#
# SPDX-License-Identifier: Apache-2.0
-#' api_clients.get
+#' R6 Class Representing a Arvados
#'
-#' api_clients.get is a method defined in Arvados class.
-#'
-#' @usage arv$api_clients.get(uuid)
-#' @param uuid The UUID of the ApiClient in question.
-#' @return ApiClient object.
-#' @name api_clients.get
-NULL
-
-#' api_clients.create
-#'
-#' api_clients.create is a method defined in Arvados class.
-#'
-#' @usage arv$api_clients.create(apiclient,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param apiClient ApiClient object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return ApiClient object.
-#' @name api_clients.create
-NULL
-
-#' api_clients.update
-#'
-#' api_clients.update is a method defined in Arvados class.
-#'
-#' @usage arv$api_clients.update(apiclient,
-#' uuid)
-#' @param apiClient ApiClient object.
-#' @param uuid The UUID of the ApiClient in question.
-#' @return ApiClient object.
-#' @name api_clients.update
-NULL
-
-#' api_clients.delete
-#'
-#' api_clients.delete is a method defined in Arvados class.
-#'
-#' @usage arv$api_clients.delete(uuid)
-#' @param uuid The UUID of the ApiClient in question.
-#' @return ApiClient object.
-#' @name api_clients.delete
-NULL
-
-#' api_clients.list
-#'
-#' api_clients.list is a method defined in Arvados class.
-#'
-#' @usage arv$api_clients.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return ApiClientList object.
-#' @name api_clients.list
-NULL
-
-#' api_client_authorizations.get
-#'
-#' api_client_authorizations.get is a method defined in Arvados class.
-#'
-#' @usage arv$api_client_authorizations.get(uuid)
-#' @param uuid The UUID of the ApiClientAuthorization in question.
-#' @return ApiClientAuthorization object.
-#' @name api_client_authorizations.get
-NULL
-
-#' api_client_authorizations.create
-#'
-#' api_client_authorizations.create is a method defined in Arvados class.
-#'
-#' @usage arv$api_client_authorizations.create(apiclientauthorization,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param apiClientAuthorization ApiClientAuthorization object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return ApiClientAuthorization object.
-#' @name api_client_authorizations.create
-NULL
-
-#' api_client_authorizations.update
-#'
-#' api_client_authorizations.update is a method defined in Arvados class.
-#'
-#' @usage arv$api_client_authorizations.update(apiclientauthorization,
-#' uuid)
-#' @param apiClientAuthorization ApiClientAuthorization object.
-#' @param uuid The UUID of the ApiClientAuthorization in question.
-#' @return ApiClientAuthorization object.
-#' @name api_client_authorizations.update
-NULL
-
-#' api_client_authorizations.delete
-#'
-#' api_client_authorizations.delete is a method defined in Arvados class.
-#'
-#' @usage arv$api_client_authorizations.delete(uuid)
-#' @param uuid The UUID of the ApiClientAuthorization in question.
-#' @return ApiClientAuthorization object.
-#' @name api_client_authorizations.delete
-NULL
-
-#' api_client_authorizations.create_system_auth
-#'
-#' api_client_authorizations.create_system_auth is a method defined in Arvados class.
-#'
-#' @usage arv$api_client_authorizations.create_system_auth(api_client_id = NULL,
-#' scopes = NULL)
-#' @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", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return ApiClientAuthorizationList object.
-#' @name api_client_authorizations.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", cluster_id = NULL)
-#' @param authorizedKey AuthorizedKey object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @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$authorized_keys.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return AuthorizedKeyList object.
-#' @name authorized_keys.list
-NULL
-
-#' collections.get
-#'
-#' collections.get is a method defined in Arvados class.
-#'
-#' @usage arv$collections.get(uuid)
-#' @param uuid The UUID of the Collection in question.
-#' @return Collection object.
-#' @name collections.get
-NULL
-
-#' collections.create
-#'
-#' collections.create is a method defined in Arvados class.
-#'
-#' @usage arv$collections.create(collection,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param collection Collection object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return Collection object.
-#' @name collections.create
-NULL
-
-#' collections.update
-#'
-#' collections.update is a method defined in Arvados class.
-#'
-#' @usage arv$collections.update(collection,
-#' uuid)
-#' @param collection Collection object.
-#' @param uuid The UUID of the Collection in question.
-#' @return Collection object.
-#' @name collections.update
-NULL
-
-#' collections.delete
-#'
-#' collections.delete is a method defined in Arvados class.
-#'
-#' @usage arv$collections.delete(uuid)
-#' @param uuid The UUID of the Collection in question.
-#' @return Collection object.
-#' @name collections.delete
-NULL
-
-#' collections.provenance
-#'
-#' collections.provenance is a method defined in Arvados class.
-#'
-#' @usage arv$collections.provenance(uuid)
-#' @param uuid
-#' @return Collection object.
-#' @name collections.provenance
-NULL
-
-#' collections.used_by
-#'
-#' collections.used_by is a method defined in Arvados class.
-#'
-#' @usage arv$collections.used_by(uuid)
-#' @param uuid
-#' @return Collection object.
-#' @name collections.used_by
-NULL
-
-#' collections.trash
-#'
-#' collections.trash is a method defined in Arvados class.
-#'
-#' @usage arv$collections.trash(uuid)
-#' @param uuid
-#' @return Collection object.
-#' @name collections.trash
-NULL
-
-#' collections.untrash
-#'
-#' collections.untrash is a method defined in Arvados class.
-#'
-#' @usage arv$collections.untrash(uuid)
-#' @param uuid
-#' @return Collection object.
-#' @name collections.untrash
-NULL
-
-#' collections.list
-#'
-#' collections.list is a method defined in Arvados class.
-#'
-#' @usage arv$collections.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL,
-#' include_trash = NULL, include_old_versions = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @param include_trash Include collections whose is_trashed attribute is true.
-#' @param include_old_versions Include past collection versions.
-#' @return CollectionList object.
-#' @name collections.list
-NULL
-
-#' containers.get
-#'
-#' containers.get is a method defined in Arvados class.
-#'
-#' @usage arv$containers.get(uuid)
-#' @param uuid The UUID of the Container in question.
-#' @return Container object.
-#' @name containers.get
-NULL
-
-#' containers.create
-#'
-#' containers.create is a method defined in Arvados class.
-#'
-#' @usage arv$containers.create(container,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param container Container object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return Container object.
-#' @name containers.create
-NULL
-
-#' containers.update
-#'
-#' containers.update is a method defined in Arvados class.
-#'
-#' @usage arv$containers.update(container,
-#' uuid)
-#' @param container Container object.
-#' @param uuid The UUID of the Container in question.
-#' @return Container object.
-#' @name containers.update
-NULL
-
-#' containers.delete
-#'
-#' containers.delete is a method defined in Arvados class.
-#'
-#' @usage arv$containers.delete(uuid)
-#' @param uuid The UUID of the Container in question.
-#' @return Container object.
-#' @name containers.delete
-NULL
-
-#' containers.auth
-#'
-#' containers.auth is a method defined in Arvados class.
-#'
-#' @usage arv$containers.auth(uuid)
-#' @param uuid
-#' @return Container object.
-#' @name containers.auth
-NULL
-
-#' containers.lock
-#'
-#' containers.lock is a method defined in Arvados class.
-#'
-#' @usage arv$containers.lock(uuid)
-#' @param uuid
-#' @return Container object.
-#' @name containers.lock
-NULL
-
-#' containers.unlock
-#'
-#' containers.unlock is a method defined in Arvados class.
-#'
-#' @usage arv$containers.unlock(uuid)
-#' @param uuid
-#' @return Container object.
-#' @name containers.unlock
-NULL
-
-#' containers.secret_mounts
-#'
-#' containers.secret_mounts is a method defined in Arvados class.
-#'
-#' @usage arv$containers.secret_mounts(uuid)
-#' @param uuid
-#' @return Container object.
-#' @name containers.secret_mounts
-NULL
-
-#' containers.current
-#'
-#' containers.current is a method defined in Arvados class.
-#'
-#' @usage arv$containers.current(NULL)
-#' @return Container object.
-#' @name containers.current
-NULL
-
-#' containers.list
-#'
-#' containers.list is a method defined in Arvados class.
-#'
-#' @usage arv$containers.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return ContainerList object.
-#' @name containers.list
-NULL
-
-#' container_requests.get
-#'
-#' container_requests.get is a method defined in Arvados class.
-#'
-#' @usage arv$container_requests.get(uuid)
-#' @param uuid The UUID of the ContainerRequest in question.
-#' @return ContainerRequest object.
-#' @name container_requests.get
-NULL
-
-#' container_requests.create
-#'
-#' container_requests.create is a method defined in Arvados class.
-#'
-#' @usage arv$container_requests.create(containerrequest,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param containerRequest ContainerRequest object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return ContainerRequest object.
-#' @name container_requests.create
-NULL
-
-#' container_requests.update
-#'
-#' container_requests.update is a method defined in Arvados class.
-#'
-#' @usage arv$container_requests.update(containerrequest,
-#' uuid)
-#' @param containerRequest ContainerRequest object.
-#' @param uuid The UUID of the ContainerRequest in question.
-#' @return ContainerRequest object.
-#' @name container_requests.update
-NULL
-
-#' container_requests.delete
-#'
-#' container_requests.delete is a method defined in Arvados class.
-#'
-#' @usage arv$container_requests.delete(uuid)
-#' @param uuid The UUID of the ContainerRequest in question.
-#' @return ContainerRequest object.
-#' @name container_requests.delete
-NULL
-
-#' container_requests.list
-#'
-#' container_requests.list is a method defined in Arvados class.
-#'
-#' @usage arv$container_requests.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL,
-#' include_trash = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @param include_trash Include container requests whose owner project is trashed.
-#' @return ContainerRequestList object.
-#' @name container_requests.list
-NULL
-
-#' groups.get
-#'
-#' groups.get is a method defined in Arvados class.
-#'
-#' @usage arv$groups.get(uuid)
-#' @param uuid The UUID of the Group in question.
-#' @return Group object.
-#' @name groups.get
-NULL
-
-#' groups.create
-#'
-#' groups.create is a method defined in Arvados class.
-#'
-#' @usage arv$groups.create(group, ensure_unique_name = "false",
-#' cluster_id = NULL, async = "false")
-#' @param group Group object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @param async defer permissions update
-#' @return Group object.
-#' @name groups.create
-NULL
-
-#' groups.update
-#'
-#' groups.update is a method defined in Arvados class.
-#'
-#' @usage arv$groups.update(group, uuid,
-#' async = "false")
-#' @param group Group object.
-#' @param uuid The UUID of the Group in question.
-#' @param async defer permissions update
-#' @return Group object.
-#' @name groups.update
-NULL
-
-#' groups.delete
-#'
-#' groups.delete is a method defined in Arvados class.
-#'
-#' @usage arv$groups.delete(uuid)
-#' @param uuid The UUID of the Group in question.
-#' @return Group object.
-#' @name groups.delete
-NULL
-
-#' groups.contents
-#'
-#' groups.contents is a method defined in Arvados class.
-#'
-#' @usage arv$groups.contents(filters = NULL,
-#' where = NULL, order = NULL, distinct = NULL,
-#' limit = "100", offset = "0", count = "exact",
-#' cluster_id = NULL, bypass_federation = NULL,
-#' include_trash = NULL, uuid = NULL, recursive = NULL,
-#' include = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @param include_trash Include items whose is_trashed attribute is true.
-#' @param uuid
-#' @param recursive Include contents from child groups recursively.
-#' @param include Include objects referred to by listed field in "included" (only owner_uuid)
-#' @return Group object.
-#' @name groups.contents
-NULL
-
-#' groups.shared
-#'
-#' groups.shared is a method defined in Arvados class.
-#'
-#' @usage arv$groups.shared(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL,
-#' include_trash = NULL, include = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @param include_trash Include items whose is_trashed attribute is true.
-#' @param include
-#' @return Group object.
-#' @name groups.shared
-NULL
-
-#' groups.trash
-#'
-#' groups.trash is a method defined in Arvados class.
-#'
-#' @usage arv$groups.trash(uuid)
-#' @param uuid
-#' @return Group object.
-#' @name groups.trash
-NULL
-
-#' groups.untrash
-#'
-#' groups.untrash is a method defined in Arvados class.
-#'
-#' @usage arv$groups.untrash(uuid)
-#' @param uuid
-#' @return Group object.
-#' @name groups.untrash
-NULL
-
-#' groups.list
-#'
-#' groups.list is a method defined in Arvados class.
-#'
-#' @usage arv$groups.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL,
-#' include_trash = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @param include_trash Include items whose is_trashed attribute is true.
-#' @return GroupList object.
-#' @name groups.list
-NULL
-
-#' keep_services.get
-#'
-#' keep_services.get is a method defined in Arvados class.
-#'
-#' @usage arv$keep_services.get(uuid)
-#' @param uuid The UUID of the KeepService in question.
-#' @return KeepService object.
-#' @name keep_services.get
-NULL
-
-#' keep_services.create
-#'
-#' keep_services.create is a method defined in Arvados class.
-#'
-#' @usage arv$keep_services.create(keepservice,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param keepService KeepService object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return KeepService object.
-#' @name keep_services.create
-NULL
-
-#' keep_services.update
-#'
-#' keep_services.update is a method defined in Arvados class.
-#'
-#' @usage arv$keep_services.update(keepservice,
-#' uuid)
-#' @param keepService KeepService object.
-#' @param uuid The UUID of the KeepService in question.
-#' @return KeepService object.
-#' @name keep_services.update
-NULL
-
-#' keep_services.delete
-#'
-#' keep_services.delete is a method defined in Arvados class.
-#'
-#' @usage arv$keep_services.delete(uuid)
-#' @param uuid The UUID of the KeepService in question.
-#' @return KeepService object.
-#' @name keep_services.delete
-NULL
-
-#' keep_services.accessible
-#'
-#' keep_services.accessible is a method defined in Arvados class.
-#'
-#' @usage arv$keep_services.accessible(NULL)
-#' @return KeepService object.
-#' @name keep_services.accessible
-NULL
-
-#' keep_services.list
-#'
-#' keep_services.list is a method defined in Arvados class.
-#'
-#' @usage arv$keep_services.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return KeepServiceList object.
-#' @name keep_services.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",
-#' cluster_id = NULL)
-#' @param link Link object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @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$links.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return LinkList object.
-#' @name links.list
-NULL
-
-#' links.get_permissions
-#'
-#' links.get_permissions is a method defined in Arvados class.
-#'
-#' @usage arv$links.get_permissions(uuid)
-#' @param uuid
-#' @return Link object.
-#' @name links.get_permissions
-NULL
-
-#' logs.get
-#'
-#' logs.get is a method defined in Arvados class.
-#'
-#' @usage arv$logs.get(uuid)
-#' @param uuid The UUID of the Log in question.
-#' @return Log object.
-#' @name logs.get
-NULL
-
-#' logs.create
-#'
-#' logs.create is a method defined in Arvados class.
-#'
-#' @usage arv$logs.create(log, ensure_unique_name = "false",
-#' cluster_id = NULL)
-#' @param log Log object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return Log object.
-#' @name logs.create
-NULL
-
-#' logs.update
-#'
-#' logs.update is a method defined in Arvados class.
-#'
-#' @usage arv$logs.update(log, uuid)
-#' @param log Log object.
-#' @param uuid The UUID of the Log in question.
-#' @return Log object.
-#' @name logs.update
-NULL
-
-#' logs.delete
-#'
-#' logs.delete is a method defined in Arvados class.
-#'
-#' @usage arv$logs.delete(uuid)
-#' @param uuid The UUID of the Log in question.
-#' @return Log object.
-#' @name logs.delete
-NULL
-
-#' logs.list
-#'
-#' logs.list is a method defined in Arvados class.
-#'
-#' @usage arv$logs.list(filters = NULL, where = NULL,
-#' order = NULL, select = NULL, distinct = NULL,
-#' limit = "100", offset = "0", count = "exact",
-#' cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return LogList object.
-#' @name logs.list
-NULL
-
-#' users.get
-#'
-#' users.get is a method defined in Arvados class.
-#'
-#' @usage arv$users.get(uuid)
-#' @param uuid The UUID of the User in question.
-#' @return User object.
-#' @name users.get
-NULL
-
-#' users.create
-#'
-#' users.create is a method defined in Arvados class.
-#'
-#' @usage arv$users.create(user, ensure_unique_name = "false",
-#' cluster_id = NULL)
-#' @param user User object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return User object.
-#' @name users.create
-NULL
-
-#' users.update
-#'
-#' users.update is a method defined in Arvados class.
-#'
-#' @usage arv$users.update(user, uuid, bypass_federation = NULL)
-#' @param user User object.
-#' @param uuid The UUID of the User in question.
-#' @param bypass_federation
-#' @return User object.
-#' @name users.update
-NULL
-
-#' users.delete
-#'
-#' users.delete is a method defined in Arvados class.
-#'
-#' @usage arv$users.delete(uuid)
-#' @param uuid The UUID of the User in question.
-#' @return User object.
-#' @name users.delete
-NULL
-
-#' users.current
-#'
-#' users.current is a method defined in Arvados class.
-#'
-#' @usage arv$users.current(NULL)
-#' @return User object.
-#' @name users.current
-NULL
-
-#' users.system
-#'
-#' users.system is a method defined in Arvados class.
-#'
-#' @usage arv$users.system(NULL)
-#' @return User object.
-#' @name users.system
-NULL
-
-#' users.activate
-#'
-#' users.activate is a method defined in Arvados class.
-#'
-#' @usage arv$users.activate(uuid)
-#' @param uuid
-#' @return User object.
-#' @name users.activate
-NULL
-
-#' users.setup
-#'
-#' users.setup is a method defined in Arvados class.
-#'
-#' @usage arv$users.setup(uuid = NULL, user = NULL,
-#' repo_name = NULL, vm_uuid = NULL, send_notification_email = "false")
-#' @param uuid
-#' @param user
-#' @param repo_name
-#' @param vm_uuid
-#' @param send_notification_email
-#' @return User object.
-#' @name users.setup
-NULL
-
-#' users.unsetup
-#'
-#' users.unsetup is a method defined in Arvados class.
-#'
-#' @usage arv$users.unsetup(uuid)
-#' @param uuid
-#' @return User object.
-#' @name users.unsetup
-NULL
-
-#' users.merge
-#'
-#' users.merge is a method defined in Arvados class.
-#'
-#' @usage arv$users.merge(new_owner_uuid,
-#' new_user_token = NULL, redirect_to_new_user = NULL,
-#' old_user_uuid = NULL, new_user_uuid = NULL)
-#' @param new_owner_uuid
-#' @param new_user_token
-#' @param redirect_to_new_user
-#' @param old_user_uuid
-#' @param new_user_uuid
-#' @return User object.
-#' @name users.merge
-NULL
-
-#' users.list
-#'
-#' users.list is a method defined in Arvados class.
-#'
-#' @usage arv$users.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return UserList object.
-#' @name users.list
-NULL
-
-#' repositories.get
-#'
-#' repositories.get is a method defined in Arvados class.
-#'
-#' @usage arv$repositories.get(uuid)
-#' @param uuid The UUID of the Repository in question.
-#' @return Repository object.
-#' @name repositories.get
-NULL
-
-#' repositories.create
-#'
-#' repositories.create is a method defined in Arvados class.
-#'
-#' @usage arv$repositories.create(repository,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param repository Repository object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return Repository object.
-#' @name repositories.create
-NULL
-
-#' repositories.update
-#'
-#' repositories.update is a method defined in Arvados class.
-#'
-#' @usage arv$repositories.update(repository,
-#' uuid)
-#' @param repository Repository object.
-#' @param uuid The UUID of the Repository in question.
-#' @return Repository object.
-#' @name repositories.update
-NULL
-
-#' repositories.delete
-#'
-#' repositories.delete is a method defined in Arvados class.
-#'
-#' @usage arv$repositories.delete(uuid)
-#' @param uuid The UUID of the Repository in question.
-#' @return Repository object.
-#' @name repositories.delete
-NULL
-
-#' repositories.get_all_permissions
-#'
-#' repositories.get_all_permissions is a method defined in Arvados class.
-#'
-#' @usage arv$repositories.get_all_permissions(NULL)
-#' @return Repository object.
-#' @name repositories.get_all_permissions
-NULL
-
-#' repositories.list
-#'
-#' repositories.list is a method defined in Arvados class.
-#'
-#' @usage arv$repositories.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return RepositoryList object.
-#' @name repositories.list
-NULL
-
-#' virtual_machines.get
-#'
-#' virtual_machines.get is a method defined in Arvados class.
-#'
-#' @usage arv$virtual_machines.get(uuid)
-#' @param uuid The UUID of the VirtualMachine in question.
-#' @return VirtualMachine object.
-#' @name virtual_machines.get
-NULL
-
-#' virtual_machines.create
-#'
-#' virtual_machines.create is a method defined in Arvados class.
-#'
-#' @usage arv$virtual_machines.create(virtualmachine,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param virtualMachine VirtualMachine object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return VirtualMachine object.
-#' @name virtual_machines.create
-NULL
-
-#' virtual_machines.update
-#'
-#' virtual_machines.update is a method defined in Arvados class.
-#'
-#' @usage arv$virtual_machines.update(virtualmachine,
-#' uuid)
-#' @param virtualMachine VirtualMachine object.
-#' @param uuid The UUID of the VirtualMachine in question.
-#' @return VirtualMachine object.
-#' @name virtual_machines.update
-NULL
-
-#' virtual_machines.delete
-#'
-#' virtual_machines.delete is a method defined in Arvados class.
-#'
-#' @usage arv$virtual_machines.delete(uuid)
-#' @param uuid The UUID of the VirtualMachine in question.
-#' @return VirtualMachine object.
-#' @name virtual_machines.delete
-NULL
-
-#' virtual_machines.logins
-#'
-#' virtual_machines.logins is a method defined in Arvados class.
-#'
-#' @usage arv$virtual_machines.logins(uuid)
-#' @param uuid
-#' @return VirtualMachine object.
-#' @name virtual_machines.logins
-NULL
-
-#' virtual_machines.get_all_logins
-#'
-#' virtual_machines.get_all_logins is a method defined in Arvados class.
-#'
-#' @usage arv$virtual_machines.get_all_logins(NULL)
-#' @return VirtualMachine object.
-#' @name virtual_machines.get_all_logins
-NULL
-
-#' virtual_machines.list
-#'
-#' virtual_machines.list is a method defined in Arvados class.
-#'
-#' @usage arv$virtual_machines.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return VirtualMachineList object.
-#' @name virtual_machines.list
-NULL
-
-#' workflows.get
-#'
-#' workflows.get is a method defined in Arvados class.
-#'
-#' @usage arv$workflows.get(uuid)
-#' @param uuid The UUID of the Workflow in question.
-#' @return Workflow object.
-#' @name workflows.get
-NULL
-
-#' workflows.create
-#'
-#' workflows.create is a method defined in Arvados class.
-#'
-#' @usage arv$workflows.create(workflow,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param workflow Workflow object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return Workflow object.
-#' @name workflows.create
-NULL
-
-#' workflows.update
-#'
-#' workflows.update is a method defined in Arvados class.
-#'
-#' @usage arv$workflows.update(workflow,
-#' uuid)
-#' @param workflow Workflow object.
-#' @param uuid The UUID of the Workflow in question.
-#' @return Workflow object.
-#' @name workflows.update
-NULL
-
-#' workflows.delete
-#'
-#' workflows.delete is a method defined in Arvados class.
-#'
-#' @usage arv$workflows.delete(uuid)
-#' @param uuid The UUID of the Workflow in question.
-#' @return Workflow object.
-#' @name workflows.delete
-NULL
-
-#' workflows.list
-#'
-#' workflows.list is a method defined in Arvados class.
-#'
-#' @usage arv$workflows.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return WorkflowList object.
-#' @name workflows.list
-NULL
-
-#' user_agreements.get
-#'
-#' user_agreements.get is a method defined in Arvados class.
-#'
-#' @usage arv$user_agreements.get(uuid)
-#' @param uuid The UUID of the UserAgreement in question.
-#' @return UserAgreement object.
-#' @name user_agreements.get
-NULL
-
-#' user_agreements.create
-#'
-#' user_agreements.create is a method defined in Arvados class.
-#'
-#' @usage arv$user_agreements.create(useragreement,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param userAgreement UserAgreement object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return UserAgreement object.
-#' @name user_agreements.create
-NULL
-
-#' user_agreements.update
-#'
-#' user_agreements.update is a method defined in Arvados class.
-#'
-#' @usage arv$user_agreements.update(useragreement,
-#' uuid)
-#' @param userAgreement UserAgreement object.
-#' @param uuid The UUID of the UserAgreement in question.
-#' @return UserAgreement object.
-#' @name user_agreements.update
-NULL
-
-#' user_agreements.delete
-#'
-#' user_agreements.delete is a method defined in Arvados class.
-#'
-#' @usage arv$user_agreements.delete(uuid)
-#' @param uuid The UUID of the UserAgreement in question.
-#' @return UserAgreement object.
-#' @name user_agreements.delete
-NULL
-
-#' user_agreements.signatures
-#'
-#' user_agreements.signatures is a method defined in Arvados class.
-#'
-#' @usage arv$user_agreements.signatures(NULL)
-#' @return UserAgreement object.
-#' @name user_agreements.signatures
-NULL
+#' @description
+#' Arvados class gives users ability to access Arvados REST API. It also allowes user to manipulate collections (and projects?)
-#' user_agreements.sign
-#'
-#' user_agreements.sign is a method defined in Arvados class.
-#'
-#' @usage arv$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$user_agreements.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return UserAgreementList object.
-#' @name user_agreements.list
-NULL
-
-#' user_agreements.new
-#'
-#' user_agreements.new is a method defined in Arvados class.
-#'
-#' @usage arv$user_agreements.new(NULL)
-#' @return UserAgreement object.
-#' @name user_agreements.new
-NULL
-
-#' configs.get
-#'
-#' configs.get is a method defined in Arvados class.
-#'
-#' @usage arv$configs.get(NULL)
-#' @return object.
-#' @name configs.get
-NULL
-
-#' project.get
-#'
-#' projects.get is equivalent to groups.get method.
-#'
-#' @usage arv$projects.get(uuid)
-#' @param uuid The UUID of the Group in question.
-#' @return Group object.
-#' @name projects.get
-NULL
-
-#' project.create
-#'
-#' projects.create wrapps groups.create method by setting group_class attribute to "project".
-#'
-#' @usage arv$projects.create(group, ensure_unique_name = "false")
-#' @param group Group object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @return Group object.
-#' @name projects.create
-NULL
-
-#' project.update
-#'
-#' projects.update wrapps groups.update method by setting group_class attribute to "project".
-#'
-#' @usage arv$projects.update(group, uuid)
-#' @param group Group object.
-#' @param uuid The UUID of the Group in question.
-#' @return Group object.
-#' @name projects.update
-NULL
-
-#' project.delete
-#'
-#' projects.delete is equivalent to groups.delete method.
-#'
-#' @usage arv$project.delete(uuid)
-#' @param uuid The UUID of the Group in question.
-#' @return Group object.
-#' @name projects.delete
-NULL
-
-#' project.list
-#'
-#' projects.list wrapps groups.list method by setting group_class attribute to "project".
-#'
-#' @usage arv$projects.list(filters = NULL,
-#' where = NULL, order = NULL, distinct = NULL,
-#' limit = "100", offset = "0", count = "exact",
-#' include_trash = NULL, uuid = NULL, recursive = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param include_trash Include items whose is_trashed attribute is true.
-#' @param uuid
-#' @param recursive Include contents from child groups recursively.
-#' @return Group object.
-#' @name projects.list
-NULL
-
-#' Arvados
-#'
-#' Arvados class gives users ability to access Arvados REST API.
-#'
-#' @section Usage:
-#' \preformatted{arv = Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)}
-#'
-#' @section Arguments:
-#' \describe{
-#' \item{authToken}{Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.}
-#' \item{hostName}{Host name. If not specified ARVADOS_API_HOST environment variable will be used.}
-#' \item{numRetries}{Number which specifies how many times to retry failed service requests.}
-#' }
-#'
-#' @section Methods:
-#' \describe{
-#' \item{}{\code{\link{api_client_authorizations.create}}}
-#' \item{}{\code{\link{api_client_authorizations.create_system_auth}}}
-#' \item{}{\code{\link{api_client_authorizations.current}}}
-#' \item{}{\code{\link{api_client_authorizations.delete}}}
-#' \item{}{\code{\link{api_client_authorizations.get}}}
-#' \item{}{\code{\link{api_client_authorizations.list}}}
-#' \item{}{\code{\link{api_client_authorizations.update}}}
-#' \item{}{\code{\link{api_clients.create}}}
-#' \item{}{\code{\link{api_clients.delete}}}
-#' \item{}{\code{\link{api_clients.get}}}
-#' \item{}{\code{\link{api_clients.list}}}
-#' \item{}{\code{\link{api_clients.update}}}
-#' \item{}{\code{\link{authorized_keys.create}}}
-#' \item{}{\code{\link{authorized_keys.delete}}}
-#' \item{}{\code{\link{authorized_keys.get}}}
-#' \item{}{\code{\link{authorized_keys.list}}}
-#' \item{}{\code{\link{authorized_keys.update}}}
-#' \item{}{\code{\link{collections.create}}}
-#' \item{}{\code{\link{collections.delete}}}
-#' \item{}{\code{\link{collections.get}}}
-#' \item{}{\code{\link{collections.list}}}
-#' \item{}{\code{\link{collections.provenance}}}
-#' \item{}{\code{\link{collections.trash}}}
-#' \item{}{\code{\link{collections.untrash}}}
-#' \item{}{\code{\link{collections.update}}}
-#' \item{}{\code{\link{collections.used_by}}}
-#' \item{}{\code{\link{configs.get}}}
-#' \item{}{\code{\link{container_requests.create}}}
-#' \item{}{\code{\link{container_requests.delete}}}
-#' \item{}{\code{\link{container_requests.get}}}
-#' \item{}{\code{\link{container_requests.list}}}
-#' \item{}{\code{\link{container_requests.update}}}
-#' \item{}{\code{\link{containers.auth}}}
-#' \item{}{\code{\link{containers.create}}}
-#' \item{}{\code{\link{containers.current}}}
-#' \item{}{\code{\link{containers.delete}}}
-#' \item{}{\code{\link{containers.get}}}
-#' \item{}{\code{\link{containers.list}}}
-#' \item{}{\code{\link{containers.lock}}}
-#' \item{}{\code{\link{containers.secret_mounts}}}
-#' \item{}{\code{\link{containers.unlock}}}
-#' \item{}{\code{\link{containers.update}}}
-#' \item{}{\code{\link{groups.contents}}}
-#' \item{}{\code{\link{groups.create}}}
-#' \item{}{\code{\link{groups.delete}}}
-#' \item{}{\code{\link{groups.get}}}
-#' \item{}{\code{\link{groups.list}}}
-#' \item{}{\code{\link{groups.shared}}}
-#' \item{}{\code{\link{groups.trash}}}
-#' \item{}{\code{\link{groups.untrash}}}
-#' \item{}{\code{\link{groups.update}}}
-#' \item{}{\code{\link{keep_services.accessible}}}
-#' \item{}{\code{\link{keep_services.create}}}
-#' \item{}{\code{\link{keep_services.delete}}}
-#' \item{}{\code{\link{keep_services.get}}}
-#' \item{}{\code{\link{keep_services.list}}}
-#' \item{}{\code{\link{keep_services.update}}}
-#' \item{}{\code{\link{links.create}}}
-#' \item{}{\code{\link{links.delete}}}
-#' \item{}{\code{\link{links.get}}}
-#' \item{}{\code{\link{links.get_permissions}}}
-#' \item{}{\code{\link{links.list}}}
-#' \item{}{\code{\link{links.update}}}
-#' \item{}{\code{\link{logs.create}}}
-#' \item{}{\code{\link{logs.delete}}}
-#' \item{}{\code{\link{logs.get}}}
-#' \item{}{\code{\link{logs.list}}}
-#' \item{}{\code{\link{logs.update}}}
-#' \item{}{\code{\link{projects.create}}}
-#' \item{}{\code{\link{projects.delete}}}
-#' \item{}{\code{\link{projects.get}}}
-#' \item{}{\code{\link{projects.list}}}
-#' \item{}{\code{\link{projects.update}}}
-#' \item{}{\code{\link{repositories.create}}}
-#' \item{}{\code{\link{repositories.delete}}}
-#' \item{}{\code{\link{repositories.get}}}
-#' \item{}{\code{\link{repositories.get_all_permissions}}}
-#' \item{}{\code{\link{repositories.list}}}
-#' \item{}{\code{\link{repositories.update}}}
-#' \item{}{\code{\link{user_agreements.create}}}
-#' \item{}{\code{\link{user_agreements.delete}}}
-#' \item{}{\code{\link{user_agreements.get}}}
-#' \item{}{\code{\link{user_agreements.list}}}
-#' \item{}{\code{\link{user_agreements.new}}}
-#' \item{}{\code{\link{user_agreements.sign}}}
-#' \item{}{\code{\link{user_agreements.signatures}}}
-#' \item{}{\code{\link{user_agreements.update}}}
-#' \item{}{\code{\link{users.activate}}}
-#' \item{}{\code{\link{users.create}}}
-#' \item{}{\code{\link{users.current}}}
-#' \item{}{\code{\link{users.delete}}}
-#' \item{}{\code{\link{users.get}}}
-#' \item{}{\code{\link{users.list}}}
-#' \item{}{\code{\link{users.merge}}}
-#' \item{}{\code{\link{users.setup}}}
-#' \item{}{\code{\link{users.system}}}
-#' \item{}{\code{\link{users.unsetup}}}
-#' \item{}{\code{\link{users.update}}}
-#' \item{}{\code{\link{virtual_machines.create}}}
-#' \item{}{\code{\link{virtual_machines.delete}}}
-#' \item{}{\code{\link{virtual_machines.get}}}
-#' \item{}{\code{\link{virtual_machines.get_all_logins}}}
-#' \item{}{\code{\link{virtual_machines.list}}}
-#' \item{}{\code{\link{virtual_machines.logins}}}
-#' \item{}{\code{\link{virtual_machines.update}}}
-#' \item{}{\code{\link{workflows.create}}}
-#' \item{}{\code{\link{workflows.delete}}}
-#' \item{}{\code{\link{workflows.get}}}
-#' \item{}{\code{\link{workflows.list}}}
-#' \item{}{\code{\link{workflows.update}}}
-#' }
-#'
-#' @name Arvados
-#' @examples
-#' \dontrun{
-#' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
-#'
-#' collection <- arv$collections.get("uuid")
-#'
-#' collectionList <- arv$collections.list(list(list("name", "like", "Test%")))
-#' collectionList <- listAll(arv$collections.list, list(list("name", "like", "Test%")))
-#'
-#' deletedCollection <- arv$collections.delete("uuid")
-#'
-#' updatedCollection <- arv$collections.update(list(name = "New name", description = "New description"),
-#' "uuid")
-#'
-#' createdCollection <- arv$collections.create(list(name = "Example",
-#' description = "This is a test collection"))
-#' }
-NULL
-
-#' @export
+#' @export Arvados
Arvados <- R6::R6Class(
- "Arvados",
-
- public = list(
-
- initialize = function(authToken = NULL, hostName = NULL, numRetries = 0)
- {
- if(!is.null(hostName))
- Sys.setenv(ARVADOS_API_HOST = hostName)
-
- if(!is.null(authToken))
- Sys.setenv(ARVADOS_API_TOKEN = authToken)
-
- hostName <- Sys.getenv("ARVADOS_API_HOST")
- token <- Sys.getenv("ARVADOS_API_TOKEN")
-
- if(hostName == "" | token == "")
- stop(paste("Please provide host name and authentification token",
- "or set ARVADOS_API_HOST and ARVADOS_API_TOKEN",
- "environment variables."))
-
- private$token <- token
- private$host <- paste0("https://", hostName, "/arvados/v1/")
- private$numRetries <- numRetries
- private$REST <- RESTService$new(token, hostName,
- HttpRequest$new(), HttpParser$new(),
- numRetries)
-
- },
-
- projects.get = function(uuid)
- {
- self$groups.get(uuid)
- },
-
- projects.create = function(group, ensure_unique_name = "false")
- {
- group <- c("group_class" = "project", group)
- self$groups.create(group, ensure_unique_name)
- },
-
- projects.update = function(group, uuid)
- {
- group <- c("group_class" = "project", group)
- self$groups.update(group, uuid)
- },
-
- projects.list = function(filters = NULL, where = NULL,
- order = NULL, select = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact",
- include_trash = NULL)
- {
- filters[[length(filters) + 1]] <- list("group_class", "=", "project")
- self$groups.list(filters, where, order, select, distinct,
- limit, offset, count, include_trash)
- },
-
- projects.delete = function(uuid)
- {
- self$groups.delete(uuid)
- },
-
- api_clients.get = function(uuid)
- {
- endPoint <- stringr::str_interp("api_clients/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_clients.create = function(apiclient,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("api_clients")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(apiclient) > 0)
- body <- jsonlite::toJSON(list(apiclient = apiclient),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_clients.update = function(apiclient, uuid)
- {
- endPoint <- stringr::str_interp("api_clients/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(apiclient) > 0)
- body <- jsonlite::toJSON(list(apiclient = apiclient),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_clients.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("api_clients/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_clients.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("api_clients")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_client_authorizations.get = function(uuid)
- {
- endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_client_authorizations.create = function(apiclientauthorization,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("api_client_authorizations")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(apiclientauthorization) > 0)
- body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_client_authorizations.update = function(apiclientauthorization, uuid)
- {
- endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(apiclientauthorization) > 0)
- body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_client_authorizations.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_client_authorizations.create_system_auth = function(api_client_id = NULL, scopes = NULL)
- {
- endPoint <- stringr::str_interp("api_client_authorizations/create_system_auth")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(api_client_id = api_client_id,
- scopes = scopes)
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_client_authorizations.current = function()
- {
- endPoint <- stringr::str_interp("api_client_authorizations/current")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_client_authorizations.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("api_client_authorizations")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$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)
- {
- endPoint <- stringr::str_interp("authorized_keys/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- authorized_keys.create = function(authorizedkey,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("authorized_keys")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(authorizedkey) > 0)
- body <- jsonlite::toJSON(list(authorizedkey = authorizedkey),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- authorized_keys.update = function(authorizedkey, uuid)
- {
- endPoint <- stringr::str_interp("authorized_keys/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(authorizedkey) > 0)
- body <- jsonlite::toJSON(list(authorizedkey = authorizedkey),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- authorized_keys.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("authorized_keys/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- authorized_keys.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("authorized_keys")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.get = function(uuid)
- {
- endPoint <- stringr::str_interp("collections/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.create = function(collection,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("collections")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(collection) > 0)
- body <- jsonlite::toJSON(list(collection = collection),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.update = function(collection, uuid)
- {
- endPoint <- stringr::str_interp("collections/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(collection) > 0)
- body <- jsonlite::toJSON(list(collection = collection),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("collections/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.provenance = function(uuid)
- {
- endPoint <- stringr::str_interp("collections/${uuid}/provenance")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.used_by = function(uuid)
- {
- endPoint <- stringr::str_interp("collections/${uuid}/used_by")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.trash = function(uuid)
- {
- endPoint <- stringr::str_interp("collections/${uuid}/trash")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.untrash = function(uuid)
- {
- endPoint <- stringr::str_interp("collections/${uuid}/untrash")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL,
- include_trash = NULL, include_old_versions = NULL)
- {
- endPoint <- stringr::str_interp("collections")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation,
- include_trash = include_trash, include_old_versions = include_old_versions)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.get = function(uuid)
- {
- endPoint <- stringr::str_interp("containers/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.create = function(container, ensure_unique_name = "false",
- cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("containers")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(container) > 0)
- body <- jsonlite::toJSON(list(container = container),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.update = function(container, uuid)
- {
- endPoint <- stringr::str_interp("containers/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(container) > 0)
- body <- jsonlite::toJSON(list(container = container),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("containers/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.auth = function(uuid)
- {
- endPoint <- stringr::str_interp("containers/${uuid}/auth")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.lock = function(uuid)
- {
- endPoint <- stringr::str_interp("containers/${uuid}/lock")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.unlock = function(uuid)
- {
- endPoint <- stringr::str_interp("containers/${uuid}/unlock")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.secret_mounts = function(uuid)
- {
- endPoint <- stringr::str_interp("containers/${uuid}/secret_mounts")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.current = function()
- {
- endPoint <- stringr::str_interp("containers/current")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("containers")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- 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$errors)
-
- resource
- },
-
- container_requests.get = function(uuid)
- {
- endPoint <- stringr::str_interp("container_requests/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- container_requests.create = function(containerrequest,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("container_requests")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(containerrequest) > 0)
- body <- jsonlite::toJSON(list(containerrequest = containerrequest),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- container_requests.update = function(containerrequest, uuid)
- {
- endPoint <- stringr::str_interp("container_requests/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(containerrequest) > 0)
- body <- jsonlite::toJSON(list(containerrequest = containerrequest),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- container_requests.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("container_requests/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- container_requests.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL,
- include_trash = NULL)
- {
- endPoint <- stringr::str_interp("container_requests")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation,
- include_trash = include_trash)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.get = function(uuid)
- {
- endPoint <- stringr::str_interp("groups/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.create = function(group, ensure_unique_name = "false",
- cluster_id = NULL, async = "false")
- {
- endPoint <- stringr::str_interp("groups")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id, async = async)
-
- if(length(group) > 0)
- body <- jsonlite::toJSON(list(group = group),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.update = function(group, uuid, async = "false")
- {
- endPoint <- stringr::str_interp("groups/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(async = async)
-
- if(length(group) > 0)
- body <- jsonlite::toJSON(list(group = group),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("groups/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.contents = function(filters = NULL,
- where = NULL, order = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact",
- cluster_id = NULL, bypass_federation = NULL,
- include_trash = NULL, uuid = NULL, recursive = NULL,
- include = NULL)
- {
- endPoint <- stringr::str_interp("groups/contents")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, distinct = distinct, limit = limit,
- offset = offset, count = count, cluster_id = cluster_id,
- bypass_federation = bypass_federation, include_trash = include_trash,
- uuid = uuid, recursive = recursive, include = include)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.shared = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL,
- include_trash = NULL, include = NULL)
- {
- endPoint <- stringr::str_interp("groups/shared")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation,
- include_trash = include_trash, include = include)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.trash = function(uuid)
- {
- endPoint <- stringr::str_interp("groups/${uuid}/trash")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.untrash = function(uuid)
- {
- endPoint <- stringr::str_interp("groups/${uuid}/untrash")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.list = function(filters = NULL, where = NULL,
- order = NULL, select = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact",
- cluster_id = NULL, bypass_federation = NULL,
- include_trash = NULL)
- {
- endPoint <- stringr::str_interp("groups")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation,
- 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$errors)
-
- resource
- },
-
- keep_services.get = function(uuid)
- {
- endPoint <- stringr::str_interp("keep_services/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- keep_services.create = function(keepservice,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("keep_services")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(keepservice) > 0)
- body <- jsonlite::toJSON(list(keepservice = keepservice),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$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
- },
-
- keep_services.update = function(keepservice, uuid)
- {
- endPoint <- stringr::str_interp("keep_services/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(keepservice) > 0)
- body <- jsonlite::toJSON(list(keepservice = keepservice),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- keep_services.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("keep_services/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- keep_services.accessible = function()
- {
- endPoint <- stringr::str_interp("keep_services/accessible")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- keep_services.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("keep_services")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$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)
- {
- endPoint <- stringr::str_interp("links/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("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",
- cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("links")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- 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$errors)
-
- resource
- },
-
- links.update = function(link, uuid)
- {
- endPoint <- stringr::str_interp("links/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(link) > 0)
- body <- jsonlite::toJSON(list(link = link),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- links.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("links/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- links.list = function(filters = NULL, where = NULL,
- order = NULL, select = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact",
- cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("links")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- links.get_permissions = function(uuid)
- {
- endPoint <- stringr::str_interp("permissions/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- logs.get = function(uuid)
- {
- endPoint <- stringr::str_interp("logs/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- logs.create = function(log, ensure_unique_name = "false",
- cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("logs")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(log) > 0)
- body <- jsonlite::toJSON(list(log = log),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- logs.update = function(log, uuid)
- {
- endPoint <- stringr::str_interp("logs/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(log) > 0)
- body <- jsonlite::toJSON(list(log = log),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- logs.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("logs/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- logs.list = function(filters = NULL, where = NULL,
- order = NULL, select = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact",
- cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("logs")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.get = function(uuid)
- {
- endPoint <- stringr::str_interp("users/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.create = function(user, ensure_unique_name = "false",
- cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("users")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(user) > 0)
- body <- jsonlite::toJSON(list(user = user),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.update = function(user, uuid, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("users/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(bypass_federation = bypass_federation)
-
- if(length(user) > 0)
- body <- jsonlite::toJSON(list(user = user),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("users/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.current = function()
- {
- endPoint <- stringr::str_interp("users/current")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.system = function()
- {
- endPoint <- stringr::str_interp("users/system")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.activate = function(uuid)
- {
- endPoint <- stringr::str_interp("users/${uuid}/activate")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.setup = function(uuid = NULL, user = NULL,
- repo_name = NULL, vm_uuid = NULL, send_notification_email = "false")
- {
- endPoint <- stringr::str_interp("users/setup")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(uuid = uuid, user = user,
- repo_name = repo_name, vm_uuid = vm_uuid,
- send_notification_email = send_notification_email)
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.unsetup = function(uuid)
- {
- endPoint <- stringr::str_interp("users/${uuid}/unsetup")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.merge = function(new_owner_uuid, new_user_token = NULL,
- redirect_to_new_user = NULL, old_user_uuid = NULL,
- new_user_uuid = NULL)
- {
- endPoint <- stringr::str_interp("users/merge")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$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,
- old_user_uuid = old_user_uuid, new_user_uuid = new_user_uuid)
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.list = function(filters = NULL, where = NULL,
- order = NULL, select = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact",
- cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("users")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$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
- },
-
- repositories.get = function(uuid)
- {
- endPoint <- stringr::str_interp("repositories/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- repositories.create = function(repository,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("repositories")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(repository) > 0)
- body <- jsonlite::toJSON(list(repository = repository),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- repositories.update = function(repository, uuid)
- {
- endPoint <- stringr::str_interp("repositories/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(repository) > 0)
- body <- jsonlite::toJSON(list(repository = repository),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- repositories.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("repositories/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- repositories.get_all_permissions = function()
- {
- endPoint <- stringr::str_interp("repositories/get_all_permissions")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- repositories.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("repositories")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- virtual_machines.get = function(uuid)
- {
- endPoint <- stringr::str_interp("virtual_machines/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- virtual_machines.create = function(virtualmachine,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("virtual_machines")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(virtualmachine) > 0)
- body <- jsonlite::toJSON(list(virtualmachine = virtualmachine),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- virtual_machines.update = function(virtualmachine, uuid)
- {
- endPoint <- stringr::str_interp("virtual_machines/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(virtualmachine) > 0)
- body <- jsonlite::toJSON(list(virtualmachine = virtualmachine),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- virtual_machines.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("virtual_machines/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- virtual_machines.logins = function(uuid)
- {
- endPoint <- stringr::str_interp("virtual_machines/${uuid}/logins")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- virtual_machines.get_all_logins = function()
- {
- endPoint <- stringr::str_interp("virtual_machines/get_all_logins")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- virtual_machines.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("virtual_machines")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- workflows.get = function(uuid)
- {
- endPoint <- stringr::str_interp("workflows/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- workflows.create = function(workflow, ensure_unique_name = "false",
- cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("workflows")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(workflow) > 0)
- body <- jsonlite::toJSON(list(workflow = workflow),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- workflows.update = function(workflow, uuid)
- {
- endPoint <- stringr::str_interp("workflows/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(workflow) > 0)
- body <- jsonlite::toJSON(list(workflow = workflow),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- workflows.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("workflows/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- workflows.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("workflows")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.get = function(uuid)
- {
- endPoint <- stringr::str_interp("user_agreements/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.create = function(useragreement,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("user_agreements")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(useragreement) > 0)
- body <- jsonlite::toJSON(list(useragreement = useragreement),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.update = function(useragreement, uuid)
- {
- endPoint <- stringr::str_interp("user_agreements/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(useragreement) > 0)
- body <- jsonlite::toJSON(list(useragreement = useragreement),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("user_agreements/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.signatures = function()
- {
- endPoint <- stringr::str_interp("user_agreements/signatures")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.sign = function()
- {
- endPoint <- stringr::str_interp("user_agreements/sign")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("user_agreements")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.new = function()
- {
- endPoint <- stringr::str_interp("user_agreements/new")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- configs.get = function()
- {
- endPoint <- stringr::str_interp("config")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$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
- },
-
- getHostName = function() private$host,
- getToken = function() private$token,
- setRESTService = function(newREST) private$REST <- newREST,
- getRESTService = function() private$REST
- ),
-
- private = list(
-
- token = NULL,
- host = NULL,
- REST = NULL,
- numRetries = NULL
- ),
-
- cloneable = FALSE
+ "Arvados",
+
+ public = list(
+
+ #' @description
+ #' Initialize new enviroment.
+ #' @param authToken ARVADOS_API_TOKEN from 'Get API Token' on Arvados.
+ #' @param hostName ARVADOS_API_HOST from 'Get API Token' on Arvados.
+ #' @param numRetries Specify number of times to retry failed service requests.
+ #' @return A new `Arvados` object.
+ #' @examples
+ #' arv <- Arvados$new(authToken = "ARVADOS_API_TOKEN", hostName = "ARVADOS_API_HOST", numRetries = 3)
+ initialize = function(authToken = NULL, hostName = NULL, numRetries = 0)
+ {
+ if(!is.null(hostName))
+ Sys.setenv(ARVADOS_API_HOST = hostName)
+
+ if(!is.null(authToken))
+ Sys.setenv(ARVADOS_API_TOKEN = authToken)
+
+ hostName <- Sys.getenv("ARVADOS_API_HOST")
+ token <- Sys.getenv("ARVADOS_API_TOKEN")
+
+ if(hostName == "" | token == "")
+ stop(paste("Please provide host name and authentification token",
+ "or set ARVADOS_API_HOST and ARVADOS_API_TOKEN",
+ "environment variables."))
+
+ private$token <- token
+ private$host <- paste0("https://", hostName, "/arvados/v1/")
+ private$numRetries <- numRetries
+ private$REST <- RESTService$new(token, hostName,
+ HttpRequest$new(), HttpParser$new(),
+ numRetries)
+
+ },
+
+ #' @description
+ #' project_exist enables checking if the project with such a UUID exist.
+ #' @param uuid The UUID of a project or a file.
+ #' @examples
+ #' arv$project_exist(uuid = projectUUID)
+ project_exist = function(uuid)
+ {
+ proj <- self$project_list(list(list("uuid", '=', uuid)))
+ value <- length(proj$items)
+
+ if (value == 1){
+ cat(format('TRUE'))
+ } else {
+ cat(format('FALSE'))
+ }
+ },
+
+ #' @description
+ #' project_get returns the demanded project.
+ #' @param uuid The UUID of the Group in question.
+ #' @examples
+ #' project <- arv$project_get(uuid = projectUUID)
+ project_get = function(uuid)
+ {
+ self$groups_get(uuid)
+ },
+
+ #' @description
+ #' project_create creates a new project of a given name and description.
+ #' @param name Name of the project.
+ #' @param description Description of the project.
+ #' @param ownerUUID The UUID of the maternal project to created one.
+ #' @param properties List of the properties of the project.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @examples
+ #' Properties <- list() # should contain a list of new properties to be added
+ #' new_project <- arv$project_create(name = "project name", description = "project description", owner_uuid = "project UUID", properties = NULL, ensureUniqueName = "false")
+ project_create = function(name, description, ownerUUID, properties = NULL, ensureUniqueName = "false")
+ {
+ group <- list(name = name, description = description, owner_uuid = ownerUUID, properties = properties)
+ group <- c("group_class" = "project", group)
+ self$groups_create(group, ensureUniqueName = ensureUniqueName)
+ },
+
+ #' @description
+ #' project_properties_set is a method defined in Arvados class that enables setting properties. Allows to set or overwrite the properties. In case there are set already it overwrites them.
+ #' @param listProperties List of new properties.
+ #' @param uuid The UUID of a project or a file.
+ #' @examples
+ #' Properties <- list() # should contain a list of new properties to be added
+ #' arv$project_properties_set(Properties, uuid)
+ project_properties_set = function(listProperties, uuid)
+ {
+ group <- c("group_class" = "project", list("properties" = listProperties))
+ self$groups_update(group, uuid)
+
+ },
+
+ #' @description
+ #' project_properties_append is a method defined in Arvados class that enables appending properties. Allows to add new properties.
+ #' @param listOfNewProperties List of new properties.
+ #' @param uuid The UUID of a project or a file.
+ #' @examples
+ #' newProperties <- list() # should contain a list of new properties to be added
+ #' arv$project_properties_append(properties = newProperties, uuid)
+ project_properties_append = function(properties, uuid)
+ {
+ proj <- self$project_list(list(list('uuid', '=', uuid)))
+ projProp <- proj$items[[1]]$properties
+
+ newListOfProperties <- c(projProp, properties)
+ uniqueProperties <- unique(unlist(newListOfProperties))
+ newListOfProperties <- suppressWarnings(newListOfProperties[which(newListOfProperties == uniqueProperties)])
+
+ group <- c("group_class" = "project", list("properties" = newListOfProperties))
+ self$groups_update(group, uuid);
+
+ },
+
+ #' @description
+ #' project_properties_get is a method defined in Arvados class that returns properties.
+ #' @param uuid The UUID of a project or a file.
+ #' @examples
+ #' arv$project_properties_get(projectUUID)
+ project_properties_get = function(uuid)
+ {
+ proj <- self$project_list(list(list('uuid', '=', uuid)))
+ proj$items[[1]]$properties
+ },
+
+ #' @description
+ #' project_properties_delete is a method defined in Arvados class that deletes list of properties.
+ #' @param oneProp Property to be deleted.
+ #' @param uuid The UUID of a project or a file.
+ #' @examples
+ #' Properties <- list() # should contain a list of new properties to be added
+ #' arv$project_properties_delete(Properties, projectUUID)
+ project_properties_delete = function(oneProp, uuid)
+ {
+ proj <- self$project_list(list(list('uuid', '=', uuid))) # find project
+ projProp <- proj$items[[1]]$properties
+ for (i in 1:length(projProp)){
+ solution <- identical(projProp[i],oneProp)
+ if (solution == TRUE) {
+ projProp <- projProp[names(projProp) != names(oneProp)]
+ self$project_properties_set(projProp, uuid)
+ }
+ }
+ },
+
+ #' @description
+ #' project_update enables updating project. New name, description and properties may be given.
+ #' @param ... Feature to be updated (name, description, properties).
+ #' @param uuid The UUID of a project in question.
+ #' @examples
+ #' newProperties <- list() # should contain a list of new properties to be added
+ #' arv$project_update(name = "new project name", properties = newProperties, uuid = projectUUID)
+ project_update = function(..., uuid) {
+ vec <- list(...)
+ for (i in 1:length(vec))
+ {
+ if (names(vec[i]) == 'properties') {
+ solution <- self$project_properties_append(vec$properties, uuid = uuid)
+ }
+ }
+ vecNew <- vec[names(vec) != "properties"]
+ vecNew <- c("group_class" = "project", vecNew)
+ z <- self$groups_update(vecNew, uuid)
+ },
+
+ #' @description
+ #' project_list enables listing project by its name, uuid, properties, permissions.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param includeTrash Include items whose is_trashed attribute is true.
+ #' @param uuid The UUID of a project in question.
+ #' @param recursive Include contents from child groups recursively.
+ #' @examples
+ #' listOfprojects <- arv$project_list(list(list("owner_uuid", "=", projectUUID))) # Sample query which show projects within the project of a given UUID
+ project_list = function(filters = NULL, where = NULL,
+ order = NULL, select = NULL, distinct = NULL,
+ limit = "100", offset = "0", count = "exact",
+ includeTrash = NULL)
+ {
+ filters[[length(filters) + 1]] <- list("group_class", "=", "project")
+ self$groups_list(filters, where, order, select, distinct,
+ limit, offset, count, includeTrash)
+ },
+
+ #' @description
+ #' project_delete trashes project of a given uuid. It can be restored from trash or deleted permanently.
+ #' @param uuid The UUID of the Group in question.
+ project_delete = function(uuid)
+ {
+ self$groups_delete(uuid)
+ },
+
+ #' @description
+ #' api_clients_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the apiClient in question.
+ api_clients_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("api_clients/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_clients_create is a method defined in Arvados class.
+ #' @param apiClient apiClient object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ api_clients_create = function(apiClient,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("api_clients")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(apiClient) > 0)
+ body <- jsonlite::toJSON(list(apiClient = apiClient),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_clients_update is a method defined in Arvados class.
+ #' @param apiClient apiClient object.
+ #' @param uuid The UUID of the apiClient in question.
+ api_clients_update = function(apiClient, uuid)
+ {
+ endPoint <- stringr::str_interp("api_clients/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(apiClient) > 0)
+ body <- jsonlite::toJSON(list(apiClient = apiClient),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_clients_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the apiClient in question.
+ api_clients_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("api_clients/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_clients_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ api_clients_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("api_clients")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' api_client_authorizations_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the apiClientAuthorization in question.
+ api_client_authorizations_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_client_authorizations_create is a method defined in Arvados class.
+ #' @param apiClientAuthorization apiClientAuthorization object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error on (ownerUUID, name) collision_
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ api_client_authorizations_create = function(apiClientAuthorization,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("api_client_authorizations")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(apiClientAuthorization) > 0)
+ body <- jsonlite::toJSON(list(apiClientAuthorization = apiClientAuthorization),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_client_authorizations_update is a method defined in Arvados class.
+ #' @param apiClientAuthorization apiClientAuthorization object.
+ #' @param uuid The UUID of the apiClientAuthorization in question.
+ api_client_authorizations_update = function(apiClientAuthorization, uuid)
+ {
+ endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(apiClientAuthorization) > 0)
+ body <- jsonlite::toJSON(list(apiClientAuthorization = apiClientAuthorization),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_client_authorizations_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the apiClientAuthorization in question.
+ api_client_authorizations_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_client_authorizations_create_system_auth is a method defined in Arvados class.
+ #' @param apiClientID
+ #' @param scopes
+ api_client_authorizations_create_system_auth = function(apiClientID = NULL, scopes = NULL)
+ {
+ endPoint <- stringr::str_interp("api_client_authorizations/create_system_auth")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(apiClientID = apiClientID,
+ scopes = scopes)
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' api_client_authorizations_current is a method defined in Arvados class.
+ api_client_authorizations_current = function()
+ {
+ endPoint <- stringr::str_interp("api_client_authorizations/current")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_client_authorizations_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ api_client_authorizations_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("api_client_authorizations")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' authorized_keys_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the authorizedKey in question.
+ authorized_keys_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("authorized_keys/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' authorized_keys_create is a method defined in Arvados class.
+ #' @param authorizedKey authorizedKey object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ authorized_keys_create = function(authorizedKey,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("authorized_keys")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ 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$errors)
+
+ resource
+ },
+
+ #' @description
+ #' authorized_keys_update is a method defined in Arvados class.
+ #' @param authorizedKey authorizedKey object.
+ #' @param uuid The UUID of the authorizedKey in question.
+ authorized_keys_update = function(authorizedKey, uuid)
+ {
+ endPoint <- stringr::str_interp("authorized_keys/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(authorizedKey) > 0)
+ body <- jsonlite::toJSON(list(authorizedKey = authorizedKey),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' authorized_keys_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the authorizedKey in question.
+ authorized_keys_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("authorized_keys/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' authorized_keys_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ authorized_keys_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("authorized_keys")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' collections_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the Collection in question.
+ #' collection <- arv$collections_get(uuid = collectionUUID)
+ collections_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("collections/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' collections_create is a method defined in Arvados class that enables collections creation.
+ #' @param name Name of the collection.
+ #' @param description Description of the collection.
+ #' @param ownerUUID UUID of the maternal project to created one.
+ #' @param properties Properties of the collection.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ #' @examples
+ #' Properties <- list() # should contain a list of new properties to be added
+ #' arv$collections_create(name = "collectionTitle", description = "collectionDescription", ownerUUID = "collectionOwner", properties = Properties)
+ collections_create = function(name, description, ownerUUID = NULL, properties = NULL, # name and description are obligatory
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("collections")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ collection <- list(name = name, description = description, owner_uuid = ownerUUID, properties = properties)
+ if(length(collection) > 0)
+ body <- jsonlite::toJSON(list(collection = collection),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors)){
+ if(identical(sub('Entity:.*',"", resource$errors), "//railsapi.internal/arvados/v1/collections: 422 Unprocessable ")){
+ resource <- cat(format("A collection with the given name already exists in this projects. If you want to update it use collections_update() instead"))
+ }else{
+ stop(resource$errors)
+ }
+ }
+
+ resource
+ },
+
+ #' @description
+ #' collections_update is a method defined in Arvados class.
+ #' @param name New name of the collection.
+ #' @param description New description of the collection.
+ #' @param ownerUUID UUID of the maternal project to created one.
+ #' @param properties New list of properties of the collection.
+ #' @param uuid The UUID of the Collection in question.
+ #' @examples
+ #' collection <- arv$collections_update(name = "newCollectionTitle", description = "newCollectionDescription", ownerUUID = "collectionOwner", properties = NULL, uuid = "collectionUUID")
+ collections_update = function(name, description, ownerUUID = NULL, properties = NULL, uuid)
+ {
+ endPoint <- stringr::str_interp("collections/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ collection <- list(name = name, description = description, ownerUUID = ownerUUID, properties = properties)
+ if(length(collection) > 0)
+ body <- jsonlite::toJSON(list(collection = collection),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' collections_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the Collection in question.
+ #' @examples
+ #' arv$collection_delete(collectionUUID)
+ collections_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("collections/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' collections_provenance is a method defined in Arvados class, it returns the collection by uuid.
+ #' @param uuid The UUID of the Collection in question.
+ #' @examples
+ #' collection <- arv$collections_provenance(collectionUUID)
+ collections_provenance = function(uuid)
+ {
+ endPoint <- stringr::str_interp("collections/${uuid}/provenance")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' collections_used_by is a method defined in Arvados class, it returns collection by portable_data_hash.
+ #' @param uuid The UUID of the Collection in question.
+ collections_used_by = function(uuid)
+ {
+ endPoint <- stringr::str_interp("collections/${uuid}/used_by")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' collections_trash is a method defined in Arvados class, it moves collection to trash.
+ #' @param uuid The UUID of the Collection in question.
+ #' @examples
+ #' arv$collections_trash(collectionUUID)
+ collections_trash = function(uuid)
+ {
+ endPoint <- stringr::str_interp("collections/${uuid}/trash")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' collections_untrash is a method defined in Arvados class, it moves collection from trash to project.
+ #' @param uuid The UUID of the Collection in question.
+ #' @examples
+ #' arv$collections_untrash(collectionUUID)
+ collections_untrash = function(uuid)
+ {
+ endPoint <- stringr::str_interp("collections/${uuid}/untrash")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' collections_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ #' @param includeTrash Include collections whose is_trashed attribute is true.
+ #' @param includeOldVersions Include past collection versions.
+ #' @examples
+ #' collectionList <- arv$collections_list(list(list("name", "=", "Example")))
+ collections_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL,
+ includeTrash = NULL, includeOldVersions = NULL)
+ {
+ endPoint <- stringr::str_interp("collections")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation,
+ includeTrash = includeTrash, includeOldVersions = includeOldVersions)
+
+ 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$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the Container in question.
+ containers_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("containers/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_create is a method defined in Arvados class.
+ #' @param container Container object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ containers_create = function(container, ensureUniqueName = "false",
+ clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("containers")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(container) > 0)
+ body <- jsonlite::toJSON(list(container = container),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_update is a method defined in Arvados class.
+ #' @param container Container object.
+ #' @param uuid The UUID of the Container in question.
+ containers_update = function(container, uuid)
+ {
+ endPoint <- stringr::str_interp("containers/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(container) > 0)
+ body <- jsonlite::toJSON(list(container = container),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the Container in question.
+ containers_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("containers/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_auth is a method defined in Arvados class.
+ #' @param uuid The UUID of the Container in question.
+ containers_auth = function(uuid)
+ {
+ endPoint <- stringr::str_interp("containers/${uuid}/auth")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_lock is a method defined in Arvados class.
+ #' @param uuid The UUID of the Container in question.
+ containers_lock = function(uuid)
+ {
+ endPoint <- stringr::str_interp("containers/${uuid}/lock")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_unlock is a method defined in Arvados class.
+ #' @param uuid The UUID of the Container in question.
+ containers_unlock = function(uuid)
+ {
+ endPoint <- stringr::str_interp("containers/${uuid}/unlock")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_secret_mounts is a method defined in Arvados class.
+ #' @param uuid The UUID of the Container in question.
+ containers_secret_mounts = function(uuid)
+ {
+ endPoint <- stringr::str_interp("containers/${uuid}/secret_mounts")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_current is a method defined in Arvados class.
+ containers_current = function()
+ {
+ endPoint <- stringr::str_interp("containers/current")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ containers_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("containers")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' container_requests_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the containerRequest in question.
+ container_requests_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("container_requests/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' container_requests_create is a method defined in Arvados class.
+ #' @param containerRequest containerRequest object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ container_requests_create = function(containerRequest,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("container_requests")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ 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$errors)
+
+ resource
+ },
+
+ #' @description
+ #' container_requests_update is a method defined in Arvados class.
+ #' @param containerRequest containerRequest object.
+ #' @param uuid The UUID of the containerRequest in question.
+ container_requests_update = function(containerRequest, uuid)
+ {
+ endPoint <- stringr::str_interp("container_requests/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(containerRequest) > 0)
+ body <- jsonlite::toJSON(list(containerRequest = containerRequest),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' container_requests_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the containerRequest in question.
+ container_requests_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("container_requests/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' container_requests_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation bypass federation behavior, list items from local instance database only
+ #' @param includeTrash Include container requests whose owner project is trashed.
+ container_requests_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL,
+ includeTrash = NULL)
+ {
+ endPoint <- stringr::str_interp("container_requests")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation,
+ includeTrash = includeTrash)
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' groups_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the Group in question.
+ groups_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("groups/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' groups_create is a method defined in Arvados class that supports project creation.
+ #' @param group Group object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ #' @param async Defer permissions update.
+ groups_create = function(group, ensureUniqueName = "false",
+ clusterID = NULL, async = "false")
+ {
+ endPoint <- stringr::str_interp("groups")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID, async = async)
+
+ if(length(group) > 0)
+ body <- jsonlite::toJSON(list(group = group),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors)){
+ if (identical(sub('#.*', "", resource$errors), "//railsapi.internal/arvados/v1/groups: 422 Unprocessable Entity: ")) {
+ #if (identical(sub('P.*', "", resource$errors), "//railsapi.internal/arvados/v1/groups: 422 Unprocessable Entity: #\u003cActiveRecord::RecordNotUnique: ")) {
+ resource <- cat(format("Project of that name already exist. If you want to update it use project_update() instead"))
+ }else{
+ stop(resource$errors)
+ }
+ }
+
+ return(resource)
+ },
+
+ #' @description
+ #' groups_update is a method defined in Arvados class.
+ #' @param group Group object.
+ #' @param uuid The UUID of the Group in question.
+ #' @param async Defer permissions update.
+ groups_update = function(group, uuid, async = "false")
+ {
+ endPoint <- stringr::str_interp("groups/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- list(async = async)
+
+ if(length(group) > 0)
+ body <- jsonlite::toJSON(list(group = group),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' groups_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the Group in question.
+ groups_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("groups/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ dataTime <- gsub("T.*", "", resource$delete_at)
+ cat("The content will be deleted permanently at", dataTime)
+
+ resource
+ },
+
+ #' @description
+ #' groups_contents is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ #' @param includeTrash Include items whose is_trashed attribute is true.
+ #' @param uuid
+ #' @param recursive Include contents from child groups recursively.
+ #' @param include Include objects referred to by listed field in "included" (only ownerUUID).
+ groups_contents = function(filters = NULL,
+ where = NULL, order = NULL, distinct = NULL,
+ limit = "100", offset = "0", count = "exact",
+ clusterID = NULL, bypassFederation = NULL,
+ includeTrash = NULL, uuid = NULL, recursive = NULL,
+ include = NULL)
+ {
+ endPoint <- stringr::str_interp("groups/contents")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- list(filters = filters, where = where,
+ order = order, distinct = distinct, limit = limit,
+ offset = offset, count = count, clusterID = clusterID,
+ bypassFederation = bypassFederation, includeTrash = includeTrash,
+ uuid = uuid, recursive = recursive, include = include)
+
+ 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$errors)
+
+ resource
+ },
+
+ #' @description
+ #' groups_shared is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ #' @param includeTrash Include items whose is_trashed attribute is true.
+ #' @param include
+ groups_shared = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL,
+ includeTrash = NULL, include = NULL)
+ {
+ endPoint <- stringr::str_interp("groups/shared")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation,
+ includeTrash = includeTrash, include = include)
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' groups_trash is a method defined in Arvados class.
+ #' @param uuid The UUID of the Group in question.
+ groups_trash = function(uuid)
+ {
+ endPoint <- stringr::str_interp("groups/${uuid}/trash")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' groups_untrash is a method defined in Arvados class.
+ #' @param uuid The UUID of the Group in question.
+ groups_untrash = function(uuid)
+ {
+ endPoint <- stringr::str_interp("groups/${uuid}/untrash")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' groups_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ #' @param includeTrash Include items whose is_trashed attribute is true.
+ groups_list = function(filters = NULL, where = NULL,
+ order = NULL, select = NULL, distinct = NULL,
+ limit = "100", offset = "0", count = "exact",
+ clusterID = NULL, bypassFederation = NULL,
+ includeTrash = NULL)
+ {
+ endPoint <- stringr::str_interp("groups")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation,
+ includeTrash = includeTrash)
+
+ 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$errors)
+
+ resource
+ },
+
+ #' @description
+ #' keep_services_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the keepService in question.
+ keep_services_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("keep_services/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' keep_services_create is a method defined in Arvados class.
+ #' @param keepService keepService object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ keep_services_create = function(keepService,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("keep_services")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(keepService) > 0)
+ body <- jsonlite::toJSON(list(keepService = keepService),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' keep_services_update is a method defined in Arvados class.
+ #' @param keepService keepService object.
+ #' @param uuid The UUID of the keepService in question.
+ keep_services_update = function(keepService, uuid)
+ {
+ endPoint <- stringr::str_interp("keep_services/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(keepService) > 0)
+ body <- jsonlite::toJSON(list(keepService = keepService),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' keep_services_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the keepService in question.
+ keep_services_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("keep_services/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' keep_services_accessible is a method defined in Arvados class.
+ keep_services_accessible = function()
+ {
+ endPoint <- stringr::str_interp("keep_services/accessible")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' keep_services_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ keep_services_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("keep_services")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' project_permission_give is a method defined in Arvados class that enables sharing files with another users.
+ #' @param type Possible options are can_read or can_write or can_manage.
+ #' @param uuid The UUID of a project or a file.
+ #' @param user The UUID of the person that gets the permission.
+ #' @examples
+ #' arv$project_permission_give(type = "can_read", uuid = objectUUID, user = userUUID)
+ project_permission_give = function(type, uuid, user)
+ {
+ endPoint <- stringr::str_interp("links")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ # it is possible to make it as pasting a list to function, not a 3 arg. What's better?
+ link <- list("link_class" = "permission", "name" = type, "head_uuid" = uuid, "tail_uuid" = user)
+
+ if(length(link) > 0)
+ body <- jsonlite::toJSON(list(link = link),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' project_permission_refuse is a method defined in Arvados class that unables sharing files with another users.
+ #' @param type Possible options are can_read or can_write or can_manage.
+ #' @param uuid The UUID of a project or a file.
+ #' @param user The UUID of a person that permissions are taken from.
+ #' @examples
+ #' arv$project_permission_refuse(type = "can_read", uuid = objectUUID, user = userUUID)
+ project_permission_refuse = function(type, uuid, user)
+ {
+ examples <- self$links_list(list(list("head_uuid","=", uuid)))
+
+ theUser <- examples[which(sapply(examples$items, "[[", "tail_uuid") == user)]
+ theType <- theUser$items[which(sapply(theUser$items, "[[", "name") == type)]
+ solution <- theType[which(sapply(theType, "[[", "link_class") == 'permission')]
+
+ if (length(solution) == 0) {
+ cat(format('No permission granted'))
+ } else {
+ self$links_delete(solution[[1]]$uuid)
+ }
+
+ },
+
+ #' @description
+ #' project_permission_update is a method defined in Arvados class that enables updating permissions.
+ #' @param typeNew New option like can_read or can_write or can_manage.
+ #' @param typeOld Old option.
+ #' @param uuid The UUID of a project or a file.
+ #' @param user The UUID of the person that the permission is being updated.
+ #' @examples
+ #' arv$project_permission_update(typeOld = "can_read", typeNew = "can_write", uuid = objectUUID, user = userUUID)
+ project_permission_update = function(typeOld, typeNew, uuid, user)
+ {
+ link <- list("name" = typeNew)
+
+ examples <- self$links_list(list(list("head_uuid","=", uuid)))
+
+ theUser <- examples[which(sapply(examples$items, "[[", "tail_uuid") == user)]
+ theType <- theUser$items[which(sapply(theUser$items, "[[", "name") == typeOld)]
+ solution <- theType[which(sapply(theType, "[[", "link_class") == 'permission')]
+
+ if (length(solution) == 0) {
+ cat(format('No permission granted'))
+ } else {
+ self$links_update(link, solution[[1]]$uuid)
+ }
+ },
+
+ #' @description
+ #' project_permission_check is a method defined in Arvados class that enables checking file permissions.
+ #' @param uuid The UUID of a project or a file.
+ #' @param user The UUID of the person that the permission is being updated.
+ #' @param type Possible options are can_read or can_write or can_manage.
+ #' @examples
+ #' arv$project_permission_check(type = "can_read", uuid = objectUUID, user = userUUID)
+ project_permission_check = function(uuid, user, type = NULL)
+ {
+ examples <- self$links_list(list(list("head_uuid","=", uuid)))
+
+ theUser <- examples[which(sapply(examples$items, "[[", "tail_uuid") == user)]
+
+ if (length(type) == 0 ){
+ theUser
+ } else {
+ theType <- theUser$items[which(sapply(theUser$items, "[[", "name") == type)]
+ permisions <- theType[which(sapply(theType, "[[", "link_class") == 'permission')]
+ print(permisions[[1]]$name)
+ }
+ },
+
+ #' @description
+ #' links_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the Link in question.
+ links_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("links/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' links_create is a method defined in Arvados class.
+ #' @param link Link object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ links_create = function(link, ensureUniqueName = "false",
+ clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("links")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ 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$errors)
+
+ resource
+ },
+
+ #' @description
+ #' links_update is a method defined in Arvados class.
+ #' @param link Link object.
+ #' @param uuid The UUID of the Link in question.
+ links_update = function(link, uuid, async = "false")
+ {
+ endPoint <- stringr::str_interp("links/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(async = async)
+
+ 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$errors)
+
+ resource
+ },
+
+ #' @description
+ #' links_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the Link in question.
+ links_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("links/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' links_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ links_list = function(filters = NULL, where = NULL,
+ order = NULL, select = NULL, distinct = NULL,
+ limit = "100", offset = "0", count = "exact",
+ clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("links")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' links_get_permissions is a method defined in Arvados class.
+ #' @param uuid The UUID of the Log in question.
+ links_get_permissions = function(uuid)
+ {
+ endPoint <- stringr::str_interp("permissions/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' logs_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the Log in question.
+ logs_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("logs/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' logs_create is a method defined in Arvados class.
+ #' @param log Log object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ logs_create = function(log, ensureUniqueName = "false",
+ clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("logs")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(log) > 0)
+ body <- jsonlite::toJSON(list(log = log),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' logs_update is a method defined in Arvados class.
+ #' @param log Log object.
+ #' @param uuid The UUID of the Log in question.
+ logs_update = function(log, uuid)
+ {
+ endPoint <- stringr::str_interp("logs/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(log) > 0)
+ body <- jsonlite::toJSON(list(log = log),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' logs_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the Log in question.
+ logs_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("logs/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' logs_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ logs_list = function(filters = NULL, where = NULL,
+ order = NULL, select = NULL, distinct = NULL,
+ limit = "100", offset = "0", count = "exact",
+ clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("logs")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' users_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the User in question.
+ users_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("users/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_create is a method defined in Arvados class.
+ #' @param user User object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ users_create = function(user, ensureUniqueName = "false",
+ clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("users")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(user) > 0)
+ body <- jsonlite::toJSON(list(user = user),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_update is a method defined in Arvados class.
+ #' @param user User object.
+ #' @param uuid The UUID of the User in question.
+ #' @param bypassFederation
+ users_update = function(user, uuid, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("users/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(bypassFederation = bypassFederation)
+
+ if(length(user) > 0)
+ body <- jsonlite::toJSON(list(user = user),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the User in question.
+ users_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("users/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_current is a method defined in Arvados class.
+ users_current = function()
+ {
+ endPoint <- stringr::str_interp("users/current")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_system is a method defined in Arvados class.
+ users_system = function()
+ {
+ endPoint <- stringr::str_interp("users/system")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_activate is a method defined in Arvados class.
+ #' @param uuid The UUID of the User in question.
+ users_activate = function(uuid)
+ {
+ endPoint <- stringr::str_interp("users/${uuid}/activate")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_setup is a method defined in Arvados class.
+ #' @param uuid
+ #' @param user
+ #' @param repo_name
+ #' @param vm_uuid
+ #' @param send_notification_email
+ users_setup = function(uuid = NULL, user = NULL,
+ repo_name = NULL, vm_uuid = NULL, send_notification_email = "false")
+ {
+ endPoint <- stringr::str_interp("users/setup")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(uuid = uuid, user = user,
+ repo_name = repo_name, vm_uuid = vm_uuid,
+ send_notification_email = send_notification_email)
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' users_unsetup is a method defined in Arvados class.
+ #' @param uuid The UUID of the User in question.
+ users_unsetup = function(uuid)
+ {
+ endPoint <- stringr::str_interp("users/${uuid}/unsetup")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_merge is a method defined in Arvados class.
+ #' @param newOwnerUUID
+ #' @param newUserToken
+ #' @param redirectToNewUser
+ #' @param oldUserUUID
+ #' @param newUserUUID
+ users_merge = function(newOwnerUUID, newUserToken = NULL,
+ redirectToNewUser = NULL, oldUserUUID = NULL,
+ newUserUUID = NULL)
+ {
+ endPoint <- stringr::str_interp("users/merge")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(newOwnerUUID = newOwnerUUID,
+ newUserToken = newUserToken, redirectToNewUser = redirectToNewUser,
+ oldUserUUID = oldUserUUID, newUserUUID = newUserUUID)
+
+ 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$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ users_list = function(filters = NULL, where = NULL,
+ order = NULL, select = NULL, distinct = NULL,
+ limit = "100", offset = "0", count = "exact",
+ clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("users")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' repositories_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the Repository in question.
+ repositories_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("repositories/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' repositories_create is a method defined in Arvados class.
+ #' @param repository Repository object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ repositories_create = function(repository,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("repositories")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(repository) > 0)
+ body <- jsonlite::toJSON(list(repository = repository),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' repositories_update is a method defined in Arvados class.
+ #' @param repository Repository object.
+ #' @param uuid The UUID of the Repository in question.
+ repositories_update = function(repository, uuid)
+ {
+ endPoint <- stringr::str_interp("repositories/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(repository) > 0)
+ body <- jsonlite::toJSON(list(repository = repository),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' repositories_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the Repository in question.
+ repositories_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("repositories/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' repositories_get_all_permissions is a method defined in Arvados class.
+ repositories_get_all_permissions = function()
+ {
+ endPoint <- stringr::str_interp("repositories/get_all_permissions")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' repositories_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ repositories_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("repositories")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ 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$errors)
+
+ resource
+ },
+
+ #' @description
+ #' virtual_machines_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the virtualMachine in question.
+ virtual_machines_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("virtual_machines/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' virtual_machines_create is a method defined in Arvados class.
+ #' @param virtualMachine virtualMachine object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ virtual_machines_create = function(virtualMachine,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("virtual_machines")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(virtualMachine) > 0)
+ body <- jsonlite::toJSON(list(virtualMachine = virtualMachine),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' virtual_machines_update is a method defined in Arvados class.
+ #' @param virtualMachine virtualMachine object.
+ #' @param uuid The UUID of the virtualMachine in question.
+ virtual_machines_update = function(virtualMachine, uuid)
+ {
+ endPoint <- stringr::str_interp("virtual_machines/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(virtualMachine) > 0)
+ body <- jsonlite::toJSON(list(virtualMachine = virtualMachine),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' virtual_machines_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the virtualMachine in question.
+ virtual_machines_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("virtual_machines/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' virtual_machines_logins is a method defined in Arvados class.
+ #' @param uuid The UUID of the virtualMachine in question.
+ virtual_machines_logins = function(uuid)
+ {
+ endPoint <- stringr::str_interp("virtual_machines/${uuid}/logins")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' virtual_machines_get_all_logins is a method defined in Arvados class.
+ virtual_machines_get_all_logins = function()
+ {
+ endPoint <- stringr::str_interp("virtual_machines/get_all_logins")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' virtual_machines_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation bypass federation behavior, list items from local instance database only
+ virtual_machines_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("virtual_machines")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' workflows_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the Workflow in question.
+ workflows_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("workflows/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' workflows_create is a method defined in Arvados class.
+ #' @param workflow Workflow object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ workflows_create = function(workflow, ensureUniqueName = "false",
+ clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("workflows")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(workflow) > 0)
+ body <- jsonlite::toJSON(list(workflow = workflow),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' workflows_update is a method defined in Arvados class.
+ #' @param workflow Workflow object.
+ #' @param uuid The UUID of the Workflow in question.
+ workflows_update = function(workflow, uuid)
+ {
+ endPoint <- stringr::str_interp("workflows/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(workflow) > 0)
+ body <- jsonlite::toJSON(list(workflow = workflow),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' workflows_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the Workflow in question.
+ workflows_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("workflows/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' workflows_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ workflows_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("workflows")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' user_agreements_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the userAgreement in question.
+ user_agreements_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("user_agreements/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' user_agreements_create is a method defined in Arvados class.
+ #' @param userAgreement userAgreement object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ user_agreements_create = function(userAgreement,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("user_agreements")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(userAgreement) > 0)
+ body <- jsonlite::toJSON(list(userAgreement = userAgreement),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' user_agreements_update is a method defined in Arvados class.
+ #' @param userAgreement userAgreement object.
+ #' @param uuid The UUID of the userAgreement in question.
+ user_agreements_update = function(userAgreement, uuid)
+ {
+ endPoint <- stringr::str_interp("user_agreements/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(userAgreement) > 0)
+ body <- jsonlite::toJSON(list(userAgreement = userAgreement),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' user_agreements_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the userAgreement in question.
+ user_agreements_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("user_agreements/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' user_agreements_signatures is a method defined in Arvados class.
+ user_agreements_signatures = function()
+ {
+ endPoint <- stringr::str_interp("user_agreements/signatures")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' user_agreements_sign is a method defined in Arvados class.
+ user_agreements_sign = function()
+ {
+ endPoint <- stringr::str_interp("user_agreements/sign")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' user_agreements_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ user_agreements_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("user_agreements")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ #' @description
+ #' user_agreements_new is a method defined in Arvados class.
+ user_agreements_new = function()
+ {
+ endPoint <- stringr::str_interp("user_agreements/new")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' configs_get is a method defined in Arvados class.
+ configs_get = function()
+ {
+ endPoint <- stringr::str_interp("config")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL=
+
+ body <- NULL
+
+ response <- private$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
+ },
+
+ getHostName = function() private$host,
+ getToken = function() private$token,
+ setRESTService = function(newREST) private$REST <- newREST,
+ getRESTService = function() private$REST
+ ),
+
+ private = list(
+
+ token = NULL,
+ host = NULL,
+ REST = NULL,
+ numRetries = NULL
+ ),
+
+ cloneable = FALSE
)
+
+
projects / arvados.git / blobdiff