function() { - #Note: We temporary set parents collection to NULL. This will ensure that - # remove method doesn't remove this subcollection from REST. + # We temporary set parents collection to NULL. This will ensure that + # remove method doesn't remove this file from REST. parent <- private$parent parentsCollection <- parent$getCollection() parent$setCollection(NULL, setRecursively = FALSE) - parent$remove(private$name) - parent$setCollection(parentsCollection, setRecursively = FALSE) } ), @@ -267,8 +304,8 @@ print.ArvadosFile = function(x, ...) relativePath <- paste0("/", relativePath) } - cat(paste0("Type: ", "\"", "ArvadosFile", "\""), sep = "\n") - cat(paste0("Name: ", "\"", x$getName(), "\""), sep = "\n") - cat(paste0("Relative path: ", "\"", relativePath, "\""), sep = "\n") - cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n") + cat(paste0("Type: ", "\"", "ArvadosFile", "\""), sep = "\n") + cat(paste0("Name: ", "\"", x$getName(), "\""), sep = "\n") + cat(paste0("Relative path: ", "\"", relativePath, "\""), sep = "\n") + cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n") } diff --git a/sdk/R/R/Collection.R b/sdk/R/R/Collection.R index 833b833c80..8869d7be67 100644 --- a/sdk/R/R/Collection.R +++ b/sdk/R/R/Collection.R @@ -23,9 +23,10 @@ source("./R/util.R") #' @section Methods: #' \describe{ #' \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.} -#' \item{create(fileNames, relativePath = "")}{Creates one or more ArvadosFiles and adds them to the collection at specified path.} +#' \item{create(files)}{Creates one or more ArvadosFiles and adds them to the collection at specified path.} #' \item{remove(fileNames)}{Remove one or more files from the collection.} -#' \item{move(content, newLocation)}{Moves ArvadosFile or Subcollection to another location in the collection.} +#' \item{move(content, destination)}{Moves ArvadosFile or Subcollection to another location in the collection.} +#' \item{copy(content, destination)}{Copies ArvadosFile or Subcollection to another location in the collection.} #' \item{getFileListing()}{Returns collections file content as character vector.} #' \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.} #' } @@ -36,9 +37,6 @@ source("./R/util.R") #' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com") #' collection <- Collection$new(arv, "uuid") #' -#' newFile <- ArvadosFile$new("myFile") -#' collection$add(newFile, "myFolder") -#' #' createdFiles <- collection$create(c("main.cpp", lib.dll), "cpp/src/") #' #' collection$remove("location/to/my/file.cpp") @@ -58,23 +56,17 @@ Collection <- R6::R6Class( public = list( uuid = NULL, - # api = NULL, initialize = function(api, uuid) { - # self$api <- api private$REST <- api$getRESTService() - self$uuid <- uuid - - private$fileContent <- private$REST$getCollectionContent(uuid) - private$tree <- CollectionTree$new(private$fileContent, self) }, add = function(content, relativePath = "") { if(is.null(private$tree)) - private$genereateCollectionTreeStructure() + private$generateCollectionTreeStructure() if(relativePath == "" || relativePath == "." || @@ -94,6 +86,9 @@ Collection <- R6::R6Class( if("ArvadosFile" %in% class(content) || "Subcollection" %in% class(content)) { + if(!is.null(content$getCollection())) + stop("Content already belongs to a collection.") + if(content$getName() == "") stop("Content has invalid name.") @@ -108,50 +103,32 @@ Collection <- R6::R6Class( } }, - create = function(fileNames, relativePath = "") + create = function(files) { if(is.null(private$tree)) - private$genereateCollectionTreeStructure() - - if(relativePath == "" || - relativePath == "." || - relativePath == "./") - { - subcollection <- private$tree$getTree() - } - else - { - relativePath <- trimFromEnd(relativePath, "/") - subcollection <- self$get(relativePath) - } - - if(is.null(subcollection)) - stop(paste("Subcollection", relativePath, "doesn't exist.")) + private$generateCollectionTreeStructure() - if(is.character(fileNames)) + if(is.character(files)) { - arvadosFiles <- NULL - sapply(fileNames, function(fileName) + sapply(files, function(file) { - childWithSameName <- subcollection$get(fileName) + childWithSameName <- self$get(file) if(!is.null(childWithSameName)) stop("Destination already contains file with same name.") - newFile <- ArvadosFile$new(fileName) - subcollection$add(newFile) + newTreeBranch <- private$tree$createBranch(file) + private$tree$addBranch(private$tree$getTree(), newTreeBranch) - arvadosFiles <<- c(arvadosFiles, newFile) + private$REST$create(file, self$uuid) + newTreeBranch$setCollection(self) }) - if(length(arvadosFiles) == 1) - return(arvadosFiles[[1]]) - else - return(arvadosFiles) + "Created" } else { stop(paste0("Expected character vector, got ", - paste0("(", paste0(class(fileNames), collapse = ", "), ")"), + paste0("(", paste0(class(files), collapse = ", "), ")"), ".")) } }, @@ -159,7 +136,7 @@ Collection <- R6::R6Class( remove = function(paths) { if(is.null(private$tree)) - private$genereateCollectionTreeStructure() + private$generateCollectionTreeStructure() if(is.character(paths)) { @@ -189,10 +166,10 @@ Collection <- R6::R6Class( } }, - move = function(content, newLocation) + move = function(content, destination) { if(is.null(private$tree)) - private$genereateCollectionTreeStructure() + private$generateCollectionTreeStructure() content <- trimFromEnd(content, "/") @@ -201,13 +178,37 @@ Collection <- R6::R6Class( if(is.null(elementToMove)) stop("Content you want to move doesn't exist in the collection.") - elementToMove$move(newLocation) + elementToMove$move(destination) + }, + + copy = function(content, destination) + { + if(is.null(private$tree)) + private$generateCollectionTreeStructure() + + content <- trimFromEnd(content, "/") + + elementToCopy <- self$get(content) + + if(is.null(elementToCopy)) + stop("Content you want to copy doesn't exist in the collection.") + + elementToCopy$copy(destination) + }, + + refresh = function() + { + if(!is.null(private$tree)) + { + private$tree$getTree()$setCollection(NULL, setRecursively = TRUE) + private$tree <- NULL + } }, getFileListing = function() { if(is.null(private$tree)) - private$genereateCollectionTreeStructure() + private$generateCollectionTreeStructure() content <- private$REST$getCollectionContent(self$uuid) content[order(tolower(content))] @@ -216,32 +217,11 @@ Collection <- R6::R6Class( get = function(relativePath) { if(is.null(private$tree)) - private$genereateCollectionTreeStructure() + private$generateCollectionTreeStructure() private$tree$getElement(relativePath) }, - toJSON = function() - { - fields <- sapply(private$classFields, function(field) - { - self[[field]] - }, USE.NAMES = TRUE) - - jsonlite::toJSON(list("collection" = - Filter(Negate(is.null), fields)), auto_unbox = TRUE) - }, - - isEmpty = function() { - fields <- sapply(private$classFields, - function(field) self[[field]]) - - if(any(sapply(fields, function(field) !is.null(field) && field != ""))) - FALSE - else - TRUE - }, - getRESTService = function() private$REST, setRESTService = function(newRESTService) private$REST <- newRESTService ), @@ -251,9 +231,8 @@ Collection <- R6::R6Class( REST = NULL, tree = NULL, fileContent = NULL, - classFields = NULL, - genereateCollectionTreeStructure = function() + generateCollectionTreeStructure = function() { if(is.null(self$uuid)) stop("Collection uuid is not defined.") diff --git a/sdk/R/R/CollectionTree.R b/sdk/R/R/CollectionTree.R index 8b2f8876b0..5f7a29455a 100644 --- a/sdk/R/R/CollectionTree.R +++ b/sdk/R/R/CollectionTree.R @@ -15,55 +15,16 @@ CollectionTree <- R6::R6Class( initialize = function(fileContent, collection) { self$pathsList <- fileContent - - treeBranches <- sapply(fileContent, function(filePath) - { - splitPath <- unlist(strsplit(filePath, "/", fixed = TRUE)) - branch <- private$createBranch(splitPath) - }) - + treeBranches <- sapply(fileContent, function(filePath) self$createBranch(filePath)) root <- Subcollection$new("") - - sapply(treeBranches, function(branch) - { - private$addBranch(root, branch) - }) - + sapply(treeBranches, function(branch) self$addBranch(root, branch)) root$setCollection(collection) private$tree <- root }, - getElement = function(relativePath) - { - relativePath <- trimFromStart(relativePath, "./") - relativePath <- trimFromEnd(relativePath, "/") - - if(endsWith(relativePath, "/")) - relativePath <- substr(relativePath, 0, nchar(relativePath) - 1) - - splitPath <- unlist(strsplit(relativePath, "/", fixed = TRUE)) - returnElement <- private$tree - - for(pathFragment in splitPath) - { - returnElement <- returnElement$get(pathFragment) - - if(is.null(returnElement)) - return(NULL) - } - - returnElement - }, - - getTree = function() private$tree - ), - - private = list( - - tree = NULL, - - createBranch = function(splitPath) + createBranch = function(filePath) { + splitPath <- unlist(strsplit(filePath, "/", fixed = TRUE)) branch <- NULL lastElementIndex <- length(splitPath) @@ -90,7 +51,11 @@ CollectionTree <- R6::R6Class( if(is.null(child)) { + # Make sure we are don't make any REST call while adding child + collection <- container$getCollection() + container$setCollection(NULL, setRecursively = FALSE) container$add(node) + container$setCollection(collection, setRecursively = FALSE) } else { @@ -100,14 +65,41 @@ CollectionTree <- R6::R6Class( # If we encounter that same name again we know # it's a folder so we need to replace ArvadosFile with Subcollection. if("ArvadosFile" %in% class(child)) - { child = private$replaceFileWithSubcollection(child) - } - private$addBranch(child, node$getFirst()) + self$addBranch(child, node$getFirst()) } }, + getElement = function(relativePath) + { + relativePath <- trimFromStart(relativePath, "./") + relativePath <- trimFromEnd(relativePath, "/") + + if(endsWith(relativePath, "/")) + relativePath <- substr(relativePath, 0, nchar(relativePath) - 1) + + splitPath <- unlist(strsplit(relativePath, "/", fixed = TRUE)) + returnElement <- private$tree + + for(pathFragment in splitPath) + { + returnElement <- returnElement$get(pathFragment) + + if(is.null(returnElement)) + return(NULL) + } + + returnElement + }, + + getTree = function() private$tree + ), + + private = list( + + tree = NULL, + replaceFileWithSubcollection = function(arvadosFile) { subcollection <- Subcollection$new(arvadosFile$getName()) diff --git a/sdk/R/R/HttpRequest.R b/sdk/R/R/HttpRequest.R index 4595fef662..07defca90f 100644 --- a/sdk/R/R/HttpRequest.R +++ b/sdk/R/R/HttpRequest.R @@ -16,7 +16,7 @@ HttpRequest <- R6::R6Class( initialize = function() { self$validContentTypes <- c("text", "raw") - self$validVerbs <- c("GET", "POST", "PUT", "DELETE", "PROPFIND", "MOVE") + self$validVerbs <- c("GET", "POST", "PUT", "DELETE", "PROPFIND", "MOVE", "COPY") }, exec = function(verb, url, headers = NULL, body = NULL, queryParams = NULL, diff --git a/sdk/R/R/RESTService.R b/sdk/R/R/RESTService.R index 867665299f..78b2c35e32 100644 --- a/sdk/R/R/RESTService.R +++ b/sdk/R/R/RESTService.R @@ -81,10 +81,10 @@ RESTService <- R6::R6Class( { collectionURL <- paste0(self$getWebDavHostName(), "c=", uuid, "/") fromURL <- paste0(collectionURL, from) - toURL <- paste0(collectionURL, to) + toURL <- paste0(collectionURL, trimFromStart(to, "/")) headers <- list("Authorization" = paste("OAuth2", self$token), - "Destination" = toURL) + "Destination" = toURL) serverResponse <- self$http$exec("MOVE", fromURL, headers, retryTimes = self$numRetries) @@ -95,6 +95,24 @@ RESTService <- R6::R6Class( serverResponse }, + copy = function(from, to, uuid) + { + collectionURL <- paste0(self$getWebDavHostName(), "c=", uuid, "/") + fromURL <- paste0(collectionURL, from) + toURL <- paste0(collectionURL, trimFromStart(to, "/")) + + headers <- list("Authorization" = paste("OAuth2", self$token), + "Destination" = toURL) + + serverResponse <- self$http$exec("COPY", fromURL, headers, + retryTimes = self$numRetries) + + if(serverResponse$status_code < 200 || serverResponse$status_code >= 300) + stop(paste("Server code:", serverResponse$status_code)) + + serverResponse + }, + getCollectionContent = function(uuid) { collectionURL <- URLencode(paste0(self$getWebDavHostName(), diff --git a/sdk/R/R/Subcollection.R b/sdk/R/R/Subcollection.R index 45fe343479..17a9ef3ee3 100644 --- a/sdk/R/R/Subcollection.R +++ b/sdk/R/R/Subcollection.R @@ -26,7 +26,8 @@ source("./R/util.R") #' \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.} #' \item{getFileListing()}{Returns subcollections file content as character vector.} #' \item{getSizeInBytes()}{Returns subcollections content size in bytes.} -#' \item{move(newLocation)}{Moves subcollection to a new location inside collection.} +#' \item{move(destination)}{Moves subcollection to a new location inside collection.} +#' \item{copy(destination)}{Copies subcollection to a new location inside collection.} #' } #' #' @name Subcollection @@ -40,6 +41,7 @@ source("./R/util.R") #' myFolder$remove("myFile") #' #' myFolder$move("newLocation/myFolder") +#' myFolder$copy("newLocation/myFolder") #' } NULL @@ -77,6 +79,9 @@ Subcollection <- R6::R6Class( if("ArvadosFile" %in% class(content) || "Subcollection" %in% class(content)) { + if(!is.null(content$getCollection())) + stop("Content already belongs to a collection.") + if(content$getName() == "") stop("Content has invalid name.") @@ -161,20 +166,18 @@ Subcollection <- R6::R6Class( return(sum(fileSizes)) }, - move = function(newLocation) + move = function(destination) { if(is.null(private$collection)) - stop("Subcollection doesn't belong to any collection") + stop("Subcollection doesn't belong to any collection.") - newLocation <- trimFromEnd(newLocation, "/") - nameAndPath <- splitToPathAndName(newLocation) + destination <- trimFromEnd(destination, "/") + nameAndPath <- splitToPathAndName(destination) newParent <- private$collection$get(nameAndPath$path) if(is.null(newParent)) - { - stop("Unable to get destination subcollection") - } + stop("Unable to get destination subcollection.") childWithSameName <- newParent$get(nameAndPath$name) @@ -187,11 +190,53 @@ Subcollection <- R6::R6Class( private$collection$uuid) private$dettachFromCurrentParent() - private$attachToNewParent(newParent) + private$attachToNewParent(self, newParent) + private$parent <- newParent private$name <- nameAndPath$name - "Content moved successfully." + self + }, + + copy = function(destination) + { + if(is.null(private$collection)) + stop("Subcollection doesn't belong to any collection.") + + destination <- trimFromEnd(destination, "/") + nameAndPath <- splitToPathAndName(destination) + + newParent <- private$collection$get(nameAndPath$path) + + if(is.null(newParent) || !("Subcollection" %in% class(newParent))) + stop("Unable to get destination subcollection.") + + childWithSameName <- newParent$get(nameAndPath$name) + + if(!is.null(childWithSameName)) + stop("Destination already contains content with same name.") + + REST <- private$collection$getRESTService() + REST$copy(self$getRelativePath(), + paste0(newParent$getRelativePath(), "/", nameAndPath$name), + private$collection$uuid) + + newContent <- self$duplicate(nameAndPath$name) + newContent$setCollection(self$getCollection(), setRecursively = TRUE) + newContent$setParent(newParent) + private$attachToNewParent(newContent, newParent) + + newContent + }, + + duplicate = function(newName = NULL) + { + name <- if(!is.null(newName)) newName else private$name + root <- Subcollection$new(name) + for(child in private$children) + root$add(child$duplicate()) + + root }, get = function(name) @@ -254,30 +299,29 @@ Subcollection <- R6::R6Class( } }, - attachToNewParent = function(newParent) + attachToNewParent = function(content, newParent) { - #Note: We temporary set parents collection to NULL. This will ensure that - # add method doesn't post file on REST. + # We temporary set parents collection to NULL. This will ensure that + # add method doesn't post this subcollection to REST. + # We also need to set content's collection to NULL because + # add method throws exception if we try to add content that already + # belongs to a collection. parentsCollection <- newParent$getCollection() + content$setCollection(NULL, setRecursively = FALSE) newParent$setCollection(NULL, setRecursively = FALSE) - - newParent$add(self) - + newParent$add(content) + content$setCollection(parentsCollection, setRecursively = FALSE) newParent$setCollection(parentsCollection, setRecursively = FALSE) - - private$parent <- newParent }, dettachFromCurrentParent = function() { - #Note: We temporary set parents collection to NULL. This will ensure that - # remove method doesn't remove this subcollection from REST. + # We temporary set parents collection to NULL. This will ensure that + # remove method doesn't remove this subcollection from REST. parent <- private$parent parentsCollection <- parent$getCollection() parent$setCollection(NULL, setRecursively = FALSE) - parent$remove(private$name) - parent$setCollection(parentsCollection, setRecursively = FALSE) }, diff --git a/sdk/R/R/zzz.R b/sdk/R/R/zzz.R index c98f803e5e..fa0cda45bf 100644 --- a/sdk/R/R/zzz.R +++ b/sdk/R/R/zzz.R @@ -1,3 +1,7 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + .onLoad <- function(libName, pkgName) { minAllowedRVersion <- "3.3.0" diff --git a/sdk/R/README.Rmd b/sdk/R/README.Rmd index be34b2fdb1..7ea226fd09 100644 --- a/sdk/R/README.Rmd +++ b/sdk/R/README.Rmd @@ -186,31 +186,16 @@ size <- arvadosSubcollection$getSizeInBytes() * Create new file in a collection: ```{r} -collection$create(fileNames, optionalRelativePath) +collection$create(files) ``` Example: ```{r} -mainFile <- collection$create("main.cpp", "cpp/src/") -fileList <- collection$create(c("main.cpp", lib.dll), "cpp/src/") +mainFile <- collection$create("cpp/src/main.cpp") +fileList <- collection$create(c("cpp/src/main.cpp", "cpp/src/util.h")) ``` -* Add existing ArvadosFile or Subcollection to a collection: - -```{r} -folder <- Subcollection$new("src") -file <- ArvadosFile$new("main.cpp") -folder$add(file) -``` - -```{r} -collection$add(folder, "cpp") -``` - -This examples will add file "main.cpp" in "./cpp/src/" folder if folder exists. -If subcollection contains more files or folders they will be added recursively. - * Delete file from a collection: ```{r} @@ -259,6 +244,28 @@ subcollection$move("newDestination/folder") Make sure to include new file name in destination. In second example file$move("newDestination/") will not work. +* Copy file or folder inside collection: + +Directley from collection + +```{r} +collection$copy("folder/file.cpp", "file.cpp") +``` + +Or from file + +```{r} +file <- collection$get("location/to/my/file.cpp") +file$copy("destination/file.cpp") +``` + +Or from subcollection + +```{r} +subcollection <- collection$get("location/to/folder") +subcollection$copy("destination/folder") +``` + #### Working with Aravdos projects * Get a project: diff --git a/sdk/R/man/Arvados.Rd b/sdk/R/man/Arvados.Rd index 95a2e5561f..51f98d81dc 100644 --- a/sdk/R/man/Arvados.Rd +++ b/sdk/R/man/Arvados.Rd @@ -166,6 +166,7 @@ Arvados class gives users ability to access Arvados REST API. \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}}} diff --git a/sdk/R/man/ArvadosFile.Rd b/sdk/R/man/ArvadosFile.Rd index b7840dc16f..514e9e846d 100644 --- a/sdk/R/man/ArvadosFile.Rd +++ b/sdk/R/man/ArvadosFile.Rd @@ -29,7 +29,8 @@ ArvadosFile class represents a file inside Arvados collection. \item{flush()}{Write connections content to a file (override current content of the file).} \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.} \item{getSizeInBytes()}{Returns file size in bytes.} - \item{move(newLocation)}{Moves file to a new location inside collection.} + \item{move(destination)}{Moves file to a new location inside collection.} + \item{copy(destination)}{Copies file to a new location inside collection.} } } @@ -40,7 +41,7 @@ myFile <- ArvadosFile$new("myFile") myFile$write("This is new file content") fileContent <- myFile$read() fileContent <- myFile$read("text") -fileContent <- myFile$read("raw", offset = 8, length = 4) +fileContent <- myFile$read("raw", offset = 8, length = 4) #Write a table: arvConnection <- myFile$connection("w") @@ -52,5 +53,6 @@ arvConnection <- myFile$connection("r") mytable <- read.table(arvConnection) myFile$move("newFolder/myFile") +myFile$copy("newFolder/myFile") } } diff --git a/sdk/R/man/Collection.Rd b/sdk/R/man/Collection.Rd index 8cf29a2ea5..fbe6038664 100644 --- a/sdk/R/man/Collection.Rd +++ b/sdk/R/man/Collection.Rd @@ -23,9 +23,10 @@ Collection class provides interface for working with Arvados collections. \describe{ \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.} - \item{create(fileNames, relativePath = "")}{Creates one or more ArvadosFiles and adds them to the collection at specified path.} + \item{create(files)}{Creates one or more ArvadosFiles and adds them to the collection at specified path.} \item{remove(fileNames)}{Remove one or more files from the collection.} - \item{move(content, newLocation)}{Moves ArvadosFile or Subcollection to another location in the collection.} + \item{move(content, destination)}{Moves ArvadosFile or Subcollection to another location in the collection.} + \item{copy(content, destination)}{Copies ArvadosFile or Subcollection to another location in the collection.} \item{getFileListing()}{Returns collections file content as character vector.} \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.} } @@ -36,9 +37,6 @@ Collection class provides interface for working with Arvados collections. arv <- Arvados$new("your Arvados token", "example.arvadosapi.com") collection <- Collection$new(arv, "uuid") -newFile <- ArvadosFile$new("myFile") -collection$add(newFile, "myFolder") - createdFiles <- collection$create(c("main.cpp", lib.dll), "cpp/src/") collection$remove("location/to/my/file.cpp") diff --git a/sdk/R/man/Subcollection.Rd b/sdk/R/man/Subcollection.Rd index df0970b30f..0b27a8bc43 100644 --- a/sdk/R/man/Subcollection.Rd +++ b/sdk/R/man/Subcollection.Rd @@ -5,7 +5,7 @@ \title{Subcollection} \description{ Subcollection class represents a folder inside Arvados collection. -It is essentially a composite of ArvadosFiles and other Subcollections. +It is essentially a composite of arvadosFiles and other subcollections. } \section{Usage}{ @@ -29,7 +29,8 @@ It is essentially a composite of ArvadosFiles and other Subcollections. \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.} \item{getFileListing()}{Returns subcollections file content as character vector.} \item{getSizeInBytes()}{Returns subcollections content size in bytes.} - \item{move(newLocation)}{Moves subcollection to a new location inside collection.} + \item{move(destination)}{Moves subcollection to a new location inside collection.} + \item{copy(destination)}{Copies subcollection to a new location inside collection.} } } @@ -43,5 +44,6 @@ myFolder$get("myFile") myFolder$remove("myFile") myFolder$move("newLocation/myFolder") +myFolder$copy("newLocation/myFolder") } } diff --git a/sdk/R/man/users.merge.Rd b/sdk/R/man/users.merge.Rd new file mode 100644 index 0000000000..a539591a6a --- /dev/null +++ b/sdk/R/man/users.merge.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Arvados.R +\name{users.merge} +\alias{users.merge} +\title{users.merge} +\usage{ +arv$users.merge(new_owner_uuid, + new_user_token, redirect_to_new_user = NULL) +} +\arguments{ +\item{new_owner_uuid}{} + +\item{new_user_token}{} + +\item{redirect_to_new_user}{} +} +\value{ +User object. +} +\description{ +users.merge is a method defined in Arvados class. +} diff --git a/sdk/R/tests/testthat/fakes/FakeHttpRequest.R b/sdk/R/tests/testthat/fakes/FakeHttpRequest.R index 2ebcda2e4d..7734e0d928 100644 --- a/sdk/R/tests/testthat/fakes/FakeHttpRequest.R +++ b/sdk/R/tests/testthat/fakes/FakeHttpRequest.R @@ -27,6 +27,7 @@ FakeHttpRequest <- R6::R6Class( numberOfPUTRequests = NULL, numberOfPOSTRequests = NULL, numberOfMOVERequests = NULL, + numberOfCOPYRequests = NULL, numberOfgetConnectionCalls = NULL, initialize = function(expectedURL = NULL, @@ -57,6 +58,7 @@ FakeHttpRequest <- R6::R6Class( self$numberOfPUTRequests <- 0 self$numberOfPOSTRequests <- 0 self$numberOfMOVERequests <- 0 + self$numberOfCOPYRequests <- 0 self$numberOfgetConnectionCalls <- 0 @@ -81,6 +83,8 @@ FakeHttpRequest <- R6::R6Class( self$numberOfDELETERequests <- self$numberOfDELETERequests + 1 else if(verb == "MOVE") self$numberOfMOVERequests <- self$numberOfMOVERequests + 1 + else if(verb == "COPY") + self$numberOfCOPYRequests <- self$numberOfCOPYRequests + 1 else if(verb == "PROPFIND") { return(self$content) diff --git a/sdk/R/tests/testthat/fakes/FakeRESTService.R b/sdk/R/tests/testthat/fakes/FakeRESTService.R index 048013f566..a91da04fd1 100644 --- a/sdk/R/tests/testthat/fakes/FakeRESTService.R +++ b/sdk/R/tests/testthat/fakes/FakeRESTService.R @@ -18,6 +18,7 @@ FakeRESTService <- R6::R6Class( createCallCount = NULL, deleteCallCount = NULL, moveCallCount = NULL, + copyCallCount = NULL, getCollectionContentCallCount = NULL, getResourceSizeCallCount = NULL, readCallCount = NULL, @@ -31,7 +32,7 @@ FakeRESTService <- R6::R6Class( collectionContent = NULL, returnContent = NULL, - initialize = function(collectionContent = NULL, returnContent = NULL, + initialize = function(collectionContent = NULL, returnContent = NULL, expectedFilterContent = NULL) { self$getResourceCallCount <- 0 @@ -44,6 +45,7 @@ FakeRESTService <- R6::R6Class( self$createCallCount <- 0 self$deleteCallCount <- 0 self$moveCallCount <- 0 + self$copyCallCount <- 0 self$getCollectionContentCallCount <- 0 self$getResourceSizeCallCount <- 0 self$readCallCount <- 0 @@ -135,6 +137,12 @@ FakeRESTService <- R6::R6Class( self$returnContent }, + copy = function(from, to, uuid) + { + self$copyCallCount <- self$copyCallCount + 1 + self$returnContent + }, + getCollectionContent = function(uuid) { self$getCollectionContentCallCount <- self$getCollectionContentCallCount + 1 @@ -146,7 +154,7 @@ FakeRESTService <- R6::R6Class( self$getResourceSizeCallCount <- self$getResourceSizeCallCount + 1 self$returnContent }, - + read = function(relativePath, uuid, contentType = "text", offset = 0, length = 0) { self$readCallCount <- self$readCallCount + 1 diff --git a/sdk/R/tests/testthat/test-ArvadosFile.R b/sdk/R/tests/testthat/test-ArvadosFile.R index 1f559e999c..e3457c993f 100644 --- a/sdk/R/tests/testthat/test-ArvadosFile.R +++ b/sdk/R/tests/testthat/test-ArvadosFile.R @@ -81,7 +81,6 @@ test_that("read raises exception if file doesn't belong to a collection", { test_that("read raises exception offset or length is negative number", { - collectionContent <- c("animal", "animal/fish") fakeREST <- FakeRESTService$new(collectionContent) @@ -156,7 +155,6 @@ test_that(paste("connection returns textConnection opened", test_that("flush sends data stored in a connection to a REST server", { - collectionContent <- c("animal", "animal/fish") fakeREST <- FakeRESTService$new(collectionContent) @@ -204,13 +202,12 @@ test_that(paste("move raises exception if arvados file", animal <- ArvadosFile$new("animal") expect_that(animal$move("new/location"), - throws_error("ArvadosFile doesn't belong to any collection")) + throws_error("ArvadosFile doesn't belong to any collection.")) }) test_that(paste("move raises exception if newLocationInCollection", "parameter is invalid"), { - collectionContent <- c("animal", "animal/fish", "animal/dog", @@ -226,7 +223,7 @@ test_that(paste("move raises exception if newLocationInCollection", dog <- collection$get("animal/dog") expect_that(dog$move("objects/dog"), - throws_error("Unable to get destination subcollection")) + throws_error("Unable to get destination subcollection.")) }) test_that("move raises exception if new location contains content with the same name", { @@ -252,7 +249,6 @@ test_that("move raises exception if new location contains content with the same test_that("move moves arvados file inside collection tree", { - collectionContent <- c("animal", "animal/fish", "animal/dog", @@ -273,3 +269,85 @@ test_that("move moves arvados file inside collection tree", { expect_that(dogIsNullOnOldLocation, is_true()) expect_that(dogExistsOnNewLocation, is_true()) }) + +test_that(paste("copy raises exception if arvados file", + "doesn't belong to any collection"), { + + animal <- ArvadosFile$new("animal") + + expect_that(animal$copy("new/location"), + throws_error("ArvadosFile doesn't belong to any collection.")) +}) + +test_that(paste("copy raises exception if location parameter is invalid"), { + + collectionContent <- c("animal", + "animal/fish", + "animal/dog", + "animal/fish/shark", + "ball") + + fakeREST <- FakeRESTService$new(collectionContent) + + api <- Arvados$new("myToken", "myHostName") + api$setRESTService(fakeREST) + + collection <- Collection$new(api, "myUUID") + dog <- collection$get("animal/dog") + + expect_that(dog$copy("objects/dog"), + throws_error("Unable to get destination subcollection.")) +}) + +test_that("copy raises exception if new location contains content with the same name", { + + + collectionContent <- c("animal", + "animal/fish", + "animal/dog", + "animal/fish/shark", + "dog") + + fakeREST <- FakeRESTService$new(collectionContent) + + api <- Arvados$new("myToken", "myHostName") + api$setRESTService(fakeREST) + collection <- Collection$new(api, "myUUID") + dog <- collection$get("animal/dog") + + expect_that(dog$copy("dog"), + throws_error("Destination already contains content with same name.")) + +}) + +test_that("copy copies arvados file inside collection tree", { + + collectionContent <- c("animal", + "animal/fish", + "animal/dog", + "animal/fish/shark", + "ball") + + fakeREST <- FakeRESTService$new(collectionContent) + + api <- Arvados$new("myToken", "myHostName") + api$setRESTService(fakeREST) + collection <- Collection$new(api, "myUUID") + dog <- collection$get("animal/dog") + + dog$copy("dog") + dogExistsOnOldLocation <- !is.null(collection$get("animal/dog")) + dogExistsOnNewLocation <- !is.null(collection$get("dog")) + + expect_that(dogExistsOnOldLocation, is_true()) + expect_that(dogExistsOnNewLocation, is_true()) +}) + +test_that("duplicate performs deep cloning of Arvados file", { + arvFile <- ArvadosFile$new("foo") + newFile1 <- arvFile$duplicate() + newFile2 <- arvFile$duplicate("bar") + + expect_that(newFile1$getFileListing(), equals(arvFile$getFileListing())) + expect_that(newFile2$getFileListing(), equals(c("bar"))) +}) diff --git a/sdk/R/tests/testthat/test-Collection.R b/sdk/R/tests/testthat/test-Collection.R index af5fabeb73..636359ae21 100644 --- a/sdk/R/tests/testthat/test-Collection.R +++ b/sdk/R/tests/testthat/test-Collection.R @@ -104,37 +104,15 @@ test_that("create raises exception if passed argumet is not character vector", { fixed = TRUE)) }) -test_that("create raises exception if relative path is not valid", { - - collectionContent <- c("animal", - "animal/fish", - "ball") - - fakeREST <- FakeRESTService$new(collectionContent) - - api <- Arvados$new("myToken", "myHostName") - api$setRESTService(fakeREST) - collection <- Collection$new(api, "myUUID") - - newPen <- ArvadosFile$new("pen") - - expect_that(collection$create(newPen, "objects"), - throws_error("Subcollection objects doesn't exist.", - fixed = TRUE)) -}) - test_that(paste("create adds files specified by fileNames", "to local tree structure and remote REST service"), { - collectionContent <- c("animal", "animal/fish", "ball") - fakeREST <- FakeRESTService$new(collectionContent) - + fakeREST <- FakeRESTService$new() api <- Arvados$new("myToken", "myHostName") api$setRESTService(fakeREST) collection <- Collection$new(api, "myUUID") - files <- c("dog", "cat") - collection$create(files, "animal") + collection$create(c("animal/dog", "animal/cat")) dog <- collection$get("animal/dog") cat <- collection$get("animal/cat") @@ -262,3 +240,58 @@ test_that("get returns arvados file or subcollection from internal tree structur expect_that(fishIsNotNull, is_true()) expect_that(fish$getName(), equals("fish")) }) + +test_that(paste("copy copies content to a new location inside file tree", + "and on REST service"), { + + collectionContent <- c("animal", "animal/dog", "ball") + fakeREST <- FakeRESTService$new(collectionContent) + + api <- Arvados$new("myToken", "myHostName") + api$setRESTService(fakeREST) + collection <- Collection$new(api, "myUUID") + + collection$copy("animal/dog", "dog") + + dogExistsOnOldLocation <- !is.null(collection$get("animal/dog")) + dogExistsOnNewLocation <- !is.null(collection$get("dog")) + + expect_that(dogExistsOnOldLocation, is_true()) + expect_that(dogExistsOnNewLocation, is_true()) + expect_that(fakeREST$copyCallCount, equals(1)) +}) + +test_that("copy raises exception if new location is not valid", { + + collectionContent <- c("animal", "animal/fish", "ball") + fakeREST <- FakeRESTService$new(collectionContent) + + api <- Arvados$new("myToken", "myHostName") + api$setRESTService(fakeREST) + collection <- Collection$new(api, "myUUID") + + expect_that(collection$copy("fish", "object"), + throws_error("Content you want to copy doesn't exist in the collection.", + fixed = TRUE)) +}) + +test_that("refresh invalidates current tree structure", { + + collectionContent <- c("animal", "animal/fish", "ball") + fakeREST <- FakeRESTService$new(collectionContent) + + api <- Arvados$new("myToken", "myHostName") + api$setRESTService(fakeREST) + collection <- Collection$new(api, "aaaaa-j7d0g-ccccccccccccccc") + + # Before refresh + fish <- collection$get("animal/fish") + expect_that(fish$getName(), equals("fish")) + expect_that(fish$getCollection()$uuid, equals("aaaaa-j7d0g-ccccccccccccccc")) + + collection$refresh() + + # After refresh + expect_that(fish$getName(), equals("fish")) + expect_true(is.null(fish$getCollection())) +}) diff --git a/sdk/R/tests/testthat/test-RESTService.R b/sdk/R/tests/testthat/test-RESTService.R index 26f459b173..64988e33db 100644 --- a/sdk/R/tests/testthat/test-RESTService.R +++ b/sdk/R/tests/testthat/test-RESTService.R @@ -135,6 +135,40 @@ test_that("move raises exception if server response code is not between 200 and throws_error("Server code: 404")) }) +test_that("copy calls REST service properly", { + + uuid <- "aaaaa-j7d0g-ccccccccccccccc" + expectedURL <- "https://webDavHost/c=aaaaa-j7d0g-ccccccccccccccc/file" + fakeHttp <- FakeHttpRequest$new(expectedURL) + fakeHttpParser <- FakeHttpParser$new() + + REST <- RESTService$new("token", "https://host/", + fakeHttp, fakeHttpParser, + 0, "https://webDavHost/") + + REST$copy("file", "newDestination/file", uuid) + + expect_that(fakeHttp$URLIsProperlyConfigured, is_true()) + expect_that(fakeHttp$requestHeaderContainsAuthorizationField, is_true()) + expect_that(fakeHttp$requestHeaderContainsDestinationField, is_true()) + expect_that(fakeHttp$numberOfCOPYRequests, equals(1)) +}) + +test_that("copy raises exception if server response code is not between 200 and 300", { + + uuid <- "aaaaa-j7d0g-ccccccccccccccc" + response <- list() + response$status_code <- 404 + fakeHttp <- FakeHttpRequest$new(serverResponse = response) + + REST <- RESTService$new("token", "https://host/", + fakeHttp, HttpParser$new(), + 0, "https://webDavHost/") + + expect_that(REST$copy("file", "newDestination/file", uuid), + throws_error("Server code: 404")) +}) + test_that("getCollectionContent retreives correct content from WebDAV server", { uuid <- "aaaaa-j7d0g-ccccccccccccccc" diff --git a/sdk/R/tests/testthat/test-Subcollection.R b/sdk/R/tests/testthat/test-Subcollection.R index 6845801e59..a6e420962b 100644 --- a/sdk/R/tests/testthat/test-Subcollection.R +++ b/sdk/R/tests/testthat/test-Subcollection.R @@ -309,7 +309,7 @@ test_that(paste("move raises exception if newLocationInCollection", fish <- collection$get("animal/fish") expect_that(fish$move("objects/dog"), - throws_error("Unable to get destination subcollection")) + throws_error("Unable to get destination subcollection.")) }) test_that("move moves subcollection inside collection tree", { @@ -358,3 +358,87 @@ test_that(paste("getSizeInBytes delegates size calculation", expect_that(resourceSize, equals(100)) }) + +######################### +test_that(paste("copy raises exception if subcollection", + "doesn't belong to any collection"), { + + animal <- Subcollection$new("animal") + + expect_that(animal$copy("new/location"), + throws_error("Subcollection doesn't belong to any collection.")) +}) + +test_that("copy raises exception if new location contains content with the same name", { + + collectionContent <- c("animal", + "animal/fish", + "animal/dog", + "animal/fish/shark", + "fish") + fakeREST <- FakeRESTService$new(collectionContent) + + api <- Arvados$new("myToken", "myHostName") + api$setRESTService(fakeREST) + collection <- Collection$new(api, "myUUID") + fish <- collection$get("animal/fish") + + expect_that(fish$copy("fish"), + throws_error("Destination already contains content with same name.")) + +}) + +test_that(paste("copy raises exception if location parameter is invalid"), { + + collectionContent <- c("animal", + "animal/fish", + "animal/dog", + "animal/fish/shark", + "ball") + fakeREST <- FakeRESTService$new(collectionContent) + + api <- Arvados$new("myToken", "myHostName") + api$setRESTService(fakeREST) + + collection <- Collection$new(api, "myUUID") + fish <- collection$get("animal/fish") + + expect_that(fish$copy("objects/dog"), + throws_error("Unable to get destination subcollection.")) +}) + +test_that("copy copies subcollection inside collection tree", { + + collectionContent <- c("animal", + "animal/fish", + "animal/dog", + "animal/fish/shark", + "ball") + fakeREST <- FakeRESTService$new(collectionContent) + + api <- Arvados$new("myToken", "myHostName") + api$setRESTService(fakeREST) + collection <- Collection$new(api, "myUUID") + fish <- collection$get("animal/fish") + + fish$copy("fish") + fishExistsOnOldLocation <- !is.null(collection$get("animal/fish")) + fishExistsOnNewLocation <- !is.null(collection$get("fish")) + + expect_that(fishExistsOnOldLocation, is_true()) + expect_that(fishExistsOnNewLocation, is_true()) +}) + +test_that("duplicate performs deep cloning of Subcollection", { + foo <- ArvadosFile$new("foo") + bar <- ArvadosFile$new("bar") + sub <- Subcollection$new("qux") + sub$add(foo) + sub$add(bar) + + newSub1 <- sub$duplicate() + newSub2 <- sub$duplicate("quux") + + expect_that(newSub1$getFileListing(), equals(sub$getFileListing())) + expect_that(sort(newSub2$getFileListing()), equals(c("quux/bar", "quux/foo"))) +})