From 342c15f625fda8746e7d74510a298286b3a52196 Mon Sep 17 00:00:00 2001 From: Fuad Muhic Date: Thu, 26 Jul 2018 16:09:14 +0200 Subject: [PATCH] Improve Collections create and move methods and update documentation Arvados-DCO-1.1-Signed-off-by: Fuad Muhic --- sdk/R/R/Arvados.R | 2816 ++++++++--------- sdk/R/R/ArvadosFile.R | 13 +- sdk/R/R/Collection.R | 56 +- sdk/R/R/CollectionTree.R | 105 +- sdk/R/R/Subcollection.R | 16 +- sdk/R/R/zzz.R | 4 + sdk/R/README.Rmd | 21 +- sdk/R/man/Collection.Rd | 8 +- ...lient_authorizations.create_system_auth.Rd | 5 + sdk/R/man/api_client_authorizations.list.Rd | 17 + sdk/R/man/api_clients.list.Rd | 17 + sdk/R/man/authorized_keys.list.Rd | 17 + sdk/R/man/collections.list.Rd | 16 + sdk/R/man/collections.provenance.Rd | 3 + sdk/R/man/collections.trash.Rd | 3 + sdk/R/man/collections.untrash.Rd | 3 + sdk/R/man/collections.used_by.Rd | 3 + sdk/R/man/container_requests.list.Rd | 17 + sdk/R/man/containers.auth.Rd | 3 + sdk/R/man/containers.list.Rd | 17 + sdk/R/man/containers.lock.Rd | 3 + sdk/R/man/containers.secret_mounts.Rd | 3 + sdk/R/man/containers.unlock.Rd | 3 + sdk/R/man/groups.contents.Rd | 16 + sdk/R/man/groups.list.Rd | 16 + sdk/R/man/groups.trash.Rd | 3 + sdk/R/man/groups.untrash.Rd | 3 + sdk/R/man/humans.list.Rd | 17 + sdk/R/man/job_tasks.list.Rd | 17 + sdk/R/man/jobs.cancel.Rd | 3 + sdk/R/man/jobs.create.Rd | 8 + sdk/R/man/jobs.list.Rd | 17 + sdk/R/man/jobs.lock.Rd | 3 + sdk/R/man/jobs.queue.Rd | 17 + sdk/R/man/keep_disks.list.Rd | 17 + sdk/R/man/keep_disks.ping.Rd | 15 + sdk/R/man/keep_services.list.Rd | 17 + sdk/R/man/links.get_permissions.Rd | 3 + sdk/R/man/links.list.Rd | 17 + sdk/R/man/logs.list.Rd | 17 + sdk/R/man/nodes.list.Rd | 17 + sdk/R/man/nodes.ping.Rd | 5 + sdk/R/man/pipeline_instances.cancel.Rd | 3 + sdk/R/man/pipeline_instances.list.Rd | 17 + sdk/R/man/pipeline_templates.list.Rd | 17 + sdk/R/man/projects.list.Rd | 16 + sdk/R/man/repositories.list.Rd | 17 + sdk/R/man/specimens.list.Rd | 17 + sdk/R/man/traits.list.Rd | 17 + sdk/R/man/user_agreements.list.Rd | 17 + sdk/R/man/users.activate.Rd | 3 + sdk/R/man/users.list.Rd | 17 + sdk/R/man/users.merge.Rd | 7 + sdk/R/man/users.setup.Rd | 11 + sdk/R/man/users.unsetup.Rd | 3 + sdk/R/man/users.update_uuid.Rd | 5 + sdk/R/man/virtual_machines.list.Rd | 17 + sdk/R/man/virtual_machines.logins.Rd | 3 + sdk/R/man/workflows.list.Rd | 17 + sdk/R/tests/testthat/test-Collection.R | 47 +- 60 files changed, 2083 insertions(+), 1565 deletions(-) diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R index de2aade4ad..744cb3c296 100644 --- a/sdk/R/R/Arvados.R +++ b/sdk/R/R/Arvados.R @@ -1,7 +1,7 @@ #' users.get -#' +#' #' users.get is a method defined in Arvados class. -#' +#' #' @usage arv$users.get(uuid) #' @param uuid The UUID of the User in question. #' @return User object. @@ -9,9 +9,9 @@ NULL #' users.create -#' +#' #' users.create is a method defined in Arvados class. -#' +#' #' @usage arv$users.create(user, ensure_unique_name = "false") #' @param user User object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -20,9 +20,9 @@ NULL NULL #' users.update -#' +#' #' users.update is a method defined in Arvados class. -#' +#' #' @usage arv$users.update(user, uuid) #' @param user User object. #' @param uuid The UUID of the User in question. @@ -31,9 +31,9 @@ NULL NULL #' users.delete -#' +#' #' users.delete is a method defined in Arvados class. -#' +#' #' @usage arv$users.delete(uuid) #' @param uuid The UUID of the User in question. #' @return User object. @@ -41,106 +41,106 @@ NULL NULL #' users.current -#' +#' #' users.current is a method defined in Arvados class. -#' +#' #' @usage arv$users.current(NULL) #' @return User object. #' @name users.current NULL #' users.system -#' +#' #' users.system is a method defined in Arvados class. -#' +#' #' @usage arv$users.system(NULL) #' @return User object. #' @name users.system NULL #' users.activate -#' +#' #' users.activate is a method defined in Arvados class. -#' +#' #' @usage arv$users.activate(uuid) -#' @param uuid +#' @param uuid #' @return User object. #' @name users.activate NULL #' users.setup -#' +#' #' users.setup is a method defined in Arvados class. -#' +#' #' @usage arv$users.setup(user = NULL, openid_prefix = NULL, #' repo_name = NULL, vm_uuid = NULL, send_notification_email = "false") -#' @param user -#' @param openid_prefix -#' @param repo_name -#' @param vm_uuid -#' @param send_notification_email +#' @param user +#' @param openid_prefix +#' @param repo_name +#' @param vm_uuid +#' @param send_notification_email #' @return User object. #' @name users.setup NULL #' users.unsetup -#' +#' #' users.unsetup is a method defined in Arvados class. -#' +#' #' @usage arv$users.unsetup(uuid) -#' @param uuid +#' @param uuid #' @return User object. #' @name users.unsetup NULL #' users.update_uuid -#' +#' #' users.update_uuid is a method defined in Arvados class. -#' +#' #' @usage arv$users.update_uuid(uuid, new_uuid) -#' @param uuid -#' @param new_uuid +#' @param uuid +#' @param new_uuid #' @return User object. #' @name users.update_uuid NULL #' users.merge -#' +#' #' users.merge is a method defined in Arvados class. -#' +#' #' @usage arv$users.merge(new_owner_uuid, #' new_user_token, redirect_to_new_user = NULL) -#' @param new_owner_uuid -#' @param new_user_token -#' @param redirect_to_new_user +#' @param new_owner_uuid +#' @param new_user_token +#' @param redirect_to_new_user #' @return User object. #' @name users.merge NULL #' users.list -#' +#' #' users.list is a method defined in Arvados class. -#' +#' #' @usage arv$users.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return UserList object. #' @name users.list NULL #' api_client_authorizations.get -#' +#' #' api_client_authorizations.get is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.get(uuid) #' @param uuid The UUID of the ApiClientAuthorization in question. #' @return ApiClientAuthorization object. @@ -148,9 +148,9 @@ NULL NULL #' api_client_authorizations.create -#' +#' #' api_client_authorizations.create is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.create(apiclientauthorization, #' ensure_unique_name = "false") #' @param apiClientAuthorization ApiClientAuthorization object. @@ -160,9 +160,9 @@ NULL NULL #' api_client_authorizations.update -#' +#' #' api_client_authorizations.update is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.update(apiclientauthorization, #' uuid) #' @param apiClientAuthorization ApiClientAuthorization object. @@ -172,9 +172,9 @@ NULL NULL #' api_client_authorizations.delete -#' +#' #' api_client_authorizations.delete is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.delete(uuid) #' @param uuid The UUID of the ApiClientAuthorization in question. #' @return ApiClientAuthorization object. @@ -182,50 +182,50 @@ NULL NULL #' api_client_authorizations.create_system_auth -#' +#' #' api_client_authorizations.create_system_auth is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.create_system_auth(api_client_id = NULL, #' scopes = NULL) -#' @param api_client_id -#' @param scopes +#' @param api_client_id +#' @param scopes #' @return ApiClientAuthorization object. #' @name api_client_authorizations.create_system_auth NULL #' api_client_authorizations.current -#' +#' #' api_client_authorizations.current is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.current(NULL) #' @return ApiClientAuthorization object. #' @name api_client_authorizations.current NULL #' api_client_authorizations.list -#' +#' #' api_client_authorizations.list is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return ApiClientAuthorizationList object. #' @name api_client_authorizations.list NULL #' containers.get -#' +#' #' containers.get is a method defined in Arvados class. -#' +#' #' @usage arv$containers.get(uuid) #' @param uuid The UUID of the Container in question. #' @return Container object. @@ -233,9 +233,9 @@ NULL NULL #' containers.create -#' +#' #' containers.create is a method defined in Arvados class. -#' +#' #' @usage arv$containers.create(container, #' ensure_unique_name = "false") #' @param container Container object. @@ -245,9 +245,9 @@ NULL NULL #' containers.update -#' +#' #' containers.update is a method defined in Arvados class. -#' +#' #' @usage arv$containers.update(container, #' uuid) #' @param container Container object. @@ -257,9 +257,9 @@ NULL NULL #' containers.delete -#' +#' #' containers.delete is a method defined in Arvados class. -#' +#' #' @usage arv$containers.delete(uuid) #' @param uuid The UUID of the Container in question. #' @return Container object. @@ -267,78 +267,78 @@ NULL NULL #' containers.auth -#' +#' #' containers.auth is a method defined in Arvados class. -#' +#' #' @usage arv$containers.auth(uuid) -#' @param uuid +#' @param uuid #' @return Container object. #' @name containers.auth NULL #' containers.lock -#' +#' #' containers.lock is a method defined in Arvados class. -#' +#' #' @usage arv$containers.lock(uuid) -#' @param uuid +#' @param uuid #' @return Container object. #' @name containers.lock NULL #' containers.unlock -#' +#' #' containers.unlock is a method defined in Arvados class. -#' +#' #' @usage arv$containers.unlock(uuid) -#' @param uuid +#' @param uuid #' @return Container object. #' @name containers.unlock NULL #' containers.secret_mounts -#' +#' #' containers.secret_mounts is a method defined in Arvados class. -#' +#' #' @usage arv$containers.secret_mounts(uuid) -#' @param uuid +#' @param uuid #' @return Container object. #' @name containers.secret_mounts NULL #' containers.current -#' +#' #' containers.current is a method defined in Arvados class. -#' +#' #' @usage arv$containers.current(NULL) #' @return Container object. #' @name containers.current NULL #' containers.list -#' +#' #' containers.list is a method defined in Arvados class. -#' +#' #' @usage arv$containers.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return ContainerList object. #' @name containers.list NULL #' api_clients.get -#' +#' #' api_clients.get is a method defined in Arvados class. -#' +#' #' @usage arv$api_clients.get(uuid) #' @param uuid The UUID of the ApiClient in question. #' @return ApiClient object. @@ -346,9 +346,9 @@ NULL NULL #' api_clients.create -#' +#' #' api_clients.create is a method defined in Arvados class. -#' +#' #' @usage arv$api_clients.create(apiclient, #' ensure_unique_name = "false") #' @param apiClient ApiClient object. @@ -358,9 +358,9 @@ NULL NULL #' api_clients.update -#' +#' #' api_clients.update is a method defined in Arvados class. -#' +#' #' @usage arv$api_clients.update(apiclient, #' uuid) #' @param apiClient ApiClient object. @@ -370,9 +370,9 @@ NULL NULL #' api_clients.delete -#' +#' #' api_clients.delete is a method defined in Arvados class. -#' +#' #' @usage arv$api_clients.delete(uuid) #' @param uuid The UUID of the ApiClient in question. #' @return ApiClient object. @@ -380,29 +380,29 @@ NULL NULL #' api_clients.list -#' +#' #' api_clients.list is a method defined in Arvados class. -#' +#' #' @usage arv$api_clients.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return ApiClientList object. #' @name api_clients.list NULL #' container_requests.get -#' +#' #' container_requests.get is a method defined in Arvados class. -#' +#' #' @usage arv$container_requests.get(uuid) #' @param uuid The UUID of the ContainerRequest in question. #' @return ContainerRequest object. @@ -410,9 +410,9 @@ NULL NULL #' container_requests.create -#' +#' #' container_requests.create is a method defined in Arvados class. -#' +#' #' @usage arv$container_requests.create(containerrequest, #' ensure_unique_name = "false") #' @param containerRequest ContainerRequest object. @@ -422,9 +422,9 @@ NULL NULL #' container_requests.update -#' +#' #' container_requests.update is a method defined in Arvados class. -#' +#' #' @usage arv$container_requests.update(containerrequest, #' uuid) #' @param containerRequest ContainerRequest object. @@ -434,9 +434,9 @@ NULL NULL #' container_requests.delete -#' +#' #' container_requests.delete is a method defined in Arvados class. -#' +#' #' @usage arv$container_requests.delete(uuid) #' @param uuid The UUID of the ContainerRequest in question. #' @return ContainerRequest object. @@ -444,29 +444,29 @@ NULL NULL #' container_requests.list -#' +#' #' container_requests.list is a method defined in Arvados class. -#' +#' #' @usage arv$container_requests.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return ContainerRequestList object. #' @name container_requests.list NULL #' authorized_keys.get -#' +#' #' authorized_keys.get is a method defined in Arvados class. -#' +#' #' @usage arv$authorized_keys.get(uuid) #' @param uuid The UUID of the AuthorizedKey in question. #' @return AuthorizedKey object. @@ -474,9 +474,9 @@ NULL NULL #' authorized_keys.create -#' +#' #' authorized_keys.create is a method defined in Arvados class. -#' +#' #' @usage arv$authorized_keys.create(authorizedkey, #' ensure_unique_name = "false") #' @param authorizedKey AuthorizedKey object. @@ -486,9 +486,9 @@ NULL NULL #' authorized_keys.update -#' +#' #' authorized_keys.update is a method defined in Arvados class. -#' +#' #' @usage arv$authorized_keys.update(authorizedkey, #' uuid) #' @param authorizedKey AuthorizedKey object. @@ -498,9 +498,9 @@ NULL NULL #' authorized_keys.delete -#' +#' #' authorized_keys.delete is a method defined in Arvados class. -#' +#' #' @usage arv$authorized_keys.delete(uuid) #' @param uuid The UUID of the AuthorizedKey in question. #' @return AuthorizedKey object. @@ -508,29 +508,29 @@ NULL NULL #' authorized_keys.list -#' +#' #' authorized_keys.list is a method defined in Arvados class. -#' +#' #' @usage arv$authorized_keys.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return AuthorizedKeyList object. #' @name authorized_keys.list NULL #' collections.get -#' +#' #' collections.get is a method defined in Arvados class. -#' +#' #' @usage arv$collections.get(uuid) #' @param uuid The UUID of the Collection in question. #' @return Collection object. @@ -538,9 +538,9 @@ NULL NULL #' collections.create -#' +#' #' collections.create is a method defined in Arvados class. -#' +#' #' @usage arv$collections.create(collection, #' ensure_unique_name = "false") #' @param collection Collection object. @@ -550,9 +550,9 @@ NULL NULL #' collections.update -#' +#' #' collections.update is a method defined in Arvados class. -#' +#' #' @usage arv$collections.update(collection, #' uuid) #' @param collection Collection object. @@ -562,9 +562,9 @@ NULL NULL #' collections.delete -#' +#' #' collections.delete is a method defined in Arvados class. -#' +#' #' @usage arv$collections.delete(uuid) #' @param uuid The UUID of the Collection in question. #' @return Collection object. @@ -572,70 +572,70 @@ NULL NULL #' collections.provenance -#' +#' #' collections.provenance is a method defined in Arvados class. -#' +#' #' @usage arv$collections.provenance(uuid) -#' @param uuid +#' @param uuid #' @return Collection object. #' @name collections.provenance NULL #' collections.used_by -#' +#' #' collections.used_by is a method defined in Arvados class. -#' +#' #' @usage arv$collections.used_by(uuid) -#' @param uuid +#' @param uuid #' @return Collection object. #' @name collections.used_by NULL #' collections.trash -#' +#' #' collections.trash is a method defined in Arvados class. -#' +#' #' @usage arv$collections.trash(uuid) -#' @param uuid +#' @param uuid #' @return Collection object. #' @name collections.trash NULL #' collections.untrash -#' +#' #' collections.untrash is a method defined in Arvados class. -#' +#' #' @usage arv$collections.untrash(uuid) -#' @param uuid +#' @param uuid #' @return Collection object. #' @name collections.untrash NULL #' collections.list -#' +#' #' collections.list is a method defined in Arvados class. -#' +#' #' @usage arv$collections.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact", include_trash = NULL) -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @param include_trash Include collections whose is_trashed attribute is true. #' @return CollectionList object. #' @name collections.list NULL #' humans.get -#' +#' #' humans.get is a method defined in Arvados class. -#' +#' #' @usage arv$humans.get(uuid) #' @param uuid The UUID of the Human in question. #' @return Human object. @@ -643,9 +643,9 @@ NULL NULL #' humans.create -#' +#' #' humans.create is a method defined in Arvados class. -#' +#' #' @usage arv$humans.create(human, ensure_unique_name = "false") #' @param human Human object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -654,9 +654,9 @@ NULL NULL #' humans.update -#' +#' #' humans.update is a method defined in Arvados class. -#' +#' #' @usage arv$humans.update(human, uuid) #' @param human Human object. #' @param uuid The UUID of the Human in question. @@ -665,9 +665,9 @@ NULL NULL #' humans.delete -#' +#' #' humans.delete is a method defined in Arvados class. -#' +#' #' @usage arv$humans.delete(uuid) #' @param uuid The UUID of the Human in question. #' @return Human object. @@ -675,29 +675,29 @@ NULL NULL #' humans.list -#' +#' #' humans.list is a method defined in Arvados class. -#' +#' #' @usage arv$humans.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return HumanList object. #' @name humans.list NULL #' job_tasks.get -#' +#' #' job_tasks.get is a method defined in Arvados class. -#' +#' #' @usage arv$job_tasks.get(uuid) #' @param uuid The UUID of the JobTask in question. #' @return JobTask object. @@ -705,9 +705,9 @@ NULL NULL #' job_tasks.create -#' +#' #' job_tasks.create is a method defined in Arvados class. -#' +#' #' @usage arv$job_tasks.create(jobtask, ensure_unique_name = "false") #' @param jobTask JobTask object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -716,9 +716,9 @@ NULL NULL #' job_tasks.update -#' +#' #' job_tasks.update is a method defined in Arvados class. -#' +#' #' @usage arv$job_tasks.update(jobtask, uuid) #' @param jobTask JobTask object. #' @param uuid The UUID of the JobTask in question. @@ -727,9 +727,9 @@ NULL NULL #' job_tasks.delete -#' +#' #' job_tasks.delete is a method defined in Arvados class. -#' +#' #' @usage arv$job_tasks.delete(uuid) #' @param uuid The UUID of the JobTask in question. #' @return JobTask object. @@ -737,29 +737,29 @@ NULL NULL #' job_tasks.list -#' +#' #' job_tasks.list is a method defined in Arvados class. -#' +#' #' @usage arv$job_tasks.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return JobTaskList object. #' @name job_tasks.list NULL #' jobs.get -#' +#' #' jobs.get is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.get(uuid) #' @param uuid The UUID of the Job in question. #' @return Job object. @@ -767,26 +767,26 @@ NULL NULL #' jobs.create -#' +#' #' jobs.create is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.create(job, ensure_unique_name = "false", #' find_or_create = "false", filters = NULL, #' minimum_script_version = NULL, exclude_script_versions = NULL) #' @param job Job object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @param find_or_create -#' @param filters -#' @param minimum_script_version -#' @param exclude_script_versions +#' @param find_or_create +#' @param filters +#' @param minimum_script_version +#' @param exclude_script_versions #' @return Job object. #' @name jobs.create NULL #' jobs.update -#' +#' #' jobs.update is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.update(job, uuid) #' @param job Job object. #' @param uuid The UUID of the Job in question. @@ -795,9 +795,9 @@ NULL NULL #' jobs.delete -#' +#' #' jobs.delete is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.delete(uuid) #' @param uuid The UUID of the Job in question. #' @return Job object. @@ -805,77 +805,77 @@ NULL NULL #' jobs.queue -#' +#' #' jobs.queue is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.queue(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return Job object. #' @name jobs.queue NULL #' jobs.queue_size -#' +#' #' jobs.queue_size is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.queue_size(NULL) #' @return Job object. #' @name jobs.queue_size NULL #' jobs.cancel -#' +#' #' jobs.cancel is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.cancel(uuid) -#' @param uuid +#' @param uuid #' @return Job object. #' @name jobs.cancel NULL #' jobs.lock -#' +#' #' jobs.lock is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.lock(uuid) -#' @param uuid +#' @param uuid #' @return Job object. #' @name jobs.lock NULL #' jobs.list -#' +#' #' jobs.list is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.list(filters = NULL, where = NULL, #' order = NULL, select = NULL, distinct = NULL, #' limit = "100", offset = "0", count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return JobList object. #' @name jobs.list NULL #' keep_disks.get -#' +#' #' keep_disks.get is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.get(uuid) #' @param uuid The UUID of the KeepDisk in question. #' @return KeepDisk object. @@ -883,9 +883,9 @@ NULL NULL #' keep_disks.create -#' +#' #' keep_disks.create is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.create(keepdisk, #' ensure_unique_name = "false") #' @param keepDisk KeepDisk object. @@ -895,9 +895,9 @@ NULL NULL #' keep_disks.update -#' +#' #' keep_disks.update is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.update(keepdisk, #' uuid) #' @param keepDisk KeepDisk object. @@ -907,9 +907,9 @@ NULL NULL #' keep_disks.delete -#' +#' #' keep_disks.delete is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.delete(uuid) #' @param uuid The UUID of the KeepDisk in question. #' @return KeepDisk object. @@ -917,47 +917,47 @@ NULL NULL #' keep_disks.ping -#' +#' #' keep_disks.ping is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.ping(uuid = NULL, #' ping_secret, node_uuid = NULL, filesystem_uuid = NULL, #' service_host = NULL, service_port, service_ssl_flag) -#' @param uuid -#' @param ping_secret -#' @param node_uuid -#' @param filesystem_uuid -#' @param service_host -#' @param service_port -#' @param service_ssl_flag +#' @param uuid +#' @param ping_secret +#' @param node_uuid +#' @param filesystem_uuid +#' @param service_host +#' @param service_port +#' @param service_ssl_flag #' @return KeepDisk object. #' @name keep_disks.ping NULL #' keep_disks.list -#' +#' #' keep_disks.list is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return KeepDiskList object. #' @name keep_disks.list NULL #' nodes.get -#' +#' #' nodes.get is a method defined in Arvados class. -#' +#' #' @usage arv$nodes.get(uuid) #' @param uuid The UUID of the Node in question. #' @return Node object. @@ -965,9 +965,9 @@ NULL NULL #' nodes.create -#' +#' #' nodes.create is a method defined in Arvados class. -#' +#' #' @usage arv$nodes.create(node, ensure_unique_name = "false", #' assign_slot = NULL) #' @param node Node object. @@ -978,9 +978,9 @@ NULL NULL #' nodes.update -#' +#' #' nodes.update is a method defined in Arvados class. -#' +#' #' @usage arv$nodes.update(node, uuid, assign_slot = NULL) #' @param node Node object. #' @param uuid The UUID of the Node in question. @@ -990,9 +990,9 @@ NULL NULL #' nodes.delete -#' +#' #' nodes.delete is a method defined in Arvados class. -#' +#' #' @usage arv$nodes.delete(uuid) #' @param uuid The UUID of the Node in question. #' @return Node object. @@ -1000,40 +1000,40 @@ NULL NULL #' nodes.ping -#' +#' #' nodes.ping is a method defined in Arvados class. -#' +#' #' @usage arv$nodes.ping(uuid, ping_secret) -#' @param uuid -#' @param ping_secret +#' @param uuid +#' @param ping_secret #' @return Node object. #' @name nodes.ping NULL #' nodes.list -#' +#' #' nodes.list is a method defined in Arvados class. -#' +#' #' @usage arv$nodes.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return NodeList object. #' @name nodes.list NULL #' links.get -#' +#' #' links.get is a method defined in Arvados class. -#' +#' #' @usage arv$links.get(uuid) #' @param uuid The UUID of the Link in question. #' @return Link object. @@ -1041,9 +1041,9 @@ NULL NULL #' links.create -#' +#' #' links.create is a method defined in Arvados class. -#' +#' #' @usage arv$links.create(link, ensure_unique_name = "false") #' @param link Link object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -1052,9 +1052,9 @@ NULL NULL #' links.update -#' +#' #' links.update is a method defined in Arvados class. -#' +#' #' @usage arv$links.update(link, uuid) #' @param link Link object. #' @param uuid The UUID of the Link in question. @@ -1063,9 +1063,9 @@ NULL NULL #' links.delete -#' +#' #' links.delete is a method defined in Arvados class. -#' +#' #' @usage arv$links.delete(uuid) #' @param uuid The UUID of the Link in question. #' @return Link object. @@ -1073,39 +1073,39 @@ NULL NULL #' links.list -#' +#' #' links.list is a method defined in Arvados class. -#' +#' #' @usage arv$links.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return LinkList object. #' @name links.list NULL #' links.get_permissions -#' +#' #' links.get_permissions is a method defined in Arvados class. -#' +#' #' @usage arv$links.get_permissions(uuid) -#' @param uuid +#' @param uuid #' @return Link object. #' @name links.get_permissions NULL #' keep_services.get -#' +#' #' keep_services.get is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.get(uuid) #' @param uuid The UUID of the KeepService in question. #' @return KeepService object. @@ -1113,9 +1113,9 @@ NULL NULL #' keep_services.create -#' +#' #' keep_services.create is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.create(keepservice, #' ensure_unique_name = "false") #' @param keepService KeepService object. @@ -1125,9 +1125,9 @@ NULL NULL #' keep_services.update -#' +#' #' keep_services.update is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.update(keepservice, #' uuid) #' @param keepService KeepService object. @@ -1137,9 +1137,9 @@ NULL NULL #' keep_services.delete -#' +#' #' keep_services.delete is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.delete(uuid) #' @param uuid The UUID of the KeepService in question. #' @return KeepService object. @@ -1147,38 +1147,38 @@ NULL NULL #' keep_services.accessible -#' +#' #' keep_services.accessible is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.accessible(NULL) #' @return KeepService object. #' @name keep_services.accessible NULL #' keep_services.list -#' +#' #' keep_services.list is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return KeepServiceList object. #' @name keep_services.list NULL #' pipeline_templates.get -#' +#' #' pipeline_templates.get is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_templates.get(uuid) #' @param uuid The UUID of the PipelineTemplate in question. #' @return PipelineTemplate object. @@ -1186,9 +1186,9 @@ NULL NULL #' pipeline_templates.create -#' +#' #' pipeline_templates.create is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_templates.create(pipelinetemplate, #' ensure_unique_name = "false") #' @param pipelineTemplate PipelineTemplate object. @@ -1198,9 +1198,9 @@ NULL NULL #' pipeline_templates.update -#' +#' #' pipeline_templates.update is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_templates.update(pipelinetemplate, #' uuid) #' @param pipelineTemplate PipelineTemplate object. @@ -1210,9 +1210,9 @@ NULL NULL #' pipeline_templates.delete -#' +#' #' pipeline_templates.delete is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_templates.delete(uuid) #' @param uuid The UUID of the PipelineTemplate in question. #' @return PipelineTemplate object. @@ -1220,29 +1220,29 @@ NULL NULL #' pipeline_templates.list -#' +#' #' pipeline_templates.list is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_templates.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return PipelineTemplateList object. #' @name pipeline_templates.list NULL #' pipeline_instances.get -#' +#' #' pipeline_instances.get is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.get(uuid) #' @param uuid The UUID of the PipelineInstance in question. #' @return PipelineInstance object. @@ -1250,9 +1250,9 @@ NULL NULL #' pipeline_instances.create -#' +#' #' pipeline_instances.create is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.create(pipelineinstance, #' ensure_unique_name = "false") #' @param pipelineInstance PipelineInstance object. @@ -1262,9 +1262,9 @@ NULL NULL #' pipeline_instances.update -#' +#' #' pipeline_instances.update is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.update(pipelineinstance, #' uuid) #' @param pipelineInstance PipelineInstance object. @@ -1274,9 +1274,9 @@ NULL NULL #' pipeline_instances.delete -#' +#' #' pipeline_instances.delete is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.delete(uuid) #' @param uuid The UUID of the PipelineInstance in question. #' @return PipelineInstance object. @@ -1284,39 +1284,39 @@ NULL NULL #' pipeline_instances.cancel -#' +#' #' pipeline_instances.cancel is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.cancel(uuid) -#' @param uuid +#' @param uuid #' @return PipelineInstance object. #' @name pipeline_instances.cancel NULL #' pipeline_instances.list -#' +#' #' pipeline_instances.list is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return PipelineInstanceList object. #' @name pipeline_instances.list NULL #' repositories.get -#' +#' #' repositories.get is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.get(uuid) #' @param uuid The UUID of the Repository in question. #' @return Repository object. @@ -1324,9 +1324,9 @@ NULL NULL #' repositories.create -#' +#' #' repositories.create is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.create(repository, #' ensure_unique_name = "false") #' @param repository Repository object. @@ -1336,9 +1336,9 @@ NULL NULL #' repositories.update -#' +#' #' repositories.update is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.update(repository, #' uuid) #' @param repository Repository object. @@ -1348,9 +1348,9 @@ NULL NULL #' repositories.delete -#' +#' #' repositories.delete is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.delete(uuid) #' @param uuid The UUID of the Repository in question. #' @return Repository object. @@ -1358,38 +1358,38 @@ NULL NULL #' repositories.get_all_permissions -#' +#' #' repositories.get_all_permissions is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.get_all_permissions(NULL) #' @return Repository object. #' @name repositories.get_all_permissions NULL #' repositories.list -#' +#' #' repositories.list is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return RepositoryList object. #' @name repositories.list NULL #' specimens.get -#' +#' #' specimens.get is a method defined in Arvados class. -#' +#' #' @usage arv$specimens.get(uuid) #' @param uuid The UUID of the Specimen in question. #' @return Specimen object. @@ -1397,9 +1397,9 @@ NULL NULL #' specimens.create -#' +#' #' specimens.create is a method defined in Arvados class. -#' +#' #' @usage arv$specimens.create(specimen, #' ensure_unique_name = "false") #' @param specimen Specimen object. @@ -1409,9 +1409,9 @@ NULL NULL #' specimens.update -#' +#' #' specimens.update is a method defined in Arvados class. -#' +#' #' @usage arv$specimens.update(specimen, #' uuid) #' @param specimen Specimen object. @@ -1421,9 +1421,9 @@ NULL NULL #' specimens.delete -#' +#' #' specimens.delete is a method defined in Arvados class. -#' +#' #' @usage arv$specimens.delete(uuid) #' @param uuid The UUID of the Specimen in question. #' @return Specimen object. @@ -1431,29 +1431,29 @@ NULL NULL #' specimens.list -#' +#' #' specimens.list is a method defined in Arvados class. -#' +#' #' @usage arv$specimens.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return SpecimenList object. #' @name specimens.list NULL #' logs.get -#' +#' #' logs.get is a method defined in Arvados class. -#' +#' #' @usage arv$logs.get(uuid) #' @param uuid The UUID of the Log in question. #' @return Log object. @@ -1461,9 +1461,9 @@ NULL NULL #' logs.create -#' +#' #' logs.create is a method defined in Arvados class. -#' +#' #' @usage arv$logs.create(log, ensure_unique_name = "false") #' @param log Log object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -1472,9 +1472,9 @@ NULL NULL #' logs.update -#' +#' #' logs.update is a method defined in Arvados class. -#' +#' #' @usage arv$logs.update(log, uuid) #' @param log Log object. #' @param uuid The UUID of the Log in question. @@ -1483,9 +1483,9 @@ NULL NULL #' logs.delete -#' +#' #' logs.delete is a method defined in Arvados class. -#' +#' #' @usage arv$logs.delete(uuid) #' @param uuid The UUID of the Log in question. #' @return Log object. @@ -1493,28 +1493,28 @@ NULL NULL #' logs.list -#' +#' #' logs.list is a method defined in Arvados class. -#' +#' #' @usage arv$logs.list(filters = NULL, where = NULL, #' order = NULL, select = NULL, distinct = NULL, #' limit = "100", offset = "0", count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return LogList object. #' @name logs.list NULL #' traits.get -#' +#' #' traits.get is a method defined in Arvados class. -#' +#' #' @usage arv$traits.get(uuid) #' @param uuid The UUID of the Trait in question. #' @return Trait object. @@ -1522,9 +1522,9 @@ NULL NULL #' traits.create -#' +#' #' traits.create is a method defined in Arvados class. -#' +#' #' @usage arv$traits.create(trait, ensure_unique_name = "false") #' @param trait Trait object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -1533,9 +1533,9 @@ NULL NULL #' traits.update -#' +#' #' traits.update is a method defined in Arvados class. -#' +#' #' @usage arv$traits.update(trait, uuid) #' @param trait Trait object. #' @param uuid The UUID of the Trait in question. @@ -1544,9 +1544,9 @@ NULL NULL #' traits.delete -#' +#' #' traits.delete is a method defined in Arvados class. -#' +#' #' @usage arv$traits.delete(uuid) #' @param uuid The UUID of the Trait in question. #' @return Trait object. @@ -1554,29 +1554,29 @@ NULL NULL #' traits.list -#' +#' #' traits.list is a method defined in Arvados class. -#' +#' #' @usage arv$traits.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return TraitList object. #' @name traits.list NULL #' virtual_machines.get -#' +#' #' virtual_machines.get is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.get(uuid) #' @param uuid The UUID of the VirtualMachine in question. #' @return VirtualMachine object. @@ -1584,9 +1584,9 @@ NULL NULL #' virtual_machines.create -#' +#' #' virtual_machines.create is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.create(virtualmachine, #' ensure_unique_name = "false") #' @param virtualMachine VirtualMachine object. @@ -1596,9 +1596,9 @@ NULL NULL #' virtual_machines.update -#' +#' #' virtual_machines.update is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.update(virtualmachine, #' uuid) #' @param virtualMachine VirtualMachine object. @@ -1608,9 +1608,9 @@ NULL NULL #' virtual_machines.delete -#' +#' #' virtual_machines.delete is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.delete(uuid) #' @param uuid The UUID of the VirtualMachine in question. #' @return VirtualMachine object. @@ -1618,48 +1618,48 @@ NULL NULL #' virtual_machines.logins -#' +#' #' virtual_machines.logins is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.logins(uuid) -#' @param uuid +#' @param uuid #' @return VirtualMachine object. #' @name virtual_machines.logins NULL #' virtual_machines.get_all_logins -#' +#' #' virtual_machines.get_all_logins is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.get_all_logins(NULL) #' @return VirtualMachine object. #' @name virtual_machines.get_all_logins NULL #' virtual_machines.list -#' +#' #' virtual_machines.list is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return VirtualMachineList object. #' @name virtual_machines.list NULL #' workflows.get -#' +#' #' workflows.get is a method defined in Arvados class. -#' +#' #' @usage arv$workflows.get(uuid) #' @param uuid The UUID of the Workflow in question. #' @return Workflow object. @@ -1667,9 +1667,9 @@ NULL NULL #' workflows.create -#' +#' #' workflows.create is a method defined in Arvados class. -#' +#' #' @usage arv$workflows.create(workflow, #' ensure_unique_name = "false") #' @param workflow Workflow object. @@ -1679,9 +1679,9 @@ NULL NULL #' workflows.update -#' +#' #' workflows.update is a method defined in Arvados class. -#' +#' #' @usage arv$workflows.update(workflow, #' uuid) #' @param workflow Workflow object. @@ -1691,9 +1691,9 @@ NULL NULL #' workflows.delete -#' +#' #' workflows.delete is a method defined in Arvados class. -#' +#' #' @usage arv$workflows.delete(uuid) #' @param uuid The UUID of the Workflow in question. #' @return Workflow object. @@ -1701,29 +1701,29 @@ NULL NULL #' workflows.list -#' +#' #' workflows.list is a method defined in Arvados class. -#' +#' #' @usage arv$workflows.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return WorkflowList object. #' @name workflows.list NULL #' groups.get -#' +#' #' groups.get is a method defined in Arvados class. -#' +#' #' @usage arv$groups.get(uuid) #' @param uuid The UUID of the Group in question. #' @return Group object. @@ -1731,9 +1731,9 @@ NULL NULL #' groups.create -#' +#' #' groups.create is a method defined in Arvados class. -#' +#' #' @usage arv$groups.create(group, ensure_unique_name = "false") #' @param group Group object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -1742,9 +1742,9 @@ NULL NULL #' groups.update -#' +#' #' groups.update is a method defined in Arvados class. -#' +#' #' @usage arv$groups.update(group, uuid) #' @param group Group object. #' @param uuid The UUID of the Group in question. @@ -1753,9 +1753,9 @@ NULL NULL #' groups.delete -#' +#' #' groups.delete is a method defined in Arvados class. -#' +#' #' @usage arv$groups.delete(uuid) #' @param uuid The UUID of the Group in question. #' @return Group object. @@ -1763,72 +1763,72 @@ NULL NULL #' groups.contents -#' +#' #' groups.contents is a method defined in Arvados class. -#' +#' #' @usage arv$groups.contents(filters = NULL, #' where = NULL, order = NULL, distinct = NULL, #' limit = "100", offset = "0", count = "exact", #' include_trash = NULL, uuid = NULL, recursive = NULL) -#' @param filters -#' @param where -#' @param order -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @param include_trash Include items whose is_trashed attribute is true. -#' @param uuid +#' @param uuid #' @param recursive Include contents from child groups recursively. #' @return Group object. #' @name groups.contents NULL #' groups.trash -#' +#' #' groups.trash is a method defined in Arvados class. -#' +#' #' @usage arv$groups.trash(uuid) -#' @param uuid +#' @param uuid #' @return Group object. #' @name groups.trash NULL #' groups.untrash -#' +#' #' groups.untrash is a method defined in Arvados class. -#' +#' #' @usage arv$groups.untrash(uuid) -#' @param uuid +#' @param uuid #' @return Group object. #' @name groups.untrash NULL #' groups.list -#' +#' #' groups.list is a method defined in Arvados class. -#' +#' #' @usage arv$groups.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact", include_trash = NULL) -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @param include_trash Include items whose is_trashed attribute is true. #' @return GroupList object. #' @name groups.list NULL #' user_agreements.get -#' +#' #' user_agreements.get is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.get(uuid) #' @param uuid The UUID of the UserAgreement in question. #' @return UserAgreement object. @@ -1836,9 +1836,9 @@ NULL NULL #' user_agreements.create -#' +#' #' user_agreements.create is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.create(useragreement, #' ensure_unique_name = "false") #' @param userAgreement UserAgreement object. @@ -1848,9 +1848,9 @@ NULL NULL #' user_agreements.update -#' +#' #' user_agreements.update is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.update(useragreement, #' uuid) #' @param userAgreement UserAgreement object. @@ -1860,9 +1860,9 @@ NULL NULL #' user_agreements.delete -#' +#' #' user_agreements.delete is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.delete(uuid) #' @param uuid The UUID of the UserAgreement in question. #' @return UserAgreement object. @@ -1870,56 +1870,56 @@ NULL NULL #' user_agreements.signatures -#' +#' #' user_agreements.signatures is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.signatures(NULL) #' @return UserAgreement object. #' @name user_agreements.signatures NULL #' user_agreements.sign -#' +#' #' user_agreements.sign is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.sign(NULL) #' @return UserAgreement object. #' @name user_agreements.sign NULL #' user_agreements.list -#' +#' #' user_agreements.list is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return UserAgreementList object. #' @name user_agreements.list NULL #' user_agreements.new -#' +#' #' user_agreements.new is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.new(NULL) #' @return UserAgreement object. #' @name user_agreements.new NULL #' project.get -#' +#' #' projects.get is equivalent to groups.get method. -#' +#' #' @usage arv$projects.get(uuid) #' @param uuid The UUID of the Group in question. #' @return Group object. @@ -1927,9 +1927,9 @@ NULL NULL #' project.create -#' +#' #' projects.create wrapps groups.create method by setting group_class attribute to "project". -#' +#' #' @usage arv$projects.create(group, ensure_unique_name = "false") #' @param group Group object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -1938,9 +1938,9 @@ NULL NULL #' project.update -#' +#' #' projects.update wrapps groups.update method by setting group_class attribute to "project". -#' +#' #' @usage arv$projects.update(group, uuid) #' @param group Group object. #' @param uuid The UUID of the Group in question. @@ -1949,9 +1949,9 @@ NULL NULL #' project.delete -#' +#' #' projects.delete is equivalent to groups.delete method. -#' +#' #' @usage arv$project.delete(uuid) #' @param uuid The UUID of the Group in question. #' @return Group object. @@ -1959,22 +1959,22 @@ NULL NULL #' project.list -#' +#' #' projects.list wrapps groups.list method by setting group_class attribute to "project". -#' +#' #' @usage arv$projects.list(filters = NULL, #' where = NULL, order = NULL, distinct = NULL, #' limit = "100", offset = "0", count = "exact", #' include_trash = NULL, uuid = NULL, recursive = NULL) -#' @param filters -#' @param where -#' @param order -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @param include_trash Include items whose is_trashed attribute is true. -#' @param uuid +#' @param uuid #' @param recursive Include contents from child groups recursively. #' @return Group object. #' @name projects.list @@ -2247,19 +2247,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2267,23 +2267,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(user) > 0) - body <- jsonlite::toJSON(list(user = user), + body <- jsonlite::toJSON(list(user = user), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2291,23 +2291,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(user) > 0) - body <- jsonlite::toJSON(list(user = user), + body <- jsonlite::toJSON(list(user = user), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2315,19 +2315,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2335,19 +2335,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/current") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2355,19 +2355,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/system") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2375,19 +2375,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}/activate") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2396,21 +2396,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/setup") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(user = user, openid_prefix = openid_prefix, repo_name = repo_name, vm_uuid = vm_uuid, send_notification_email = send_notification_email) - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2418,19 +2418,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}/unsetup") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2438,19 +2438,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}/update_uuid") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(new_uuid = new_uuid) - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2459,20 +2459,20 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/merge") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(new_owner_uuid = new_owner_uuid, new_user_token = new_user_token, redirect_to_new_user = redirect_to_new_user) - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2482,21 +2482,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2504,19 +2504,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2525,23 +2525,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(apiclientauthorization) > 0) - body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), + body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2549,23 +2549,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(apiclientauthorization) > 0) - body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), + body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2573,19 +2573,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2593,20 +2593,20 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations/create_system_auth") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(api_client_id = api_client_id, scopes = scopes) - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2614,19 +2614,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations/current") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2637,21 +2637,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2659,19 +2659,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2679,23 +2679,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(container) > 0) - body <- jsonlite::toJSON(list(container = container), + body <- jsonlite::toJSON(list(container = container), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2703,23 +2703,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(container) > 0) - body <- jsonlite::toJSON(list(container = container), + body <- jsonlite::toJSON(list(container = container), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2727,19 +2727,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2747,19 +2747,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}/auth") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2767,19 +2767,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}/lock") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2787,19 +2787,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}/unlock") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2807,19 +2807,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}/secret_mounts") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2827,19 +2827,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/current") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2850,21 +2850,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2872,19 +2872,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2892,23 +2892,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_clients") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(apiclient) > 0) - body <- jsonlite::toJSON(list(apiclient = apiclient), + body <- jsonlite::toJSON(list(apiclient = apiclient), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2916,23 +2916,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(apiclient) > 0) - body <- jsonlite::toJSON(list(apiclient = apiclient), + body <- jsonlite::toJSON(list(apiclient = apiclient), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2940,19 +2940,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2963,21 +2963,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_clients") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2985,19 +2985,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3006,23 +3006,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("container_requests") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(containerrequest) > 0) - body <- jsonlite::toJSON(list(containerrequest = containerrequest), + 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$errors) - + resource }, @@ -3030,23 +3030,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(containerrequest) > 0) - body <- jsonlite::toJSON(list(containerrequest = containerrequest), + body <- jsonlite::toJSON(list(containerrequest = containerrequest), auto_unbox = TRUE) else body <- NULL - + response <- private$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 }, @@ -3054,19 +3054,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3077,21 +3077,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("container_requests") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3099,19 +3099,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3120,23 +3120,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("authorized_keys") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(authorizedkey) > 0) - body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), + body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), auto_unbox = TRUE) else body <- NULL - + response <- private$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 }, @@ -3144,23 +3144,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(authorizedkey) > 0) - body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), + 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$errors) - + resource }, @@ -3168,19 +3168,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3191,21 +3191,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("authorized_keys") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3213,19 +3213,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3233,23 +3233,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(collection) > 0) - body <- jsonlite::toJSON(list(collection = collection), + body <- jsonlite::toJSON(list(collection = collection), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3257,23 +3257,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(collection) > 0) - body <- jsonlite::toJSON(list(collection = collection), + body <- jsonlite::toJSON(list(collection = collection), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3281,19 +3281,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3301,19 +3301,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}/provenance") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3321,19 +3321,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}/used_by") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3341,19 +3341,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}/trash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3361,19 +3361,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}/untrash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3384,22 +3384,22 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count, include_trash = include_trash) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3407,19 +3407,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("humans/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3427,23 +3427,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("humans") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(human) > 0) - body <- jsonlite::toJSON(list(human = human), + body <- jsonlite::toJSON(list(human = human), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3451,23 +3451,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("humans/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(human) > 0) - body <- jsonlite::toJSON(list(human = human), + body <- jsonlite::toJSON(list(human = human), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3475,19 +3475,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("humans/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3497,21 +3497,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("humans") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3519,19 +3519,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3539,23 +3539,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("job_tasks") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(jobtask) > 0) - body <- jsonlite::toJSON(list(jobtask = jobtask), + body <- jsonlite::toJSON(list(jobtask = jobtask), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3563,23 +3563,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(jobtask) > 0) - body <- jsonlite::toJSON(list(jobtask = jobtask), + body <- jsonlite::toJSON(list(jobtask = jobtask), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3587,19 +3587,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3610,21 +3610,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("job_tasks") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3632,19 +3632,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3654,26 +3654,26 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name, find_or_create = find_or_create, filters = filters, minimum_script_version = minimum_script_version, exclude_script_versions = exclude_script_versions) - + if(length(job) > 0) - body <- jsonlite::toJSON(list(job = job), + body <- jsonlite::toJSON(list(job = job), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3681,23 +3681,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(job) > 0) - body <- jsonlite::toJSON(list(job = job), + body <- jsonlite::toJSON(list(job = job), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3705,19 +3705,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3727,21 +3727,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs/queue") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3749,19 +3749,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs/queue_size") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3769,19 +3769,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs/${uuid}/cancel") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3789,19 +3789,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs/${uuid}/lock") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$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 }, @@ -3811,21 +3811,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3833,19 +3833,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3853,23 +3853,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_disks") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(keepdisk) > 0) - body <- jsonlite::toJSON(list(keepdisk = keepdisk), + body <- jsonlite::toJSON(list(keepdisk = keepdisk), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3877,23 +3877,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(keepdisk) > 0) - body <- jsonlite::toJSON(list(keepdisk = keepdisk), + body <- jsonlite::toJSON(list(keepdisk = keepdisk), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3901,19 +3901,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3923,22 +3923,22 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_disks/ping") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(uuid = uuid, ping_secret = ping_secret, node_uuid = node_uuid, filesystem_uuid = filesystem_uuid, service_host = service_host, service_port = service_port, service_ssl_flag = service_ssl_flag) - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3949,21 +3949,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_disks") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3971,19 +3971,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("nodes/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3992,24 +3992,24 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("nodes") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name, assign_slot = assign_slot) - + if(length(node) > 0) - body <- jsonlite::toJSON(list(node = node), + body <- jsonlite::toJSON(list(node = node), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4017,23 +4017,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("nodes/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(assign_slot = assign_slot) - + if(length(node) > 0) - body <- jsonlite::toJSON(list(node = node), + body <- jsonlite::toJSON(list(node = node), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4041,19 +4041,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("nodes/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4061,19 +4061,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("nodes/${uuid}/ping") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ping_secret = ping_secret) - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4083,21 +4083,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("nodes") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4105,19 +4105,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4125,23 +4125,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("links") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(link) > 0) - body <- jsonlite::toJSON(list(link = link), + body <- jsonlite::toJSON(list(link = link), auto_unbox = TRUE) else body <- NULL - + response <- private$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 }, @@ -4149,23 +4149,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(link) > 0) - body <- jsonlite::toJSON(list(link = link), + 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$errors) - + resource }, @@ -4173,19 +4173,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4195,21 +4195,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("links") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4217,19 +4217,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("permissions/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- 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$errors) - + resource }, @@ -4237,19 +4237,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4258,23 +4258,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_services") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(keepservice) > 0) - body <- jsonlite::toJSON(list(keepservice = keepservice), + body <- jsonlite::toJSON(list(keepservice = keepservice), auto_unbox = TRUE) else body <- NULL - + response <- private$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 }, @@ -4282,23 +4282,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(keepservice) > 0) - body <- jsonlite::toJSON(list(keepservice = keepservice), + 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$errors) - + resource }, @@ -4306,19 +4306,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4326,19 +4326,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_services/accessible") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4349,21 +4349,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_services") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4371,19 +4371,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4392,23 +4392,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_templates") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(pipelinetemplate) > 0) - body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), + body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4416,23 +4416,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(pipelinetemplate) > 0) - body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), + body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4440,19 +4440,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4463,21 +4463,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_templates") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4485,19 +4485,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4506,23 +4506,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_instances") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(pipelineinstance) > 0) - body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), + body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4530,23 +4530,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(pipelineinstance) > 0) - body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), + body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4554,19 +4554,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4574,19 +4574,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_instances/${uuid}/cancel") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- 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$errors) - + resource }, @@ -4597,21 +4597,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_instances") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4619,19 +4619,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4639,23 +4639,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(repository) > 0) - body <- jsonlite::toJSON(list(repository = repository), + body <- jsonlite::toJSON(list(repository = repository), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4663,23 +4663,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(repository) > 0) - body <- jsonlite::toJSON(list(repository = repository), + body <- jsonlite::toJSON(list(repository = repository), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4687,19 +4687,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4707,19 +4707,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories/get_all_permissions") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4730,21 +4730,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4752,19 +4752,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("specimens/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4772,23 +4772,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("specimens") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(specimen) > 0) - body <- jsonlite::toJSON(list(specimen = specimen), + body <- jsonlite::toJSON(list(specimen = specimen), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4796,23 +4796,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("specimens/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(specimen) > 0) - body <- jsonlite::toJSON(list(specimen = specimen), + body <- jsonlite::toJSON(list(specimen = specimen), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4820,19 +4820,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("specimens/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4843,21 +4843,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("specimens") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4865,19 +4865,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4885,23 +4885,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("logs") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(log) > 0) - body <- jsonlite::toJSON(list(log = log), + body <- jsonlite::toJSON(list(log = log), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4909,23 +4909,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(log) > 0) - body <- jsonlite::toJSON(list(log = log), + body <- jsonlite::toJSON(list(log = log), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4933,19 +4933,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4955,21 +4955,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("logs") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4977,19 +4977,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("traits/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4997,23 +4997,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("traits") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(trait) > 0) - body <- jsonlite::toJSON(list(trait = trait), + body <- jsonlite::toJSON(list(trait = trait), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5021,23 +5021,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("traits/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(trait) > 0) - body <- jsonlite::toJSON(list(trait = trait), + body <- jsonlite::toJSON(list(trait = trait), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5045,19 +5045,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("traits/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5067,21 +5067,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("traits") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5089,19 +5089,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5110,23 +5110,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(virtualmachine) > 0) - body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), + body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5134,23 +5134,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(virtualmachine) > 0) - body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), + body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5158,19 +5158,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5178,19 +5178,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines/${uuid}/logins") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5198,19 +5198,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines/get_all_logins") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5221,21 +5221,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5243,19 +5243,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("workflows/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5263,23 +5263,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("workflows") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(workflow) > 0) - body <- jsonlite::toJSON(list(workflow = workflow), + body <- jsonlite::toJSON(list(workflow = workflow), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5287,23 +5287,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("workflows/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(workflow) > 0) - body <- jsonlite::toJSON(list(workflow = workflow), + body <- jsonlite::toJSON(list(workflow = workflow), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5311,19 +5311,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("workflows/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5334,21 +5334,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("workflows") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5356,19 +5356,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5376,23 +5376,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(group) > 0) - body <- jsonlite::toJSON(list(group = group), + body <- jsonlite::toJSON(list(group = group), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5400,23 +5400,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(group) > 0) - body <- jsonlite::toJSON(list(group = group), + body <- jsonlite::toJSON(list(group = group), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5424,19 +5424,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5447,22 +5447,22 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/contents") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, distinct = distinct, limit = limit, offset = offset, count = count, include_trash = include_trash, uuid = uuid, recursive = recursive) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5470,19 +5470,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/${uuid}/trash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5490,19 +5490,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/${uuid}/untrash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5513,22 +5513,22 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count, include_trash = include_trash) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5536,19 +5536,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5557,23 +5557,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(useragreement) > 0) - body <- jsonlite::toJSON(list(useragreement = useragreement), + body <- jsonlite::toJSON(list(useragreement = useragreement), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5581,23 +5581,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(useragreement) > 0) - body <- jsonlite::toJSON(list(useragreement = useragreement), + body <- jsonlite::toJSON(list(useragreement = useragreement), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5605,19 +5605,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5625,19 +5625,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/signatures") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5645,19 +5645,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/sign") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5668,21 +5668,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5690,19 +5690,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/new") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, diff --git a/sdk/R/R/ArvadosFile.R b/sdk/R/R/ArvadosFile.R index 2257d99bfe..70bb4450ec 100644 --- a/sdk/R/R/ArvadosFile.R +++ b/sdk/R/R/ArvadosFile.R @@ -258,18 +258,23 @@ ArvadosFile <- R6::R6Class( attachToNewParent = function(content, newParent) { - #Note: We temporary set parents collection to NULL. This will ensure that - # add method doesn't post this file on REST. + # We temporary set parents collection to NULL. This will ensure that + # add method doesn't post this file on REST. + # We also need to set content's collection to NULL because + # add method throws exception if we try to add content that already + # belongs to a collection. parentsCollection <- newParent$getCollection() + content$setCollection(NULL, setRecursively = FALSE) newParent$setCollection(NULL, setRecursively = FALSE) newParent$add(content) + content$setCollection(parentsCollection, setRecursively = FALSE) newParent$setCollection(parentsCollection, setRecursively = FALSE) }, dettachFromCurrentParent = function() { - #Note: We temporary set parents collection to NULL. This will ensure that - # remove method doesn't remove this file from REST. + # We temporary set parents collection to NULL. This will ensure that + # remove method doesn't remove this file from REST. parent <- private$parent parentsCollection <- parent$getCollection() parent$setCollection(NULL, setRecursively = FALSE) diff --git a/sdk/R/R/Collection.R b/sdk/R/R/Collection.R index f88eb0e7cd..8869d7be67 100644 --- a/sdk/R/R/Collection.R +++ b/sdk/R/R/Collection.R @@ -23,9 +23,10 @@ source("./R/util.R") #' @section Methods: #' \describe{ #' \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.} -#' \item{create(fileNames, relativePath = "")}{Creates one or more ArvadosFiles and adds them to the collection at specified path.} +#' \item{create(files)}{Creates one or more ArvadosFiles and adds them to the collection at specified path.} #' \item{remove(fileNames)}{Remove one or more files from the collection.} -#' \item{move(content, newLocation)}{Moves ArvadosFile or Subcollection to another location in the collection.} +#' \item{move(content, destination)}{Moves ArvadosFile or Subcollection to another location in the collection.} +#' \item{copy(content, destination)}{Copies ArvadosFile or Subcollection to another location in the collection.} #' \item{getFileListing()}{Returns collections file content as character vector.} #' \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.} #' } @@ -36,9 +37,6 @@ source("./R/util.R") #' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com") #' collection <- Collection$new(arv, "uuid") #' -#' newFile <- ArvadosFile$new("myFile") -#' collection$add(newFile, "myFolder") -#' #' createdFiles <- collection$create(c("main.cpp", lib.dll), "cpp/src/") #' #' collection$remove("location/to/my/file.cpp") @@ -88,6 +86,9 @@ Collection <- R6::R6Class( if("ArvadosFile" %in% class(content) || "Subcollection" %in% class(content)) { + if(!is.null(content$getCollection())) + stop("Content already belongs to a collection.") + if(content$getName() == "") stop("Content has invalid name.") @@ -102,50 +103,32 @@ Collection <- R6::R6Class( } }, - create = function(fileNames, relativePath = "") + create = function(files) { if(is.null(private$tree)) private$generateCollectionTreeStructure() - if(relativePath == "" || - relativePath == "." || - relativePath == "./") - { - subcollection <- private$tree$getTree() - } - else - { - relativePath <- trimFromEnd(relativePath, "/") - subcollection <- self$get(relativePath) - } - - if(is.null(subcollection)) - stop(paste("Subcollection", relativePath, "doesn't exist.")) - - if(is.character(fileNames)) + if(is.character(files)) { - arvadosFiles <- NULL - sapply(fileNames, function(fileName) + sapply(files, function(file) { - childWithSameName <- subcollection$get(fileName) + childWithSameName <- self$get(file) if(!is.null(childWithSameName)) stop("Destination already contains file with same name.") - newFile <- ArvadosFile$new(fileName) - subcollection$add(newFile) + newTreeBranch <- private$tree$createBranch(file) + private$tree$addBranch(private$tree$getTree(), newTreeBranch) - arvadosFiles <<- c(arvadosFiles, newFile) + private$REST$create(file, self$uuid) + newTreeBranch$setCollection(self) }) - if(length(arvadosFiles) == 1) - return(arvadosFiles[[1]]) - else - return(arvadosFiles) + "Created" } else { stop(paste0("Expected character vector, got ", - paste0("(", paste0(class(fileNames), collapse = ", "), ")"), + paste0("(", paste0(class(files), collapse = ", "), ")"), ".")) } }, @@ -215,8 +198,11 @@ Collection <- R6::R6Class( refresh = function() { - private$tree$getTree()$setCollection(NULL, setRecursively = TRUE) - private$tree <- NULL + if(!is.null(private$tree)) + { + private$tree$getTree()$setCollection(NULL, setRecursively = TRUE) + private$tree <- NULL + } }, getFileListing = function() diff --git a/sdk/R/R/CollectionTree.R b/sdk/R/R/CollectionTree.R index 2d4af094aa..5f7a29455a 100644 --- a/sdk/R/R/CollectionTree.R +++ b/sdk/R/R/CollectionTree.R @@ -15,55 +15,16 @@ CollectionTree <- R6::R6Class( initialize = function(fileContent, collection) { self$pathsList <- fileContent - - treeBranches <- sapply(fileContent, function(filePath) - { - splitPath <- unlist(strsplit(filePath, "/", fixed = TRUE)) - branch <- private$createBranch(splitPath) - }) - + treeBranches <- sapply(fileContent, function(filePath) self$createBranch(filePath)) root <- Subcollection$new("") - - sapply(treeBranches, function(branch) - { - private$addBranch(root, branch) - }) - + sapply(treeBranches, function(branch) self$addBranch(root, branch)) root$setCollection(collection) private$tree <- root }, - getElement = function(relativePath) - { - relativePath <- trimFromStart(relativePath, "./") - relativePath <- trimFromEnd(relativePath, "/") - - if(endsWith(relativePath, "/")) - relativePath <- substr(relativePath, 0, nchar(relativePath) - 1) - - splitPath <- unlist(strsplit(relativePath, "/", fixed = TRUE)) - returnElement <- private$tree - - for(pathFragment in splitPath) - { - returnElement <- returnElement$get(pathFragment) - - if(is.null(returnElement)) - return(NULL) - } - - returnElement - }, - - getTree = function() private$tree - ), - - private = list( - - tree = NULL, - - createBranch = function(splitPath) + createBranch = function(filePath) { + splitPath <- unlist(strsplit(filePath, "/", fixed = TRUE)) branch <- NULL lastElementIndex <- length(splitPath) @@ -90,7 +51,11 @@ CollectionTree <- R6::R6Class( if(is.null(child)) { + # Make sure we are don't make any REST call while adding child + collection <- container$getCollection() + container$setCollection(NULL, setRecursively = FALSE) container$add(node) + container$setCollection(collection, setRecursively = FALSE) } else { @@ -100,14 +65,41 @@ CollectionTree <- R6::R6Class( # If we encounter that same name again we know # it's a folder so we need to replace ArvadosFile with Subcollection. if("ArvadosFile" %in% class(child)) - { child = private$replaceFileWithSubcollection(child) - } - private$addBranch(child, node$getFirst()) + self$addBranch(child, node$getFirst()) } }, + getElement = function(relativePath) + { + relativePath <- trimFromStart(relativePath, "./") + relativePath <- trimFromEnd(relativePath, "/") + + if(endsWith(relativePath, "/")) + relativePath <- substr(relativePath, 0, nchar(relativePath) - 1) + + splitPath <- unlist(strsplit(relativePath, "/", fixed = TRUE)) + returnElement <- private$tree + + for(pathFragment in splitPath) + { + returnElement <- returnElement$get(pathFragment) + + if(is.null(returnElement)) + return(NULL) + } + + returnElement + }, + + getTree = function() private$tree + ), + + private = list( + + tree = NULL, + replaceFileWithSubcollection = function(arvadosFile) { subcollection <- Subcollection$new(arvadosFile$getName()) @@ -121,24 +113,3 @@ CollectionTree <- R6::R6Class( } ) ) - -# deepCopyArvadosComposite = function(composite) -# { - # if("ArvadosFile" %in% class(content)) - # { - # newFile <- ArvadosFile$new(content$name) - # newFile$setCollection(content$getCollection()) - - # return(newFile) - # } - # else if("Subcollection" %in% class(content)) - # { - # root <- Subcollection$new(content$name) - # root$setCollection(content$getCollection()) - # } - # else - # stop("Arvados composite is corrupted. It can contain only ArvadosFile or Subcollection.") - - - -# } diff --git a/sdk/R/R/Subcollection.R b/sdk/R/R/Subcollection.R index 5fd21c192a..17a9ef3ee3 100644 --- a/sdk/R/R/Subcollection.R +++ b/sdk/R/R/Subcollection.R @@ -79,6 +79,9 @@ Subcollection <- R6::R6Class( if("ArvadosFile" %in% class(content) || "Subcollection" %in% class(content)) { + if(!is.null(content$getCollection())) + stop("Content already belongs to a collection.") + if(content$getName() == "") stop("Content has invalid name.") @@ -298,18 +301,23 @@ Subcollection <- R6::R6Class( attachToNewParent = function(content, newParent) { - #Note: We temporary set parents collection to NULL. This will ensure that - # add method doesn't post this file on REST. + # We temporary set parents collection to NULL. This will ensure that + # add method doesn't post this subcollection to REST. + # We also need to set content's collection to NULL because + # add method throws exception if we try to add content that already + # belongs to a collection. parentsCollection <- newParent$getCollection() + content$setCollection(NULL, setRecursively = FALSE) newParent$setCollection(NULL, setRecursively = FALSE) newParent$add(content) + content$setCollection(parentsCollection, setRecursively = FALSE) newParent$setCollection(parentsCollection, setRecursively = FALSE) }, dettachFromCurrentParent = function() { - #Note: We temporary set parents collection to NULL. This will ensure that - # remove method doesn't remove this subcollection from REST. + # We temporary set parents collection to NULL. This will ensure that + # remove method doesn't remove this subcollection from REST. parent <- private$parent parentsCollection <- parent$getCollection() parent$setCollection(NULL, setRecursively = FALSE) diff --git a/sdk/R/R/zzz.R b/sdk/R/R/zzz.R index c98f803e5e..fa0cda45bf 100644 --- a/sdk/R/R/zzz.R +++ b/sdk/R/R/zzz.R @@ -1,3 +1,7 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + .onLoad <- function(libName, pkgName) { minAllowedRVersion <- "3.3.0" diff --git a/sdk/R/README.Rmd b/sdk/R/README.Rmd index 001a3efc13..7ea226fd09 100644 --- a/sdk/R/README.Rmd +++ b/sdk/R/README.Rmd @@ -186,31 +186,16 @@ size <- arvadosSubcollection$getSizeInBytes() * Create new file in a collection: ```{r} -collection$create(fileNames, optionalRelativePath) +collection$create(files) ``` Example: ```{r} -mainFile <- collection$create("main.cpp", "cpp/src/") -fileList <- collection$create(c("main.cpp", lib.dll), "cpp/src/") +mainFile <- collection$create("cpp/src/main.cpp") +fileList <- collection$create(c("cpp/src/main.cpp", "cpp/src/util.h")) ``` -* Add existing ArvadosFile or Subcollection to a collection: - -```{r} -folder <- Subcollection$new("src") -file <- ArvadosFile$new("main.cpp") -folder$add(file) -``` - -```{r} -collection$add(folder, "cpp") -``` - -This examples will add file "main.cpp" in "./cpp/src/" folder if folder exists. -If subcollection contains more files or folders they will be added recursively. - * Delete file from a collection: ```{r} diff --git a/sdk/R/man/Collection.Rd b/sdk/R/man/Collection.Rd index 8cf29a2ea5..fbe6038664 100644 --- a/sdk/R/man/Collection.Rd +++ b/sdk/R/man/Collection.Rd @@ -23,9 +23,10 @@ Collection class provides interface for working with Arvados collections. \describe{ \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.} - \item{create(fileNames, relativePath = "")}{Creates one or more ArvadosFiles and adds them to the collection at specified path.} + \item{create(files)}{Creates one or more ArvadosFiles and adds them to the collection at specified path.} \item{remove(fileNames)}{Remove one or more files from the collection.} - \item{move(content, newLocation)}{Moves ArvadosFile or Subcollection to another location in the collection.} + \item{move(content, destination)}{Moves ArvadosFile or Subcollection to another location in the collection.} + \item{copy(content, destination)}{Copies ArvadosFile or Subcollection to another location in the collection.} \item{getFileListing()}{Returns collections file content as character vector.} \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.} } @@ -36,9 +37,6 @@ Collection class provides interface for working with Arvados collections. arv <- Arvados$new("your Arvados token", "example.arvadosapi.com") collection <- Collection$new(arv, "uuid") -newFile <- ArvadosFile$new("myFile") -collection$add(newFile, "myFolder") - createdFiles <- collection$create(c("main.cpp", lib.dll), "cpp/src/") collection$remove("location/to/my/file.cpp") diff --git a/sdk/R/man/api_client_authorizations.create_system_auth.Rd b/sdk/R/man/api_client_authorizations.create_system_auth.Rd index 5bef96f9c5..3eb172aabf 100644 --- a/sdk/R/man/api_client_authorizations.create_system_auth.Rd +++ b/sdk/R/man/api_client_authorizations.create_system_auth.Rd @@ -7,6 +7,11 @@ arv$api_client_authorizations.create_system_auth(api_client_id = NULL, scopes = NULL) } +\arguments{ +\item{api_client_id}{} + +\item{scopes}{} +} \value{ ApiClientAuthorization object. } diff --git a/sdk/R/man/api_client_authorizations.list.Rd b/sdk/R/man/api_client_authorizations.list.Rd index 983bf4478d..7c8ae69cd5 100644 --- a/sdk/R/man/api_client_authorizations.list.Rd +++ b/sdk/R/man/api_client_authorizations.list.Rd @@ -9,6 +9,23 @@ arv$api_client_authorizations.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ ApiClientAuthorizationList object. } diff --git a/sdk/R/man/api_clients.list.Rd b/sdk/R/man/api_clients.list.Rd index 21523096d0..0679c9c12e 100644 --- a/sdk/R/man/api_clients.list.Rd +++ b/sdk/R/man/api_clients.list.Rd @@ -9,6 +9,23 @@ arv$api_clients.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ ApiClientList object. } diff --git a/sdk/R/man/authorized_keys.list.Rd b/sdk/R/man/authorized_keys.list.Rd index c477b54a92..cd19bc60c0 100644 --- a/sdk/R/man/authorized_keys.list.Rd +++ b/sdk/R/man/authorized_keys.list.Rd @@ -9,6 +9,23 @@ arv$authorized_keys.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ AuthorizedKeyList object. } diff --git a/sdk/R/man/collections.list.Rd b/sdk/R/man/collections.list.Rd index cc5badebe4..87f6f78e33 100644 --- a/sdk/R/man/collections.list.Rd +++ b/sdk/R/man/collections.list.Rd @@ -10,6 +10,22 @@ arv$collections.list(filters = NULL, count = "exact", include_trash = NULL) } \arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} + \item{include_trash}{Include collections whose is_trashed attribute is true.} } \value{ diff --git a/sdk/R/man/collections.provenance.Rd b/sdk/R/man/collections.provenance.Rd index 72b164e50e..001a7b47c7 100644 --- a/sdk/R/man/collections.provenance.Rd +++ b/sdk/R/man/collections.provenance.Rd @@ -6,6 +6,9 @@ \usage{ arv$collections.provenance(uuid) } +\arguments{ +\item{uuid}{} +} \value{ Collection object. } diff --git a/sdk/R/man/collections.trash.Rd b/sdk/R/man/collections.trash.Rd index f01c191db0..4862109b9f 100644 --- a/sdk/R/man/collections.trash.Rd +++ b/sdk/R/man/collections.trash.Rd @@ -6,6 +6,9 @@ \usage{ arv$collections.trash(uuid) } +\arguments{ +\item{uuid}{} +} \value{ Collection object. } diff --git a/sdk/R/man/collections.untrash.Rd b/sdk/R/man/collections.untrash.Rd index 6e63fd4f37..c41bc3d904 100644 --- a/sdk/R/man/collections.untrash.Rd +++ b/sdk/R/man/collections.untrash.Rd @@ -6,6 +6,9 @@ \usage{ arv$collections.untrash(uuid) } +\arguments{ +\item{uuid}{} +} \value{ Collection object. } diff --git a/sdk/R/man/collections.used_by.Rd b/sdk/R/man/collections.used_by.Rd index 0ea0dc3240..53b8e493f7 100644 --- a/sdk/R/man/collections.used_by.Rd +++ b/sdk/R/man/collections.used_by.Rd @@ -6,6 +6,9 @@ \usage{ arv$collections.used_by(uuid) } +\arguments{ +\item{uuid}{} +} \value{ Collection object. } diff --git a/sdk/R/man/container_requests.list.Rd b/sdk/R/man/container_requests.list.Rd index b0ce4de0d9..9c2412beed 100644 --- a/sdk/R/man/container_requests.list.Rd +++ b/sdk/R/man/container_requests.list.Rd @@ -9,6 +9,23 @@ arv$container_requests.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ ContainerRequestList object. } diff --git a/sdk/R/man/containers.auth.Rd b/sdk/R/man/containers.auth.Rd index 2aa51cacce..a594d2f196 100644 --- a/sdk/R/man/containers.auth.Rd +++ b/sdk/R/man/containers.auth.Rd @@ -6,6 +6,9 @@ \usage{ arv$containers.auth(uuid) } +\arguments{ +\item{uuid}{} +} \value{ Container object. } diff --git a/sdk/R/man/containers.list.Rd b/sdk/R/man/containers.list.Rd index 7b3d2fccc5..d445796135 100644 --- a/sdk/R/man/containers.list.Rd +++ b/sdk/R/man/containers.list.Rd @@ -9,6 +9,23 @@ arv$containers.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ ContainerList object. } diff --git a/sdk/R/man/containers.lock.Rd b/sdk/R/man/containers.lock.Rd index b8d7c08650..72bcdf0f81 100644 --- a/sdk/R/man/containers.lock.Rd +++ b/sdk/R/man/containers.lock.Rd @@ -6,6 +6,9 @@ \usage{ arv$containers.lock(uuid) } +\arguments{ +\item{uuid}{} +} \value{ Container object. } diff --git a/sdk/R/man/containers.secret_mounts.Rd b/sdk/R/man/containers.secret_mounts.Rd index 2cccba3aaa..d0f8444fa4 100644 --- a/sdk/R/man/containers.secret_mounts.Rd +++ b/sdk/R/man/containers.secret_mounts.Rd @@ -6,6 +6,9 @@ \usage{ arv$containers.secret_mounts(uuid) } +\arguments{ +\item{uuid}{} +} \value{ Container object. } diff --git a/sdk/R/man/containers.unlock.Rd b/sdk/R/man/containers.unlock.Rd index 2bba7ee5a9..5c41f2059a 100644 --- a/sdk/R/man/containers.unlock.Rd +++ b/sdk/R/man/containers.unlock.Rd @@ -6,6 +6,9 @@ \usage{ arv$containers.unlock(uuid) } +\arguments{ +\item{uuid}{} +} \value{ Container object. } diff --git a/sdk/R/man/groups.contents.Rd b/sdk/R/man/groups.contents.Rd index 1273f445d5..26647df4f7 100644 --- a/sdk/R/man/groups.contents.Rd +++ b/sdk/R/man/groups.contents.Rd @@ -10,8 +10,24 @@ arv$groups.contents(filters = NULL, include_trash = NULL, uuid = NULL, recursive = NULL) } \arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} + \item{include_trash}{Include items whose is_trashed attribute is true.} +\item{uuid}{} + \item{recursive}{Include contents from child groups recursively.} } \value{ diff --git a/sdk/R/man/groups.list.Rd b/sdk/R/man/groups.list.Rd index c76a27ad9e..7699f3ef4b 100644 --- a/sdk/R/man/groups.list.Rd +++ b/sdk/R/man/groups.list.Rd @@ -10,6 +10,22 @@ arv$groups.list(filters = NULL, count = "exact", include_trash = NULL) } \arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} + \item{include_trash}{Include items whose is_trashed attribute is true.} } \value{ diff --git a/sdk/R/man/groups.trash.Rd b/sdk/R/man/groups.trash.Rd index ecd2b10c86..c529618f71 100644 --- a/sdk/R/man/groups.trash.Rd +++ b/sdk/R/man/groups.trash.Rd @@ -6,6 +6,9 @@ \usage{ arv$groups.trash(uuid) } +\arguments{ +\item{uuid}{} +} \value{ Group object. } diff --git a/sdk/R/man/groups.untrash.Rd b/sdk/R/man/groups.untrash.Rd index ef1f19a106..014190c8fe 100644 --- a/sdk/R/man/groups.untrash.Rd +++ b/sdk/R/man/groups.untrash.Rd @@ -6,6 +6,9 @@ \usage{ arv$groups.untrash(uuid) } +\arguments{ +\item{uuid}{} +} \value{ Group object. } diff --git a/sdk/R/man/humans.list.Rd b/sdk/R/man/humans.list.Rd index c9fad5fd32..a8db4c7f69 100644 --- a/sdk/R/man/humans.list.Rd +++ b/sdk/R/man/humans.list.Rd @@ -9,6 +9,23 @@ arv$humans.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ HumanList object. } diff --git a/sdk/R/man/job_tasks.list.Rd b/sdk/R/man/job_tasks.list.Rd index 2184d9655e..51c4b4942c 100644 --- a/sdk/R/man/job_tasks.list.Rd +++ b/sdk/R/man/job_tasks.list.Rd @@ -9,6 +9,23 @@ arv$job_tasks.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ JobTaskList object. } diff --git a/sdk/R/man/jobs.cancel.Rd b/sdk/R/man/jobs.cancel.Rd index 16cda4aa6a..7399d28a8d 100644 --- a/sdk/R/man/jobs.cancel.Rd +++ b/sdk/R/man/jobs.cancel.Rd @@ -6,6 +6,9 @@ \usage{ arv$jobs.cancel(uuid) } +\arguments{ +\item{uuid}{} +} \value{ Job object. } diff --git a/sdk/R/man/jobs.create.Rd b/sdk/R/man/jobs.create.Rd index d8e52d4f94..4c4d61ae76 100644 --- a/sdk/R/man/jobs.create.Rd +++ b/sdk/R/man/jobs.create.Rd @@ -12,6 +12,14 @@ arv$jobs.create(job, ensure_unique_name = "false", \item{job}{Job object.} \item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.} + +\item{find_or_create}{} + +\item{filters}{} + +\item{minimum_script_version}{} + +\item{exclude_script_versions}{} } \value{ Job object. diff --git a/sdk/R/man/jobs.list.Rd b/sdk/R/man/jobs.list.Rd index 33840b0a49..53055f5878 100644 --- a/sdk/R/man/jobs.list.Rd +++ b/sdk/R/man/jobs.list.Rd @@ -8,6 +8,23 @@ arv$jobs.list(filters = NULL, where = NULL, order = NULL, select = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ JobList object. } diff --git a/sdk/R/man/jobs.lock.Rd b/sdk/R/man/jobs.lock.Rd index 51500fc44d..3c2e232809 100644 --- a/sdk/R/man/jobs.lock.Rd +++ b/sdk/R/man/jobs.lock.Rd @@ -6,6 +6,9 @@ \usage{ arv$jobs.lock(uuid) } +\arguments{ +\item{uuid}{} +} \value{ Job object. } diff --git a/sdk/R/man/jobs.queue.Rd b/sdk/R/man/jobs.queue.Rd index e92d01063f..a9deaa971c 100644 --- a/sdk/R/man/jobs.queue.Rd +++ b/sdk/R/man/jobs.queue.Rd @@ -9,6 +9,23 @@ arv$jobs.queue(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ Job object. } diff --git a/sdk/R/man/keep_disks.list.Rd b/sdk/R/man/keep_disks.list.Rd index 79d7b0a636..fdb599f70f 100644 --- a/sdk/R/man/keep_disks.list.Rd +++ b/sdk/R/man/keep_disks.list.Rd @@ -9,6 +9,23 @@ arv$keep_disks.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ KeepDiskList object. } diff --git a/sdk/R/man/keep_disks.ping.Rd b/sdk/R/man/keep_disks.ping.Rd index 2952c31e12..6ae55955f6 100644 --- a/sdk/R/man/keep_disks.ping.Rd +++ b/sdk/R/man/keep_disks.ping.Rd @@ -8,6 +8,21 @@ arv$keep_disks.ping(uuid = NULL, ping_secret, node_uuid = NULL, filesystem_uuid = NULL, service_host = NULL, service_port, service_ssl_flag) } +\arguments{ +\item{uuid}{} + +\item{ping_secret}{} + +\item{node_uuid}{} + +\item{filesystem_uuid}{} + +\item{service_host}{} + +\item{service_port}{} + +\item{service_ssl_flag}{} +} \value{ KeepDisk object. } diff --git a/sdk/R/man/keep_services.list.Rd b/sdk/R/man/keep_services.list.Rd index 73f5fb854a..22aa3aa107 100644 --- a/sdk/R/man/keep_services.list.Rd +++ b/sdk/R/man/keep_services.list.Rd @@ -9,6 +9,23 @@ arv$keep_services.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ KeepServiceList object. } diff --git a/sdk/R/man/links.get_permissions.Rd b/sdk/R/man/links.get_permissions.Rd index 457c38e149..982dbb9691 100644 --- a/sdk/R/man/links.get_permissions.Rd +++ b/sdk/R/man/links.get_permissions.Rd @@ -6,6 +6,9 @@ \usage{ arv$links.get_permissions(uuid) } +\arguments{ +\item{uuid}{} +} \value{ Link object. } diff --git a/sdk/R/man/links.list.Rd b/sdk/R/man/links.list.Rd index a3fc988a38..540fdc1683 100644 --- a/sdk/R/man/links.list.Rd +++ b/sdk/R/man/links.list.Rd @@ -9,6 +9,23 @@ arv$links.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ LinkList object. } diff --git a/sdk/R/man/logs.list.Rd b/sdk/R/man/logs.list.Rd index 88c8bbdc7c..58dbdb71ea 100644 --- a/sdk/R/man/logs.list.Rd +++ b/sdk/R/man/logs.list.Rd @@ -8,6 +8,23 @@ arv$logs.list(filters = NULL, where = NULL, order = NULL, select = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ LogList object. } diff --git a/sdk/R/man/nodes.list.Rd b/sdk/R/man/nodes.list.Rd index 6074a38a65..7ccfad6d93 100644 --- a/sdk/R/man/nodes.list.Rd +++ b/sdk/R/man/nodes.list.Rd @@ -9,6 +9,23 @@ arv$nodes.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ NodeList object. } diff --git a/sdk/R/man/nodes.ping.Rd b/sdk/R/man/nodes.ping.Rd index b8775a2e0d..e77d2b5b89 100644 --- a/sdk/R/man/nodes.ping.Rd +++ b/sdk/R/man/nodes.ping.Rd @@ -6,6 +6,11 @@ \usage{ arv$nodes.ping(uuid, ping_secret) } +\arguments{ +\item{uuid}{} + +\item{ping_secret}{} +} \value{ Node object. } diff --git a/sdk/R/man/pipeline_instances.cancel.Rd b/sdk/R/man/pipeline_instances.cancel.Rd index 6de3134054..026de816fb 100644 --- a/sdk/R/man/pipeline_instances.cancel.Rd +++ b/sdk/R/man/pipeline_instances.cancel.Rd @@ -6,6 +6,9 @@ \usage{ arv$pipeline_instances.cancel(uuid) } +\arguments{ +\item{uuid}{} +} \value{ PipelineInstance object. } diff --git a/sdk/R/man/pipeline_instances.list.Rd b/sdk/R/man/pipeline_instances.list.Rd index 74b5db2bb9..407f94446d 100644 --- a/sdk/R/man/pipeline_instances.list.Rd +++ b/sdk/R/man/pipeline_instances.list.Rd @@ -9,6 +9,23 @@ arv$pipeline_instances.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ PipelineInstanceList object. } diff --git a/sdk/R/man/pipeline_templates.list.Rd b/sdk/R/man/pipeline_templates.list.Rd index 846008e4d1..c6c7413d5e 100644 --- a/sdk/R/man/pipeline_templates.list.Rd +++ b/sdk/R/man/pipeline_templates.list.Rd @@ -9,6 +9,23 @@ arv$pipeline_templates.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ PipelineTemplateList object. } diff --git a/sdk/R/man/projects.list.Rd b/sdk/R/man/projects.list.Rd index 22b5175ceb..ff4c1c9edb 100644 --- a/sdk/R/man/projects.list.Rd +++ b/sdk/R/man/projects.list.Rd @@ -10,8 +10,24 @@ arv$projects.list(filters = NULL, include_trash = NULL, uuid = NULL, recursive = NULL) } \arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} + \item{include_trash}{Include items whose is_trashed attribute is true.} +\item{uuid}{} + \item{recursive}{Include contents from child groups recursively.} } \value{ diff --git a/sdk/R/man/repositories.list.Rd b/sdk/R/man/repositories.list.Rd index e19c87c6ca..d1f4772e74 100644 --- a/sdk/R/man/repositories.list.Rd +++ b/sdk/R/man/repositories.list.Rd @@ -9,6 +9,23 @@ arv$repositories.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ RepositoryList object. } diff --git a/sdk/R/man/specimens.list.Rd b/sdk/R/man/specimens.list.Rd index c05ce5f26c..4e07f4ab28 100644 --- a/sdk/R/man/specimens.list.Rd +++ b/sdk/R/man/specimens.list.Rd @@ -9,6 +9,23 @@ arv$specimens.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ SpecimenList object. } diff --git a/sdk/R/man/traits.list.Rd b/sdk/R/man/traits.list.Rd index 77a13cae38..e91b929949 100644 --- a/sdk/R/man/traits.list.Rd +++ b/sdk/R/man/traits.list.Rd @@ -9,6 +9,23 @@ arv$traits.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ TraitList object. } diff --git a/sdk/R/man/user_agreements.list.Rd b/sdk/R/man/user_agreements.list.Rd index c9914d5f16..5e6986189d 100644 --- a/sdk/R/man/user_agreements.list.Rd +++ b/sdk/R/man/user_agreements.list.Rd @@ -9,6 +9,23 @@ arv$user_agreements.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ UserAgreementList object. } diff --git a/sdk/R/man/users.activate.Rd b/sdk/R/man/users.activate.Rd index bba8162322..201caf4c89 100644 --- a/sdk/R/man/users.activate.Rd +++ b/sdk/R/man/users.activate.Rd @@ -6,6 +6,9 @@ \usage{ arv$users.activate(uuid) } +\arguments{ +\item{uuid}{} +} \value{ User object. } diff --git a/sdk/R/man/users.list.Rd b/sdk/R/man/users.list.Rd index 98fa2141a3..71319433b8 100644 --- a/sdk/R/man/users.list.Rd +++ b/sdk/R/man/users.list.Rd @@ -9,6 +9,23 @@ arv$users.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ UserList object. } diff --git a/sdk/R/man/users.merge.Rd b/sdk/R/man/users.merge.Rd index ee97244f30..a539591a6a 100644 --- a/sdk/R/man/users.merge.Rd +++ b/sdk/R/man/users.merge.Rd @@ -7,6 +7,13 @@ arv$users.merge(new_owner_uuid, new_user_token, redirect_to_new_user = NULL) } +\arguments{ +\item{new_owner_uuid}{} + +\item{new_user_token}{} + +\item{redirect_to_new_user}{} +} \value{ User object. } diff --git a/sdk/R/man/users.setup.Rd b/sdk/R/man/users.setup.Rd index 764bc52596..869403d3ed 100644 --- a/sdk/R/man/users.setup.Rd +++ b/sdk/R/man/users.setup.Rd @@ -7,6 +7,17 @@ arv$users.setup(user = NULL, openid_prefix = NULL, repo_name = NULL, vm_uuid = NULL, send_notification_email = "false") } +\arguments{ +\item{user}{} + +\item{openid_prefix}{} + +\item{repo_name}{} + +\item{vm_uuid}{} + +\item{send_notification_email}{} +} \value{ User object. } diff --git a/sdk/R/man/users.unsetup.Rd b/sdk/R/man/users.unsetup.Rd index 0753a34d23..85de6f9782 100644 --- a/sdk/R/man/users.unsetup.Rd +++ b/sdk/R/man/users.unsetup.Rd @@ -6,6 +6,9 @@ \usage{ arv$users.unsetup(uuid) } +\arguments{ +\item{uuid}{} +} \value{ User object. } diff --git a/sdk/R/man/users.update_uuid.Rd b/sdk/R/man/users.update_uuid.Rd index 591599dfe8..af62c2c825 100644 --- a/sdk/R/man/users.update_uuid.Rd +++ b/sdk/R/man/users.update_uuid.Rd @@ -6,6 +6,11 @@ \usage{ arv$users.update_uuid(uuid, new_uuid) } +\arguments{ +\item{uuid}{} + +\item{new_uuid}{} +} \value{ User object. } diff --git a/sdk/R/man/virtual_machines.list.Rd b/sdk/R/man/virtual_machines.list.Rd index 0f3b440b82..42ed58b0e1 100644 --- a/sdk/R/man/virtual_machines.list.Rd +++ b/sdk/R/man/virtual_machines.list.Rd @@ -9,6 +9,23 @@ arv$virtual_machines.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ VirtualMachineList object. } diff --git a/sdk/R/man/virtual_machines.logins.Rd b/sdk/R/man/virtual_machines.logins.Rd index bb6d21ed91..7e25110aa4 100644 --- a/sdk/R/man/virtual_machines.logins.Rd +++ b/sdk/R/man/virtual_machines.logins.Rd @@ -6,6 +6,9 @@ \usage{ arv$virtual_machines.logins(uuid) } +\arguments{ +\item{uuid}{} +} \value{ VirtualMachine object. } diff --git a/sdk/R/man/workflows.list.Rd b/sdk/R/man/workflows.list.Rd index b8a6a03ec7..e24b74d030 100644 --- a/sdk/R/man/workflows.list.Rd +++ b/sdk/R/man/workflows.list.Rd @@ -9,6 +9,23 @@ arv$workflows.list(filters = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") } +\arguments{ +\item{filters}{} + +\item{where}{} + +\item{order}{} + +\item{select}{} + +\item{distinct}{} + +\item{limit}{} + +\item{offset}{} + +\item{count}{} +} \value{ WorkflowList object. } diff --git a/sdk/R/tests/testthat/test-Collection.R b/sdk/R/tests/testthat/test-Collection.R index 76668c2eb0..636359ae21 100644 --- a/sdk/R/tests/testthat/test-Collection.R +++ b/sdk/R/tests/testthat/test-Collection.R @@ -104,37 +104,15 @@ test_that("create raises exception if passed argumet is not character vector", { fixed = TRUE)) }) -test_that("create raises exception if relative path is not valid", { - - collectionContent <- c("animal", - "animal/fish", - "ball") - - fakeREST <- FakeRESTService$new(collectionContent) - - api <- Arvados$new("myToken", "myHostName") - api$setRESTService(fakeREST) - collection <- Collection$new(api, "myUUID") - - newPen <- ArvadosFile$new("pen") - - expect_that(collection$create(newPen, "objects"), - throws_error("Subcollection objects doesn't exist.", - fixed = TRUE)) -}) - test_that(paste("create adds files specified by fileNames", "to local tree structure and remote REST service"), { - collectionContent <- c("animal", "animal/fish", "ball") - fakeREST <- FakeRESTService$new(collectionContent) - + fakeREST <- FakeRESTService$new() api <- Arvados$new("myToken", "myHostName") api$setRESTService(fakeREST) collection <- Collection$new(api, "myUUID") - files <- c("dog", "cat") - collection$create(files, "animal") + collection$create(c("animal/dog", "animal/cat")) dog <- collection$get("animal/dog") cat <- collection$get("animal/cat") @@ -296,3 +274,24 @@ test_that("copy raises exception if new location is not valid", { throws_error("Content you want to copy doesn't exist in the collection.", fixed = TRUE)) }) + +test_that("refresh invalidates current tree structure", { + + collectionContent <- c("animal", "animal/fish", "ball") + fakeREST <- FakeRESTService$new(collectionContent) + + api <- Arvados$new("myToken", "myHostName") + api$setRESTService(fakeREST) + collection <- Collection$new(api, "aaaaa-j7d0g-ccccccccccccccc") + + # Before refresh + fish <- collection$get("animal/fish") + expect_that(fish$getName(), equals("fish")) + expect_that(fish$getCollection()$uuid, equals("aaaaa-j7d0g-ccccccccccccccc")) + + collection$refresh() + + # After refresh + expect_that(fish$getName(), equals("fish")) + expect_true(is.null(fish$getCollection())) +}) -- 2.30.2