X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/2b11ab27a8508a49bb5e2c87babbbae9e95f4e3d..6eeb2b1a7b30e356514f1f842c5d7ecafd126732:/sdk/R/R/Arvados.R diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R index 7c077c03a1..368ca52237 100644 --- a/sdk/R/R/Arvados.R +++ b/sdk/R/R/Arvados.R @@ -1,3 +1,1796 @@ +#' users.get is a method defined in Arvados class. +#' +#' @usage arv$users.get(uuid) +#' @param uuid The UUID of the User in question. +#' @return User object. +#' @name users.get +NULL + +#' users.create is a method defined in Arvados class. +#' +#' @usage arv$users.create(user, ensure_unique_name = "false") +#' @param user User object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return User object. +#' @name users.create +NULL + +#' users.update is a method defined in Arvados class. +#' +#' @usage arv$users.update(user, uuid) +#' @param user User object. +#' @param uuid The UUID of the User in question. +#' @return User object. +#' @name users.update +NULL + +#' users.delete is a method defined in Arvados class. +#' +#' @usage arv$users.delete(uuid) +#' @param uuid The UUID of the User in question. +#' @return User object. +#' @name users.delete +NULL + +#' users.current is a method defined in Arvados class. +#' +#' @usage arv$users.current(NULL) +#' @return User object. +#' @name users.current +NULL + +#' users.system is a method defined in Arvados class. +#' +#' @usage arv$users.system(NULL) +#' @return User object. +#' @name users.system +NULL + +#' users.activate is a method defined in Arvados class. +#' +#' @usage arv$users.activate(uuid) +#' @param uuid +#' @return User object. +#' @name users.activate +NULL + +#' users.setup is a method defined in Arvados class. +#' +#' @usage arv$users.setup(user = NULL, openid_prefix = NULL, +#' repo_name = NULL, vm_uuid = NULL, send_notification_email = "false") +#' @param user +#' @param openid_prefix +#' @param repo_name +#' @param vm_uuid +#' @param send_notification_email +#' @return User object. +#' @name users.setup +NULL + +#' users.unsetup is a method defined in Arvados class. +#' +#' @usage arv$users.unsetup(uuid) +#' @param uuid +#' @return User object. +#' @name users.unsetup +NULL + +#' users.update_uuid is a method defined in Arvados class. +#' +#' @usage arv$users.update_uuid(uuid, new_uuid) +#' @param uuid +#' @param new_uuid +#' @return User object. +#' @name users.update_uuid +NULL + +#' users.list is a method defined in Arvados class. +#' +#' @usage arv$users.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return UserList object. +#' @name users.list +NULL + +#' api_client_authorizations.get is a method defined in Arvados class. +#' +#' @usage arv$api_client_authorizations.get(uuid) +#' @param uuid The UUID of the ApiClientAuthorization in question. +#' @return ApiClientAuthorization object. +#' @name api_client_authorizations.get +NULL + +#' api_client_authorizations.create is a method defined in Arvados class. +#' +#' @usage arv$api_client_authorizations.create(apiclientauthorization, +#' ensure_unique_name = "false") +#' @param apiClientAuthorization ApiClientAuthorization object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return ApiClientAuthorization object. +#' @name api_client_authorizations.create +NULL + +#' api_client_authorizations.update is a method defined in Arvados class. +#' +#' @usage arv$api_client_authorizations.update(apiclientauthorization, +#' uuid) +#' @param apiClientAuthorization ApiClientAuthorization object. +#' @param uuid The UUID of the ApiClientAuthorization in question. +#' @return ApiClientAuthorization object. +#' @name api_client_authorizations.update +NULL + +#' api_client_authorizations.delete is a method defined in Arvados class. +#' +#' @usage arv$api_client_authorizations.delete(uuid) +#' @param uuid The UUID of the ApiClientAuthorization in question. +#' @return ApiClientAuthorization object. +#' @name api_client_authorizations.delete +NULL + +#' api_client_authorizations.create_system_auth is a method defined in Arvados class. +#' +#' @usage arv$api_client_authorizations.create_system_auth(api_client_id = NULL, +#' scopes = NULL) +#' @param api_client_id +#' @param scopes +#' @return ApiClientAuthorization object. +#' @name api_client_authorizations.create_system_auth +NULL + +#' api_client_authorizations.current is a method defined in Arvados class. +#' +#' @usage arv$api_client_authorizations.current(NULL) +#' @return ApiClientAuthorization object. +#' @name api_client_authorizations.current +NULL + +#' api_client_authorizations.list is a method defined in Arvados class. +#' +#' @usage arv$api_client_authorizations.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return ApiClientAuthorizationList object. +#' @name api_client_authorizations.list +NULL + +#' containers.get is a method defined in Arvados class. +#' +#' @usage arv$containers.get(uuid) +#' @param uuid The UUID of the Container in question. +#' @return Container object. +#' @name containers.get +NULL + +#' containers.create is a method defined in Arvados class. +#' +#' @usage arv$containers.create(container, +#' ensure_unique_name = "false") +#' @param container Container object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Container object. +#' @name containers.create +NULL + +#' containers.update is a method defined in Arvados class. +#' +#' @usage arv$containers.update(container, +#' uuid) +#' @param container Container object. +#' @param uuid The UUID of the Container in question. +#' @return Container object. +#' @name containers.update +NULL + +#' containers.delete is a method defined in Arvados class. +#' +#' @usage arv$containers.delete(uuid) +#' @param uuid The UUID of the Container in question. +#' @return Container object. +#' @name containers.delete +NULL + +#' containers.auth is a method defined in Arvados class. +#' +#' @usage arv$containers.auth(uuid) +#' @param uuid +#' @return Container object. +#' @name containers.auth +NULL + +#' containers.lock is a method defined in Arvados class. +#' +#' @usage arv$containers.lock(uuid) +#' @param uuid +#' @return Container object. +#' @name containers.lock +NULL + +#' containers.unlock is a method defined in Arvados class. +#' +#' @usage arv$containers.unlock(uuid) +#' @param uuid +#' @return Container object. +#' @name containers.unlock +NULL + +#' containers.secret_mounts is a method defined in Arvados class. +#' +#' @usage arv$containers.secret_mounts(uuid) +#' @param uuid +#' @return Container object. +#' @name containers.secret_mounts +NULL + +#' containers.current is a method defined in Arvados class. +#' +#' @usage arv$containers.current(NULL) +#' @return Container object. +#' @name containers.current +NULL + +#' containers.list is a method defined in Arvados class. +#' +#' @usage arv$containers.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return ContainerList object. +#' @name containers.list +NULL + +#' api_clients.get is a method defined in Arvados class. +#' +#' @usage arv$api_clients.get(uuid) +#' @param uuid The UUID of the ApiClient in question. +#' @return ApiClient object. +#' @name api_clients.get +NULL + +#' api_clients.create is a method defined in Arvados class. +#' +#' @usage arv$api_clients.create(apiclient, +#' ensure_unique_name = "false") +#' @param apiClient ApiClient object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return ApiClient object. +#' @name api_clients.create +NULL + +#' api_clients.update is a method defined in Arvados class. +#' +#' @usage arv$api_clients.update(apiclient, +#' uuid) +#' @param apiClient ApiClient object. +#' @param uuid The UUID of the ApiClient in question. +#' @return ApiClient object. +#' @name api_clients.update +NULL + +#' api_clients.delete is a method defined in Arvados class. +#' +#' @usage arv$api_clients.delete(uuid) +#' @param uuid The UUID of the ApiClient in question. +#' @return ApiClient object. +#' @name api_clients.delete +NULL + +#' api_clients.list is a method defined in Arvados class. +#' +#' @usage arv$api_clients.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return ApiClientList object. +#' @name api_clients.list +NULL + +#' authorized_keys.get is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.get(uuid) +#' @param uuid The UUID of the AuthorizedKey in question. +#' @return AuthorizedKey object. +#' @name authorized_keys.get +NULL + +#' authorized_keys.create is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.create(authorizedkey, +#' ensure_unique_name = "false") +#' @param authorizedKey AuthorizedKey object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return AuthorizedKey object. +#' @name authorized_keys.create +NULL + +#' authorized_keys.update is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.update(authorizedkey, +#' uuid) +#' @param authorizedKey AuthorizedKey object. +#' @param uuid The UUID of the AuthorizedKey in question. +#' @return AuthorizedKey object. +#' @name authorized_keys.update +NULL + +#' authorized_keys.delete is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.delete(uuid) +#' @param uuid The UUID of the AuthorizedKey in question. +#' @return AuthorizedKey object. +#' @name authorized_keys.delete +NULL + +#' authorized_keys.list is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return AuthorizedKeyList object. +#' @name authorized_keys.list +NULL + +#' container_requests.get is a method defined in Arvados class. +#' +#' @usage arv$container_requests.get(uuid) +#' @param uuid The UUID of the ContainerRequest in question. +#' @return ContainerRequest object. +#' @name container_requests.get +NULL + +#' container_requests.create is a method defined in Arvados class. +#' +#' @usage arv$container_requests.create(containerrequest, +#' ensure_unique_name = "false") +#' @param containerRequest ContainerRequest object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return ContainerRequest object. +#' @name container_requests.create +NULL + +#' container_requests.update is a method defined in Arvados class. +#' +#' @usage arv$container_requests.update(containerrequest, +#' uuid) +#' @param containerRequest ContainerRequest object. +#' @param uuid The UUID of the ContainerRequest in question. +#' @return ContainerRequest object. +#' @name container_requests.update +NULL + +#' container_requests.delete is a method defined in Arvados class. +#' +#' @usage arv$container_requests.delete(uuid) +#' @param uuid The UUID of the ContainerRequest in question. +#' @return ContainerRequest object. +#' @name container_requests.delete +NULL + +#' container_requests.list is a method defined in Arvados class. +#' +#' @usage arv$container_requests.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return ContainerRequestList object. +#' @name container_requests.list +NULL + +#' collections.get is a method defined in Arvados class. +#' +#' @usage arv$collections.get(uuid) +#' @param uuid The UUID of the Collection in question. +#' @return Collection object. +#' @name collections.get +NULL + +#' collections.create is a method defined in Arvados class. +#' +#' @usage arv$collections.create(collection, +#' ensure_unique_name = "false") +#' @param collection Collection object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Collection object. +#' @name collections.create +NULL + +#' collections.update is a method defined in Arvados class. +#' +#' @usage arv$collections.update(collection, +#' uuid) +#' @param collection Collection object. +#' @param uuid The UUID of the Collection in question. +#' @return Collection object. +#' @name collections.update +NULL + +#' collections.delete is a method defined in Arvados class. +#' +#' @usage arv$collections.delete(uuid) +#' @param uuid The UUID of the Collection in question. +#' @return Collection object. +#' @name collections.delete +NULL + +#' collections.provenance is a method defined in Arvados class. +#' +#' @usage arv$collections.provenance(uuid) +#' @param uuid +#' @return Collection object. +#' @name collections.provenance +NULL + +#' collections.used_by is a method defined in Arvados class. +#' +#' @usage arv$collections.used_by(uuid) +#' @param uuid +#' @return Collection object. +#' @name collections.used_by +NULL + +#' collections.trash is a method defined in Arvados class. +#' +#' @usage arv$collections.trash(uuid) +#' @param uuid +#' @return Collection object. +#' @name collections.trash +NULL + +#' collections.untrash is a method defined in Arvados class. +#' +#' @usage arv$collections.untrash(uuid) +#' @param uuid +#' @return Collection object. +#' @name collections.untrash +NULL + +#' collections.list is a method defined in Arvados class. +#' +#' @usage arv$collections.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact", include_trash = NULL) +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @param include_trash Include collections whose is_trashed attribute is true. +#' @return CollectionList object. +#' @name collections.list +NULL + +#' humans.get is a method defined in Arvados class. +#' +#' @usage arv$humans.get(uuid) +#' @param uuid The UUID of the Human in question. +#' @return Human object. +#' @name humans.get +NULL + +#' humans.create is a method defined in Arvados class. +#' +#' @usage arv$humans.create(human, ensure_unique_name = "false") +#' @param human Human object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Human object. +#' @name humans.create +NULL + +#' humans.update is a method defined in Arvados class. +#' +#' @usage arv$humans.update(human, uuid) +#' @param human Human object. +#' @param uuid The UUID of the Human in question. +#' @return Human object. +#' @name humans.update +NULL + +#' humans.delete is a method defined in Arvados class. +#' +#' @usage arv$humans.delete(uuid) +#' @param uuid The UUID of the Human in question. +#' @return Human object. +#' @name humans.delete +NULL + +#' humans.list is a method defined in Arvados class. +#' +#' @usage arv$humans.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return HumanList object. +#' @name humans.list +NULL + +#' job_tasks.get is a method defined in Arvados class. +#' +#' @usage arv$job_tasks.get(uuid) +#' @param uuid The UUID of the JobTask in question. +#' @return JobTask object. +#' @name job_tasks.get +NULL + +#' job_tasks.create is a method defined in Arvados class. +#' +#' @usage arv$job_tasks.create(jobtask, ensure_unique_name = "false") +#' @param jobTask JobTask object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return JobTask object. +#' @name job_tasks.create +NULL + +#' job_tasks.update is a method defined in Arvados class. +#' +#' @usage arv$job_tasks.update(jobtask, uuid) +#' @param jobTask JobTask object. +#' @param uuid The UUID of the JobTask in question. +#' @return JobTask object. +#' @name job_tasks.update +NULL + +#' job_tasks.delete is a method defined in Arvados class. +#' +#' @usage arv$job_tasks.delete(uuid) +#' @param uuid The UUID of the JobTask in question. +#' @return JobTask object. +#' @name job_tasks.delete +NULL + +#' job_tasks.list is a method defined in Arvados class. +#' +#' @usage arv$job_tasks.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return JobTaskList object. +#' @name job_tasks.list +NULL + +#' links.get is a method defined in Arvados class. +#' +#' @usage arv$links.get(uuid) +#' @param uuid The UUID of the Link in question. +#' @return Link object. +#' @name links.get +NULL + +#' links.create is a method defined in Arvados class. +#' +#' @usage arv$links.create(link, ensure_unique_name = "false") +#' @param link Link object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Link object. +#' @name links.create +NULL + +#' links.update is a method defined in Arvados class. +#' +#' @usage arv$links.update(link, uuid) +#' @param link Link object. +#' @param uuid The UUID of the Link in question. +#' @return Link object. +#' @name links.update +NULL + +#' links.delete is a method defined in Arvados class. +#' +#' @usage arv$links.delete(uuid) +#' @param uuid The UUID of the Link in question. +#' @return Link object. +#' @name links.delete +NULL + +#' links.list is a method defined in Arvados class. +#' +#' @usage arv$links.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return LinkList object. +#' @name links.list +NULL + +#' links.get_permissions is a method defined in Arvados class. +#' +#' @usage arv$links.get_permissions(uuid) +#' @param uuid +#' @return Link object. +#' @name links.get_permissions +NULL + +#' jobs.get is a method defined in Arvados class. +#' +#' @usage arv$jobs.get(uuid) +#' @param uuid The UUID of the Job in question. +#' @return Job object. +#' @name jobs.get +NULL + +#' jobs.create is a method defined in Arvados class. +#' +#' @usage arv$jobs.create(job, ensure_unique_name = "false", +#' find_or_create = "false", filters = NULL, +#' minimum_script_version = NULL, exclude_script_versions = NULL) +#' @param job Job object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @param find_or_create +#' @param filters +#' @param minimum_script_version +#' @param exclude_script_versions +#' @return Job object. +#' @name jobs.create +NULL + +#' jobs.update is a method defined in Arvados class. +#' +#' @usage arv$jobs.update(job, uuid) +#' @param job Job object. +#' @param uuid The UUID of the Job in question. +#' @return Job object. +#' @name jobs.update +NULL + +#' jobs.delete is a method defined in Arvados class. +#' +#' @usage arv$jobs.delete(uuid) +#' @param uuid The UUID of the Job in question. +#' @return Job object. +#' @name jobs.delete +NULL + +#' jobs.queue is a method defined in Arvados class. +#' +#' @usage arv$jobs.queue(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return Job object. +#' @name jobs.queue +NULL + +#' jobs.queue_size is a method defined in Arvados class. +#' +#' @usage arv$jobs.queue_size(NULL) +#' @return Job object. +#' @name jobs.queue_size +NULL + +#' jobs.cancel is a method defined in Arvados class. +#' +#' @usage arv$jobs.cancel(uuid) +#' @param uuid +#' @return Job object. +#' @name jobs.cancel +NULL + +#' jobs.lock is a method defined in Arvados class. +#' +#' @usage arv$jobs.lock(uuid) +#' @param uuid +#' @return Job object. +#' @name jobs.lock +NULL + +#' jobs.list is a method defined in Arvados class. +#' +#' @usage arv$jobs.list(filters = NULL, where = NULL, +#' order = NULL, select = NULL, distinct = NULL, +#' limit = "100", offset = "0", count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return JobList object. +#' @name jobs.list +NULL + +#' keep_disks.get is a method defined in Arvados class. +#' +#' @usage arv$keep_disks.get(uuid) +#' @param uuid The UUID of the KeepDisk in question. +#' @return KeepDisk object. +#' @name keep_disks.get +NULL + +#' keep_disks.create is a method defined in Arvados class. +#' +#' @usage arv$keep_disks.create(keepdisk, +#' ensure_unique_name = "false") +#' @param keepDisk KeepDisk object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return KeepDisk object. +#' @name keep_disks.create +NULL + +#' keep_disks.update is a method defined in Arvados class. +#' +#' @usage arv$keep_disks.update(keepdisk, +#' uuid) +#' @param keepDisk KeepDisk object. +#' @param uuid The UUID of the KeepDisk in question. +#' @return KeepDisk object. +#' @name keep_disks.update +NULL + +#' keep_disks.delete is a method defined in Arvados class. +#' +#' @usage arv$keep_disks.delete(uuid) +#' @param uuid The UUID of the KeepDisk in question. +#' @return KeepDisk object. +#' @name keep_disks.delete +NULL + +#' keep_disks.ping is a method defined in Arvados class. +#' +#' @usage arv$keep_disks.ping(uuid = NULL, +#' ping_secret, node_uuid = NULL, filesystem_uuid = NULL, +#' service_host = NULL, service_port, service_ssl_flag) +#' @param uuid +#' @param ping_secret +#' @param node_uuid +#' @param filesystem_uuid +#' @param service_host +#' @param service_port +#' @param service_ssl_flag +#' @return KeepDisk object. +#' @name keep_disks.ping +NULL + +#' keep_disks.list is a method defined in Arvados class. +#' +#' @usage arv$keep_disks.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return KeepDiskList object. +#' @name keep_disks.list +NULL + +#' keep_services.get is a method defined in Arvados class. +#' +#' @usage arv$keep_services.get(uuid) +#' @param uuid The UUID of the KeepService in question. +#' @return KeepService object. +#' @name keep_services.get +NULL + +#' keep_services.create is a method defined in Arvados class. +#' +#' @usage arv$keep_services.create(keepservice, +#' ensure_unique_name = "false") +#' @param keepService KeepService object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return KeepService object. +#' @name keep_services.create +NULL + +#' keep_services.update is a method defined in Arvados class. +#' +#' @usage arv$keep_services.update(keepservice, +#' uuid) +#' @param keepService KeepService object. +#' @param uuid The UUID of the KeepService in question. +#' @return KeepService object. +#' @name keep_services.update +NULL + +#' keep_services.delete is a method defined in Arvados class. +#' +#' @usage arv$keep_services.delete(uuid) +#' @param uuid The UUID of the KeepService in question. +#' @return KeepService object. +#' @name keep_services.delete +NULL + +#' keep_services.accessible is a method defined in Arvados class. +#' +#' @usage arv$keep_services.accessible(NULL) +#' @return KeepService object. +#' @name keep_services.accessible +NULL + +#' keep_services.list is a method defined in Arvados class. +#' +#' @usage arv$keep_services.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return KeepServiceList object. +#' @name keep_services.list +NULL + +#' pipeline_templates.get is a method defined in Arvados class. +#' +#' @usage arv$pipeline_templates.get(uuid) +#' @param uuid The UUID of the PipelineTemplate in question. +#' @return PipelineTemplate object. +#' @name pipeline_templates.get +NULL + +#' pipeline_templates.create is a method defined in Arvados class. +#' +#' @usage arv$pipeline_templates.create(pipelinetemplate, +#' ensure_unique_name = "false") +#' @param pipelineTemplate PipelineTemplate object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return PipelineTemplate object. +#' @name pipeline_templates.create +NULL + +#' pipeline_templates.update is a method defined in Arvados class. +#' +#' @usage arv$pipeline_templates.update(pipelinetemplate, +#' uuid) +#' @param pipelineTemplate PipelineTemplate object. +#' @param uuid The UUID of the PipelineTemplate in question. +#' @return PipelineTemplate object. +#' @name pipeline_templates.update +NULL + +#' pipeline_templates.delete is a method defined in Arvados class. +#' +#' @usage arv$pipeline_templates.delete(uuid) +#' @param uuid The UUID of the PipelineTemplate in question. +#' @return PipelineTemplate object. +#' @name pipeline_templates.delete +NULL + +#' pipeline_templates.list is a method defined in Arvados class. +#' +#' @usage arv$pipeline_templates.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return PipelineTemplateList object. +#' @name pipeline_templates.list +NULL + +#' pipeline_instances.get is a method defined in Arvados class. +#' +#' @usage arv$pipeline_instances.get(uuid) +#' @param uuid The UUID of the PipelineInstance in question. +#' @return PipelineInstance object. +#' @name pipeline_instances.get +NULL + +#' pipeline_instances.create is a method defined in Arvados class. +#' +#' @usage arv$pipeline_instances.create(pipelineinstance, +#' ensure_unique_name = "false") +#' @param pipelineInstance PipelineInstance object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return PipelineInstance object. +#' @name pipeline_instances.create +NULL + +#' pipeline_instances.update is a method defined in Arvados class. +#' +#' @usage arv$pipeline_instances.update(pipelineinstance, +#' uuid) +#' @param pipelineInstance PipelineInstance object. +#' @param uuid The UUID of the PipelineInstance in question. +#' @return PipelineInstance object. +#' @name pipeline_instances.update +NULL + +#' pipeline_instances.delete is a method defined in Arvados class. +#' +#' @usage arv$pipeline_instances.delete(uuid) +#' @param uuid The UUID of the PipelineInstance in question. +#' @return PipelineInstance object. +#' @name pipeline_instances.delete +NULL + +#' pipeline_instances.cancel is a method defined in Arvados class. +#' +#' @usage arv$pipeline_instances.cancel(uuid) +#' @param uuid +#' @return PipelineInstance object. +#' @name pipeline_instances.cancel +NULL + +#' pipeline_instances.list is a method defined in Arvados class. +#' +#' @usage arv$pipeline_instances.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return PipelineInstanceList object. +#' @name pipeline_instances.list +NULL + +#' nodes.get is a method defined in Arvados class. +#' +#' @usage arv$nodes.get(uuid) +#' @param uuid The UUID of the Node in question. +#' @return Node object. +#' @name nodes.get +NULL + +#' nodes.create is a method defined in Arvados class. +#' +#' @usage arv$nodes.create(node, ensure_unique_name = "false", +#' assign_slot = NULL) +#' @param node Node object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @param assign_slot assign slot and hostname +#' @return Node object. +#' @name nodes.create +NULL + +#' nodes.update is a method defined in Arvados class. +#' +#' @usage arv$nodes.update(node, uuid, assign_slot = NULL) +#' @param node Node object. +#' @param uuid The UUID of the Node in question. +#' @param assign_slot assign slot and hostname +#' @return Node object. +#' @name nodes.update +NULL + +#' nodes.delete is a method defined in Arvados class. +#' +#' @usage arv$nodes.delete(uuid) +#' @param uuid The UUID of the Node in question. +#' @return Node object. +#' @name nodes.delete +NULL + +#' nodes.ping is a method defined in Arvados class. +#' +#' @usage arv$nodes.ping(uuid, ping_secret) +#' @param uuid +#' @param ping_secret +#' @return Node object. +#' @name nodes.ping +NULL + +#' nodes.list is a method defined in Arvados class. +#' +#' @usage arv$nodes.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return NodeList object. +#' @name nodes.list +NULL + +#' repositories.get is a method defined in Arvados class. +#' +#' @usage arv$repositories.get(uuid) +#' @param uuid The UUID of the Repository in question. +#' @return Repository object. +#' @name repositories.get +NULL + +#' repositories.create is a method defined in Arvados class. +#' +#' @usage arv$repositories.create(repository, +#' ensure_unique_name = "false") +#' @param repository Repository object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Repository object. +#' @name repositories.create +NULL + +#' repositories.update is a method defined in Arvados class. +#' +#' @usage arv$repositories.update(repository, +#' uuid) +#' @param repository Repository object. +#' @param uuid The UUID of the Repository in question. +#' @return Repository object. +#' @name repositories.update +NULL + +#' repositories.delete is a method defined in Arvados class. +#' +#' @usage arv$repositories.delete(uuid) +#' @param uuid The UUID of the Repository in question. +#' @return Repository object. +#' @name repositories.delete +NULL + +#' repositories.get_all_permissions is a method defined in Arvados class. +#' +#' @usage arv$repositories.get_all_permissions(NULL) +#' @return Repository object. +#' @name repositories.get_all_permissions +NULL + +#' repositories.list is a method defined in Arvados class. +#' +#' @usage arv$repositories.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return RepositoryList object. +#' @name repositories.list +NULL + +#' specimens.get is a method defined in Arvados class. +#' +#' @usage arv$specimens.get(uuid) +#' @param uuid The UUID of the Specimen in question. +#' @return Specimen object. +#' @name specimens.get +NULL + +#' specimens.create is a method defined in Arvados class. +#' +#' @usage arv$specimens.create(specimen, +#' ensure_unique_name = "false") +#' @param specimen Specimen object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Specimen object. +#' @name specimens.create +NULL + +#' specimens.update is a method defined in Arvados class. +#' +#' @usage arv$specimens.update(specimen, +#' uuid) +#' @param specimen Specimen object. +#' @param uuid The UUID of the Specimen in question. +#' @return Specimen object. +#' @name specimens.update +NULL + +#' specimens.delete is a method defined in Arvados class. +#' +#' @usage arv$specimens.delete(uuid) +#' @param uuid The UUID of the Specimen in question. +#' @return Specimen object. +#' @name specimens.delete +NULL + +#' specimens.list is a method defined in Arvados class. +#' +#' @usage arv$specimens.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return SpecimenList object. +#' @name specimens.list +NULL + +#' logs.get is a method defined in Arvados class. +#' +#' @usage arv$logs.get(uuid) +#' @param uuid The UUID of the Log in question. +#' @return Log object. +#' @name logs.get +NULL + +#' logs.create is a method defined in Arvados class. +#' +#' @usage arv$logs.create(log, ensure_unique_name = "false") +#' @param log Log object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Log object. +#' @name logs.create +NULL + +#' logs.update is a method defined in Arvados class. +#' +#' @usage arv$logs.update(log, uuid) +#' @param log Log object. +#' @param uuid The UUID of the Log in question. +#' @return Log object. +#' @name logs.update +NULL + +#' logs.delete is a method defined in Arvados class. +#' +#' @usage arv$logs.delete(uuid) +#' @param uuid The UUID of the Log in question. +#' @return Log object. +#' @name logs.delete +NULL + +#' logs.list is a method defined in Arvados class. +#' +#' @usage arv$logs.list(filters = NULL, where = NULL, +#' order = NULL, select = NULL, distinct = NULL, +#' limit = "100", offset = "0", count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return LogList object. +#' @name logs.list +NULL + +#' traits.get is a method defined in Arvados class. +#' +#' @usage arv$traits.get(uuid) +#' @param uuid The UUID of the Trait in question. +#' @return Trait object. +#' @name traits.get +NULL + +#' traits.create is a method defined in Arvados class. +#' +#' @usage arv$traits.create(trait, ensure_unique_name = "false") +#' @param trait Trait object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Trait object. +#' @name traits.create +NULL + +#' traits.update is a method defined in Arvados class. +#' +#' @usage arv$traits.update(trait, uuid) +#' @param trait Trait object. +#' @param uuid The UUID of the Trait in question. +#' @return Trait object. +#' @name traits.update +NULL + +#' traits.delete is a method defined in Arvados class. +#' +#' @usage arv$traits.delete(uuid) +#' @param uuid The UUID of the Trait in question. +#' @return Trait object. +#' @name traits.delete +NULL + +#' traits.list is a method defined in Arvados class. +#' +#' @usage arv$traits.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return TraitList object. +#' @name traits.list +NULL + +#' virtual_machines.get is a method defined in Arvados class. +#' +#' @usage arv$virtual_machines.get(uuid) +#' @param uuid The UUID of the VirtualMachine in question. +#' @return VirtualMachine object. +#' @name virtual_machines.get +NULL + +#' virtual_machines.create is a method defined in Arvados class. +#' +#' @usage arv$virtual_machines.create(virtualmachine, +#' ensure_unique_name = "false") +#' @param virtualMachine VirtualMachine object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return VirtualMachine object. +#' @name virtual_machines.create +NULL + +#' virtual_machines.update is a method defined in Arvados class. +#' +#' @usage arv$virtual_machines.update(virtualmachine, +#' uuid) +#' @param virtualMachine VirtualMachine object. +#' @param uuid The UUID of the VirtualMachine in question. +#' @return VirtualMachine object. +#' @name virtual_machines.update +NULL + +#' virtual_machines.delete is a method defined in Arvados class. +#' +#' @usage arv$virtual_machines.delete(uuid) +#' @param uuid The UUID of the VirtualMachine in question. +#' @return VirtualMachine object. +#' @name virtual_machines.delete +NULL + +#' virtual_machines.logins is a method defined in Arvados class. +#' +#' @usage arv$virtual_machines.logins(uuid) +#' @param uuid +#' @return VirtualMachine object. +#' @name virtual_machines.logins +NULL + +#' virtual_machines.get_all_logins is a method defined in Arvados class. +#' +#' @usage arv$virtual_machines.get_all_logins(NULL) +#' @return VirtualMachine object. +#' @name virtual_machines.get_all_logins +NULL + +#' virtual_machines.list is a method defined in Arvados class. +#' +#' @usage arv$virtual_machines.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return VirtualMachineList object. +#' @name virtual_machines.list +NULL + +#' workflows.get is a method defined in Arvados class. +#' +#' @usage arv$workflows.get(uuid) +#' @param uuid The UUID of the Workflow in question. +#' @return Workflow object. +#' @name workflows.get +NULL + +#' workflows.create is a method defined in Arvados class. +#' +#' @usage arv$workflows.create(workflow, +#' ensure_unique_name = "false") +#' @param workflow Workflow object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Workflow object. +#' @name workflows.create +NULL + +#' workflows.update is a method defined in Arvados class. +#' +#' @usage arv$workflows.update(workflow, +#' uuid) +#' @param workflow Workflow object. +#' @param uuid The UUID of the Workflow in question. +#' @return Workflow object. +#' @name workflows.update +NULL + +#' workflows.delete is a method defined in Arvados class. +#' +#' @usage arv$workflows.delete(uuid) +#' @param uuid The UUID of the Workflow in question. +#' @return Workflow object. +#' @name workflows.delete +NULL + +#' workflows.list is a method defined in Arvados class. +#' +#' @usage arv$workflows.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return WorkflowList object. +#' @name workflows.list +NULL + +#' groups.get is a method defined in Arvados class. +#' +#' @usage arv$groups.get(uuid) +#' @param uuid The UUID of the Group in question. +#' @return Group object. +#' @name groups.get +NULL + +#' groups.create is a method defined in Arvados class. +#' +#' @usage arv$groups.create(group, ensure_unique_name = "false") +#' @param group Group object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Group object. +#' @name groups.create +NULL + +#' groups.update is a method defined in Arvados class. +#' +#' @usage arv$groups.update(group, uuid) +#' @param group Group object. +#' @param uuid The UUID of the Group in question. +#' @return Group object. +#' @name groups.update +NULL + +#' groups.delete is a method defined in Arvados class. +#' +#' @usage arv$groups.delete(uuid) +#' @param uuid The UUID of the Group in question. +#' @return Group object. +#' @name groups.delete +NULL + +#' groups.contents is a method defined in Arvados class. +#' +#' @usage arv$groups.contents(filters = NULL, +#' where = NULL, order = NULL, distinct = NULL, +#' limit = "100", offset = "0", count = "exact", +#' include_trash = NULL, uuid = NULL, recursive = NULL) +#' @param filters +#' @param where +#' @param order +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @param include_trash Include items whose is_trashed attribute is true. +#' @param uuid +#' @param recursive Include contents from child groups recursively. +#' @return Group object. +#' @name groups.contents +NULL + +#' groups.trash is a method defined in Arvados class. +#' +#' @usage arv$groups.trash(uuid) +#' @param uuid +#' @return Group object. +#' @name groups.trash +NULL + +#' groups.untrash is a method defined in Arvados class. +#' +#' @usage arv$groups.untrash(uuid) +#' @param uuid +#' @return Group object. +#' @name groups.untrash +NULL + +#' groups.list is a method defined in Arvados class. +#' +#' @usage arv$groups.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact", include_trash = NULL) +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @param include_trash Include items whose is_trashed attribute is true. +#' @return GroupList object. +#' @name groups.list +NULL + +#' user_agreements.get is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.get(uuid) +#' @param uuid The UUID of the UserAgreement in question. +#' @return UserAgreement object. +#' @name user_agreements.get +NULL + +#' user_agreements.create is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.create(useragreement, +#' ensure_unique_name = "false") +#' @param userAgreement UserAgreement object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return UserAgreement object. +#' @name user_agreements.create +NULL + +#' user_agreements.update is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.update(useragreement, +#' uuid) +#' @param userAgreement UserAgreement object. +#' @param uuid The UUID of the UserAgreement in question. +#' @return UserAgreement object. +#' @name user_agreements.update +NULL + +#' user_agreements.delete is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.delete(uuid) +#' @param uuid The UUID of the UserAgreement in question. +#' @return UserAgreement object. +#' @name user_agreements.delete +NULL + +#' user_agreements.signatures is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.signatures(NULL) +#' @return UserAgreement object. +#' @name user_agreements.signatures +NULL + +#' user_agreements.sign is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.sign(NULL) +#' @return UserAgreement object. +#' @name user_agreements.sign +NULL + +#' user_agreements.list is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return UserAgreementList object. +#' @name user_agreements.list +NULL + +#' user_agreements.new is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.new(NULL) +#' @return UserAgreement object. +#' @name user_agreements.new +NULL + +#' Arvados +#' +#' Arvados class gives users ability to manipulate collections and projects. +#' +#' @section Usage: +#' \preformatted{arv = Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)} +#' +#' @section Arguments: +#' \describe{ +#' \item{authToken}{Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.} +#' \item{hostName}{Host name. If not specified ARVADOS_API_HOST environment variable will be used.} +#' \item{numRetries}{Number which specifies how many times to retry failed service requests.} +#' } +#' +#' @section Methods: +#' \describe{ +#' \item{}{\code{\link{api_client_authorizations.create}}} +#' \item{}{\code{\link{api_client_authorizations.create_system_auth}}} +#' \item{}{\code{\link{api_client_authorizations.current}}} +#' \item{}{\code{\link{api_client_authorizations.delete}}} +#' \item{}{\code{\link{api_client_authorizations.get}}} +#' \item{}{\code{\link{api_client_authorizations.list}}} +#' \item{}{\code{\link{api_client_authorizations.update}}} +#' \item{}{\code{\link{api_clients.create}}} +#' \item{}{\code{\link{api_clients.delete}}} +#' \item{}{\code{\link{api_clients.get}}} +#' \item{}{\code{\link{api_clients.list}}} +#' \item{}{\code{\link{api_clients.update}}} +#' \item{}{\code{\link{authorized_keys.create}}} +#' \item{}{\code{\link{authorized_keys.delete}}} +#' \item{}{\code{\link{authorized_keys.get}}} +#' \item{}{\code{\link{authorized_keys.list}}} +#' \item{}{\code{\link{authorized_keys.update}}} +#' \item{}{\code{\link{collections.create}}} +#' \item{}{\code{\link{collections.delete}}} +#' \item{}{\code{\link{collections.get}}} +#' \item{}{\code{\link{collections.list}}} +#' \item{}{\code{\link{collections.provenance}}} +#' \item{}{\code{\link{collections.trash}}} +#' \item{}{\code{\link{collections.untrash}}} +#' \item{}{\code{\link{collections.update}}} +#' \item{}{\code{\link{collections.used_by}}} +#' \item{}{\code{\link{container_requests.create}}} +#' \item{}{\code{\link{container_requests.delete}}} +#' \item{}{\code{\link{container_requests.get}}} +#' \item{}{\code{\link{container_requests.list}}} +#' \item{}{\code{\link{container_requests.update}}} +#' \item{}{\code{\link{containers.auth}}} +#' \item{}{\code{\link{containers.create}}} +#' \item{}{\code{\link{containers.current}}} +#' \item{}{\code{\link{containers.delete}}} +#' \item{}{\code{\link{containers.get}}} +#' \item{}{\code{\link{containers.list}}} +#' \item{}{\code{\link{containers.lock}}} +#' \item{}{\code{\link{containers.secret_mounts}}} +#' \item{}{\code{\link{containers.unlock}}} +#' \item{}{\code{\link{containers.update}}} +#' \item{}{\code{\link{groups.contents}}} +#' \item{}{\code{\link{groups.create}}} +#' \item{}{\code{\link{groups.delete}}} +#' \item{}{\code{\link{groups.get}}} +#' \item{}{\code{\link{groups.list}}} +#' \item{}{\code{\link{groups.trash}}} +#' \item{}{\code{\link{groups.untrash}}} +#' \item{}{\code{\link{groups.update}}} +#' \item{}{\code{\link{humans.create}}} +#' \item{}{\code{\link{humans.delete}}} +#' \item{}{\code{\link{humans.get}}} +#' \item{}{\code{\link{humans.list}}} +#' \item{}{\code{\link{humans.update}}} +#' \item{}{\code{\link{jobs.cancel}}} +#' \item{}{\code{\link{jobs.create}}} +#' \item{}{\code{\link{jobs.delete}}} +#' \item{}{\code{\link{jobs.get}}} +#' \item{}{\code{\link{jobs.list}}} +#' \item{}{\code{\link{jobs.lock}}} +#' \item{}{\code{\link{jobs.queue}}} +#' \item{}{\code{\link{jobs.queue_size}}} +#' \item{}{\code{\link{jobs.update}}} +#' \item{}{\code{\link{job_tasks.create}}} +#' \item{}{\code{\link{job_tasks.delete}}} +#' \item{}{\code{\link{job_tasks.get}}} +#' \item{}{\code{\link{job_tasks.list}}} +#' \item{}{\code{\link{job_tasks.update}}} +#' \item{}{\code{\link{keep_disks.create}}} +#' \item{}{\code{\link{keep_disks.delete}}} +#' \item{}{\code{\link{keep_disks.get}}} +#' \item{}{\code{\link{keep_disks.list}}} +#' \item{}{\code{\link{keep_disks.ping}}} +#' \item{}{\code{\link{keep_disks.update}}} +#' \item{}{\code{\link{keep_services.accessible}}} +#' \item{}{\code{\link{keep_services.create}}} +#' \item{}{\code{\link{keep_services.delete}}} +#' \item{}{\code{\link{keep_services.get}}} +#' \item{}{\code{\link{keep_services.list}}} +#' \item{}{\code{\link{keep_services.update}}} +#' \item{}{\code{\link{links.create}}} +#' \item{}{\code{\link{links.delete}}} +#' \item{}{\code{\link{links.get}}} +#' \item{}{\code{\link{links.get_permissions}}} +#' \item{}{\code{\link{links.list}}} +#' \item{}{\code{\link{links.update}}} +#' \item{}{\code{\link{logs.create}}} +#' \item{}{\code{\link{logs.delete}}} +#' \item{}{\code{\link{logs.get}}} +#' \item{}{\code{\link{logs.list}}} +#' \item{}{\code{\link{logs.update}}} +#' \item{}{\code{\link{nodes.create}}} +#' \item{}{\code{\link{nodes.delete}}} +#' \item{}{\code{\link{nodes.get}}} +#' \item{}{\code{\link{nodes.list}}} +#' \item{}{\code{\link{nodes.ping}}} +#' \item{}{\code{\link{nodes.update}}} +#' \item{}{\code{\link{pipeline_instances.cancel}}} +#' \item{}{\code{\link{pipeline_instances.create}}} +#' \item{}{\code{\link{pipeline_instances.delete}}} +#' \item{}{\code{\link{pipeline_instances.get}}} +#' \item{}{\code{\link{pipeline_instances.list}}} +#' \item{}{\code{\link{pipeline_instances.update}}} +#' \item{}{\code{\link{pipeline_templates.create}}} +#' \item{}{\code{\link{pipeline_templates.delete}}} +#' \item{}{\code{\link{pipeline_templates.get}}} +#' \item{}{\code{\link{pipeline_templates.list}}} +#' \item{}{\code{\link{pipeline_templates.update}}} +#' \item{}{\code{\link{projects.create}}} +#' \item{}{\code{\link{projects.delete}}} +#' \item{}{\code{\link{projects.get}}} +#' \item{}{\code{\link{projects.list}}} +#' \item{}{\code{\link{projects.update}}} +#' \item{}{\code{\link{repositories.create}}} +#' \item{}{\code{\link{repositories.delete}}} +#' \item{}{\code{\link{repositories.get}}} +#' \item{}{\code{\link{repositories.get_all_permissions}}} +#' \item{}{\code{\link{repositories.list}}} +#' \item{}{\code{\link{repositories.update}}} +#' \item{}{\code{\link{specimens.create}}} +#' \item{}{\code{\link{specimens.delete}}} +#' \item{}{\code{\link{specimens.get}}} +#' \item{}{\code{\link{specimens.list}}} +#' \item{}{\code{\link{specimens.update}}} +#' \item{}{\code{\link{traits.create}}} +#' \item{}{\code{\link{traits.delete}}} +#' \item{}{\code{\link{traits.get}}} +#' \item{}{\code{\link{traits.list}}} +#' \item{}{\code{\link{traits.update}}} +#' \item{}{\code{\link{user_agreements.create}}} +#' \item{}{\code{\link{user_agreements.delete}}} +#' \item{}{\code{\link{user_agreements.get}}} +#' \item{}{\code{\link{user_agreements.list}}} +#' \item{}{\code{\link{user_agreements.new}}} +#' \item{}{\code{\link{user_agreements.sign}}} +#' \item{}{\code{\link{user_agreements.signatures}}} +#' \item{}{\code{\link{user_agreements.update}}} +#' \item{}{\code{\link{users.activate}}} +#' \item{}{\code{\link{users.create}}} +#' \item{}{\code{\link{users.current}}} +#' \item{}{\code{\link{users.delete}}} +#' \item{}{\code{\link{users.get}}} +#' \item{}{\code{\link{users.list}}} +#' \item{}{\code{\link{users.setup}}} +#' \item{}{\code{\link{users.system}}} +#' \item{}{\code{\link{users.unsetup}}} +#' \item{}{\code{\link{users.update}}} +#' \item{}{\code{\link{users.update_uuid}}} +#' \item{}{\code{\link{virtual_machines.create}}} +#' \item{}{\code{\link{virtual_machines.delete}}} +#' \item{}{\code{\link{virtual_machines.get}}} +#' \item{}{\code{\link{virtual_machines.get_all_logins}}} +#' \item{}{\code{\link{virtual_machines.list}}} +#' \item{}{\code{\link{virtual_machines.logins}}} +#' \item{}{\code{\link{virtual_machines.update}}} +#' \item{}{\code{\link{workflows.create}}} +#' \item{}{\code{\link{workflows.delete}}} +#' \item{}{\code{\link{workflows.get}}} +#' \item{}{\code{\link{workflows.list}}} +#' \item{}{\code{\link{workflows.update}}} +#' } +#' +#' @name Arvados +#' @examples +#' \dontrun{ +#' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com") +#' +#' collection <- arv$collections.get("uuid") +#' +#' collectionList <- arv$collections.list(list(list("name", "like", "Test%"))) +#' collectionList <- listAll(arv$collections.list, list(list("name", "like", "Test%"))) +#' +#' deletedCollection <- arv$collections.delete("uuid") +#' +#' updatedCollection <- arv$collections.update(list(name = "New name", description = "New description") +#' "uuid") +#' +#' createdCollection <- arv$collections.create(list(name = "Example", +#' description = "This is a test collection")) +#' } +NULL + #' @export Arvados <- R6::R6Class( @@ -30,48 +1823,46 @@ Arvados <- R6::R6Class( }, - users.get = function(uuid) + projects.get = function(uuid) { - endPoint <- stringr::str_interp("users/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - 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$errors) - - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + self$groups.get(uuid) }, - users.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + projects.create = function(group, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("users") + group <- c("group_class" = "project", group) + self$groups.create(group, ensure_unique_name) + }, + + projects.update = function(group, uuid) + { + group <- c("group_class" = "project", group) + self$groups.update(group, uuid) + }, + + projects.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact", + include_trash = NULL) + { + filters[[length(filters) + 1]] <- list("group_class", "=", "project") + self$groups.list(filters, where, order, select, distinct, + limit, offset, count, include_trash) + }, + + projects.delete = function(uuid) + { + self$groups.delete(uuid) + }, + + users.get = function(uuid) + { + endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -81,11 +1872,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, users.create = function(user, ensure_unique_name = "false") @@ -95,7 +1882,12 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- user$toJSON() + + if(length(user) > 0) + body <- jsonlite::toJSON(list(user = user), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -104,17 +1896,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, users.update = function(user, uuid) @@ -123,8 +1905,13 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- user$toJSON() + queryArgs <- NULL + + if(length(user) > 0) + body <- jsonlite::toJSON(list(user = user), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -133,17 +1920,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, users.delete = function(uuid) @@ -152,7 +1929,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -162,17 +1940,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, users.current = function() @@ -182,6 +1950,7 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -191,17 +1960,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, users.system = function() @@ -211,6 +1970,7 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -220,17 +1980,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, users.activate = function(uuid) @@ -239,7 +1989,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -249,31 +2000,20 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, - users.setup = function( - user = NULL, openid_prefix = NULL, repo_name = NULL, - vm_uuid = NULL, send_notification_email = "false") + users.setup = function(user = NULL, openid_prefix = NULL, + repo_name = NULL, vm_uuid = NULL, send_notification_email = "false") { endPoint <- stringr::str_interp("users/setup") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - user = user, openid_prefix = openid_prefix, - repo_name = repo_name, vm_uuid = vm_uuid, - send_notification_email = send_notification_email) + queryArgs <- list(user = user, openid_prefix = openid_prefix, + repo_name = repo_name, vm_uuid = vm_uuid, + send_notification_email = send_notification_email) + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -283,17 +2023,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, users.unsetup = function(uuid) @@ -302,7 +2032,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -312,17 +2043,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, users.update_uuid = function(uuid, new_uuid) @@ -331,7 +2052,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid, new_uuid = new_uuid) + queryArgs <- list(new_uuid = new_uuid) + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -341,32 +2063,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, - users.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + users.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { endPoint <- stringr::str_interp("users") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -376,20 +2087,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - users.show = function(uuid) + api_client_authorizations.get = function(uuid) { - endPoint <- stringr::str_interp("users/${uuid}") + endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -399,113 +2107,88 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, - users.destroy = function(uuid) + api_client_authorizations.create = function(apiclientauthorization, + ensure_unique_name = "false") { - endPoint <- stringr::str_interp("users/${uuid}") + endPoint <- stringr::str_interp("api_client_authorizations") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - response <- private$REST$http$exec("DELETE", url, headers, body, + if(length(apiclientauthorization) > 0) + body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, - api_client_authorizations.get = function(uuid) + api_client_authorizations.update = function(apiclientauthorization, uuid) { endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + if(length(apiclientauthorization) > 0) + body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, - api_client_authorizations.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + api_client_authorizations.delete = function(uuid) { - endPoint <- stringr::str_interp("api_client_authorizations") + endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorizationList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - api_client_authorizations.create = function( - api_client_authorization, ensure_unique_name = "false") + api_client_authorizations.create_system_auth = function(api_client_id = NULL, scopes = NULL) { - endPoint <- stringr::str_interp("api_client_authorizations") + endPoint <- stringr::str_interp("api_client_authorizations/create_system_auth") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- api_client_authorization$toJSON() + queryArgs <- list(api_client_id = api_client_id, + scopes = scopes) + + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -514,81 +2197,88 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, - api_client_authorizations.update = function(api_client_authorization, uuid) + api_client_authorizations.current = function() { - endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") + endPoint <- stringr::str_interp("api_client_authorizations/current") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- api_client_authorization$toJSON() + queryArgs <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, - api_client_authorizations.delete = function(uuid) + api_client_authorizations.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") + endPoint <- stringr::str_interp("api_client_authorizations") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, - api_client_authorizations.create_system_auth = function(api_client_id = NULL, scopes = NULL) + containers.get = function(uuid) { - endPoint <- stringr::str_interp("api_client_authorizations/create_system_auth") + endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - api_client_id = api_client_id, scopes = scopes) + queryArgs <- NULL + body <- NULL + response <- private$REST$http$exec("GET", url, headers, body, + queryArgs, private$numRetries) + resource <- private$REST$httpParser$parseJSONResponse(response) + + if(!is.null(resource$errors)) + stop(resource$errors) + + resource + }, + + containers.create = function(container, ensure_unique_name = "false") + { + endPoint <- stringr::str_interp("containers") + url <- paste0(private$host, endPoint) + headers <- list(Authorization = paste("OAuth2", private$token), + "Content-Type" = "application/json") + queryArgs <- list(ensure_unique_name = ensure_unique_name) + + if(length(container) > 0) + body <- jsonlite::toJSON(list(container = container), + auto_unbox = TRUE) + else + body <- NULL + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -596,80 +2286,61 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, - api_client_authorizations.current = function() + containers.update = function(container, uuid) { - endPoint <- stringr::str_interp("api_client_authorizations/current") + endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + if(length(container) > 0) + body <- jsonlite::toJSON(list(container = container), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, - api_client_authorizations.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + containers.delete = function(uuid) { - endPoint <- stringr::str_interp("api_client_authorizations") + endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorizationList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - api_client_authorizations.show = function(uuid) + containers.auth = function(uuid) { - endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}/auth") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -679,82 +2350,57 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, - api_client_authorizations.destroy = function(uuid) + containers.lock = function(uuid) { - endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}/lock") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, - api_clients.get = function(uuid) + containers.unlock = function(uuid) { - endPoint <- stringr::str_interp("api_clients/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}/unlock") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ApiClient$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - url_prefix = resource$url_prefix, created_at = resource$created_at, - updated_at = resource$updated_at, is_trusted = resource$is_trusted) + resource }, - api_clients.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + containers.secret_mounts = function(uuid) { - endPoint <- stringr::str_interp("api_clients") + endPoint <- stringr::str_interp("containers/${uuid}/secret_mounts") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -764,149 +2410,130 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - api_clients.create = function(api_client, ensure_unique_name = "false") + containers.current = function() { - endPoint <- stringr::str_interp("api_clients") + endPoint <- stringr::str_interp("containers/current") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- api_client$toJSON() + queryArgs <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ApiClient$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - url_prefix = resource$url_prefix, created_at = resource$created_at, - updated_at = resource$updated_at, is_trusted = resource$is_trusted) + resource }, - api_clients.update = function(api_client, uuid) + containers.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("api_clients/${uuid}") + endPoint <- stringr::str_interp("containers") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- api_client$toJSON() + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - response <- private$REST$http$exec("PUT", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ApiClient$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - url_prefix = resource$url_prefix, created_at = resource$created_at, - updated_at = resource$updated_at, is_trusted = resource$is_trusted) + resource }, - api_clients.delete = function(uuid) + api_clients.get = function(uuid) { endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ApiClient$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - url_prefix = resource$url_prefix, created_at = resource$created_at, - updated_at = resource$updated_at, is_trusted = resource$is_trusted) + resource }, - api_clients.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + api_clients.create = function(apiclient, ensure_unique_name = "false") { endPoint <- stringr::str_interp("api_clients") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - response <- private$REST$http$exec("GET", url, headers, body, + if(length(apiclient) > 0) + body <- jsonlite::toJSON(list(apiclient = apiclient), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ApiClientList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - api_clients.show = function(uuid) + api_clients.update = function(apiclient, uuid) { endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + if(length(apiclient) > 0) + body <- jsonlite::toJSON(list(apiclient = apiclient), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ApiClient$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - url_prefix = resource$url_prefix, created_at = resource$created_at, - updated_at = resource$updated_at, is_trusted = resource$is_trusted) + resource }, - api_clients.destroy = function(uuid) + api_clients.delete = function(uuid) { endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -916,22 +2543,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClient$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - url_prefix = resource$url_prefix, created_at = resource$created_at, - updated_at = resource$updated_at, is_trusted = resource$is_trusted) + resource }, - container_requests.get = function(uuid) + api_clients.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("container_requests/${uuid}") + endPoint <- stringr::str_interp("api_clients") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -941,41 +2568,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequest$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - properties = resource$properties, state = resource$state, - requesting_container_uuid = resource$requesting_container_uuid, - container_uuid = resource$container_uuid, - container_count_max = resource$container_count_max, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - container_image = resource$container_image, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - priority = resource$priority, expires_at = resource$expires_at, - filters = resource$filters, updated_at = resource$updated_at, - container_count = resource$container_count, - use_existing = resource$use_existing, scheduling_parameters = resource$scheduling_parameters, - output_uuid = resource$output_uuid, log_uuid = resource$log_uuid, - output_name = resource$output_name, output_ttl = resource$output_ttl) + resource }, - container_requests.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + authorized_keys.get = function(uuid) { - endPoint <- stringr::str_interp("container_requests") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -985,22 +2588,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequestList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - container_requests.create = function( - container_request, ensure_unique_name = "false") + authorized_keys.create = function(authorizedkey, + ensure_unique_name = "false") { - endPoint <- stringr::str_interp("container_requests") + endPoint <- stringr::str_interp("authorized_keys") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- container_request$toJSON() + + if(length(authorizedkey) > 0) + body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -1009,36 +2613,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequest$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - properties = resource$properties, state = resource$state, - requesting_container_uuid = resource$requesting_container_uuid, - container_uuid = resource$container_uuid, - container_count_max = resource$container_count_max, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - container_image = resource$container_image, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - priority = resource$priority, expires_at = resource$expires_at, - filters = resource$filters, updated_at = resource$updated_at, - container_count = resource$container_count, - use_existing = resource$use_existing, scheduling_parameters = resource$scheduling_parameters, - output_uuid = resource$output_uuid, log_uuid = resource$log_uuid, - output_name = resource$output_name, output_ttl = resource$output_ttl) + resource }, - container_requests.update = function(container_request, uuid) + authorized_keys.update = function(authorizedkey, uuid) { - endPoint <- stringr::str_interp("container_requests/${uuid}") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- container_request$toJSON() + queryArgs <- NULL + + if(length(authorizedkey) > 0) + body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -1047,35 +2637,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequest$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - properties = resource$properties, state = resource$state, - requesting_container_uuid = resource$requesting_container_uuid, - container_uuid = resource$container_uuid, - container_count_max = resource$container_count_max, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - container_image = resource$container_image, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - priority = resource$priority, expires_at = resource$expires_at, - filters = resource$filters, updated_at = resource$updated_at, - container_count = resource$container_count, - use_existing = resource$use_existing, scheduling_parameters = resource$scheduling_parameters, - output_uuid = resource$output_uuid, log_uuid = resource$log_uuid, - output_name = resource$output_name, output_ttl = resource$output_ttl) + resource }, - container_requests.delete = function(uuid) + authorized_keys.delete = function(uuid) { - endPoint <- stringr::str_interp("container_requests/${uuid}") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -1085,41 +2657,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequest$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - properties = resource$properties, state = resource$state, - requesting_container_uuid = resource$requesting_container_uuid, - container_uuid = resource$container_uuid, - container_count_max = resource$container_count_max, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - container_image = resource$container_image, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - priority = resource$priority, expires_at = resource$expires_at, - filters = resource$filters, updated_at = resource$updated_at, - container_count = resource$container_count, - use_existing = resource$use_existing, scheduling_parameters = resource$scheduling_parameters, - output_uuid = resource$output_uuid, log_uuid = resource$log_uuid, - output_name = resource$output_name, output_ttl = resource$output_ttl) + resource }, - container_requests.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + authorized_keys.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("container_requests") + endPoint <- stringr::str_interp("authorized_keys") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1129,20 +2682,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequestList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - container_requests.show = function(uuid) + container_requests.get = function(uuid) { endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1152,262 +2702,179 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequest$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - properties = resource$properties, state = resource$state, - requesting_container_uuid = resource$requesting_container_uuid, - container_uuid = resource$container_uuid, - container_count_max = resource$container_count_max, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - container_image = resource$container_image, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - priority = resource$priority, expires_at = resource$expires_at, - filters = resource$filters, updated_at = resource$updated_at, - container_count = resource$container_count, - use_existing = resource$use_existing, scheduling_parameters = resource$scheduling_parameters, - output_uuid = resource$output_uuid, log_uuid = resource$log_uuid, - output_name = resource$output_name, output_ttl = resource$output_ttl) + resource }, - container_requests.destroy = function(uuid) + container_requests.create = function(containerrequest, + ensure_unique_name = "false") { - endPoint <- stringr::str_interp("container_requests/${uuid}") + endPoint <- stringr::str_interp("container_requests") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - response <- private$REST$http$exec("DELETE", url, headers, body, + if(length(containerrequest) > 0) + body <- jsonlite::toJSON(list(containerrequest = containerrequest), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequest$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - properties = resource$properties, state = resource$state, - requesting_container_uuid = resource$requesting_container_uuid, - container_uuid = resource$container_uuid, - container_count_max = resource$container_count_max, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - container_image = resource$container_image, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - priority = resource$priority, expires_at = resource$expires_at, - filters = resource$filters, updated_at = resource$updated_at, - container_count = resource$container_count, - use_existing = resource$use_existing, scheduling_parameters = resource$scheduling_parameters, - output_uuid = resource$output_uuid, log_uuid = resource$log_uuid, - output_name = resource$output_name, output_ttl = resource$output_ttl) + resource }, - authorized_keys.get = function(uuid) + container_requests.update = function(containerrequest, uuid) { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") + endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + if(length(containerrequest) > 0) + body <- jsonlite::toJSON(list(containerrequest = containerrequest), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - AuthorizedKey$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - key_type = resource$key_type, authorized_user_uuid = resource$authorized_user_uuid, - public_key = resource$public_key, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - authorized_keys.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + container_requests.delete = function(uuid) { - endPoint <- stringr::str_interp("authorized_keys") + endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - AuthorizedKeyList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - authorized_keys.create = function( - authorized_key, ensure_unique_name = "false") + container_requests.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("authorized_keys") + endPoint <- stringr::str_interp("container_requests") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- authorized_key$toJSON() + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - response <- private$REST$http$exec("POST", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - AuthorizedKey$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - key_type = resource$key_type, authorized_user_uuid = resource$authorized_user_uuid, - public_key = resource$public_key, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - authorized_keys.update = function(authorized_key, uuid) + collections.get = function(uuid) { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- authorized_key$toJSON() + queryArgs <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - AuthorizedKey$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - key_type = resource$key_type, authorized_user_uuid = resource$authorized_user_uuid, - public_key = resource$public_key, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - authorized_keys.delete = function(uuid) + collections.create = function(collection, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") + endPoint <- stringr::str_interp("collections") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - 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$errors) + queryArgs <- list(ensure_unique_name = ensure_unique_name) - AuthorizedKey$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - key_type = resource$key_type, authorized_user_uuid = resource$authorized_user_uuid, - public_key = resource$public_key, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at) - }, - - authorized_keys.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("authorized_keys") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL + if(length(collection) > 0) + body <- jsonlite::toJSON(list(collection = collection), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - AuthorizedKeyList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - authorized_keys.show = function(uuid) + collections.update = function(collection, uuid) { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + if(length(collection) > 0) + body <- jsonlite::toJSON(list(collection = collection), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - AuthorizedKey$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - key_type = resource$key_type, authorized_user_uuid = resource$authorized_user_uuid, - public_key = resource$public_key, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - authorized_keys.destroy = function(uuid) + collections.delete = function(uuid) { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -1417,23 +2884,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - AuthorizedKey$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - key_type = resource$key_type, authorized_user_uuid = resource$authorized_user_uuid, - public_key = resource$public_key, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - collections.get = function(uuid) + collections.provenance = function(uuid) { - endPoint <- stringr::str_interp("collections/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}/provenance") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1443,38 +2904,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - collections.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact", include_trash = NULL) + collections.used_by = function(uuid) { - endPoint <- stringr::str_interp("collections") + endPoint <- stringr::str_interp("collections/${uuid}/used_by") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count, include_trash = include_trash) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1484,21 +2924,18 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - CollectionList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - collections.create = function(collection, ensure_unique_name = "false") + collections.trash = function(uuid) { - endPoint <- stringr::str_interp("collections") + endPoint <- stringr::str_interp("collections/${uuid}/trash") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- collection$toJSON() + queryArgs <- NULL + + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -1507,102 +2944,43 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - collections.update = function(collection, uuid) + collections.untrash = function(uuid) { - endPoint <- stringr::str_interp("collections/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}/untrash") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- collection$toJSON() - - response <- private$REST$http$exec("PUT", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + queryArgs <- NULL - collection$setRESTService(private$REST) - collection - }, - - collections.delete = function(uuid) - { - endPoint <- stringr::str_interp("collections/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - collections.provenance = function(uuid) + collections.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact", include_trash = NULL) { - endPoint <- stringr::str_interp("collections/${uuid}/provenance") + endPoint <- stringr::str_interp("collections") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count, + include_trash = include_trash) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1612,32 +2990,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - collections.used_by = function(uuid) + humans.get = function(uuid) { - endPoint <- stringr::str_interp("collections/${uuid}/used_by") + endPoint <- stringr::str_interp("humans/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1647,68 +3010,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - collections.trash = function(uuid) + humans.create = function(human, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("collections/${uuid}/trash") + endPoint <- stringr::str_interp("humans") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = 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$errors) - - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + queryArgs <- list(ensure_unique_name = ensure_unique_name) - collection$setRESTService(private$REST) - collection - }, - - collections.untrash = function(uuid) - { - endPoint <- stringr::str_interp("collections/${uuid}/untrash") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + if(length(human) > 0) + body <- jsonlite::toJSON(list(human = human), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -1717,96 +3034,41 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - collections.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact", include_trash = NULL) + humans.update = function(human, uuid) { - endPoint <- stringr::str_interp("collections") + endPoint <- stringr::str_interp("humans/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count, include_trash = include_trash) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) + queryArgs <- NULL - CollectionList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) - }, - - collections.show = function(uuid) - { - endPoint <- stringr::str_interp("collections/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + if(length(human) > 0) + body <- jsonlite::toJSON(list(human = human), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - collections.destroy = function(uuid) + humans.delete = function(uuid) { - endPoint <- stringr::str_interp("collections/${uuid}") + endPoint <- stringr::str_interp("humans/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -1816,32 +3078,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - containers.get = function(uuid) + humans.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("containers/${uuid}") + endPoint <- stringr::str_interp("humans") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1851,36 +3102,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + job_tasks.get = function(uuid) { - endPoint <- stringr::str_interp("containers") + endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1890,21 +3122,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ContainerList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - containers.create = function(container, ensure_unique_name = "false") + job_tasks.create = function(jobtask, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("containers") + endPoint <- stringr::str_interp("job_tasks") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- container$toJSON() + + if(length(jobtask) > 0) + body <- jsonlite::toJSON(list(jobtask = jobtask), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -1913,31 +3146,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.update = function(container, uuid) + job_tasks.update = function(jobtask, uuid) { - endPoint <- stringr::str_interp("containers/${uuid}") + endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- container$toJSON() + queryArgs <- NULL + + if(length(jobtask) > 0) + body <- jsonlite::toJSON(list(jobtask = jobtask), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -1946,30 +3170,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.delete = function(uuid) + job_tasks.delete = function(uuid) { - endPoint <- stringr::str_interp("containers/${uuid}") + endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -1979,30 +3190,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.auth = function(uuid) + job_tasks.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("containers/${uuid}/auth") + endPoint <- stringr::str_interp("job_tasks") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2012,64 +3215,42 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.lock = function(uuid) + links.get = function(uuid) { - endPoint <- stringr::str_interp("containers/${uuid}/lock") + endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.unlock = function(uuid) + links.create = function(link, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("containers/${uuid}/unlock") + endPoint <- stringr::str_interp("links") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) + + if(length(link) > 0) + body <- jsonlite::toJSON(list(link = link), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -2078,92 +3259,65 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.current = function() + links.update = function(link, uuid) { - endPoint <- stringr::str_interp("containers/current") + endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + if(length(link) > 0) + body <- jsonlite::toJSON(list(link = link), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + links.delete = function(uuid) { - endPoint <- stringr::str_interp("containers") + endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ContainerList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - containers.show = function(uuid) + links.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("containers/${uuid}") + endPoint <- stringr::str_interp("links") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2173,63 +3327,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.destroy = function(uuid) + links.get_permissions = function(uuid) { - endPoint <- stringr::str_interp("containers/${uuid}") + endPoint <- stringr::str_interp("permissions/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - 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$errors) + queryArgs <- NULL - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) - }, - - humans.get = function(uuid) - { - endPoint <- stringr::str_interp("humans/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2239,27 +3347,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Human$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, properties = resource$properties, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - humans.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + jobs.get = function(uuid) { - endPoint <- stringr::str_interp("humans") + endPoint <- stringr::str_interp("jobs/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2269,21 +3367,27 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - HumanList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - humans.create = function(human, ensure_unique_name = "false") + jobs.create = function(job, ensure_unique_name = "false", + find_or_create = "false", filters = NULL, + minimum_script_version = NULL, exclude_script_versions = NULL) { - endPoint <- stringr::str_interp("humans") + endPoint <- stringr::str_interp("jobs") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- human$toJSON() + queryArgs <- list(ensure_unique_name = ensure_unique_name, + find_or_create = find_or_create, filters = filters, + minimum_script_version = minimum_script_version, + exclude_script_versions = exclude_script_versions) + + if(length(job) > 0) + body <- jsonlite::toJSON(list(job = job), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -2292,22 +3396,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Human$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, properties = resource$properties, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - humans.update = function(human, uuid) + jobs.update = function(job, uuid) { - endPoint <- stringr::str_interp("humans/${uuid}") + endPoint <- stringr::str_interp("jobs/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- human$toJSON() + queryArgs <- NULL + + if(length(job) > 0) + body <- jsonlite::toJSON(list(job = job), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -2316,21 +3420,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Human$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, properties = resource$properties, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - humans.delete = function(uuid) + jobs.delete = function(uuid) { - endPoint <- stringr::str_interp("humans/${uuid}") + endPoint <- stringr::str_interp("jobs/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -2340,27 +3440,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Human$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, properties = resource$properties, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - humans.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + jobs.queue = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("humans") + endPoint <- stringr::str_interp("jobs/queue") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2370,1887 +3464,57 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - HumanList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - humans.show = function(uuid) + jobs.queue_size = function() { - endPoint <- stringr::str_interp("humans/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - Human$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, properties = resource$properties, - created_at = resource$created_at, updated_at = resource$updated_at) - }, - - humans.destroy = function(uuid) - { - endPoint <- stringr::str_interp("humans/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - Human$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, properties = resource$properties, - created_at = resource$created_at, updated_at = resource$updated_at) - }, - - job_tasks.get = function(uuid) - { - endPoint <- stringr::str_interp("job_tasks/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - JobTask$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, job_uuid = resource$job_uuid, - sequence = resource$sequence, parameters = resource$parameters, - output = resource$output, progress = resource$progress, - success = resource$success, created_at = resource$created_at, - updated_at = resource$updated_at, created_by_job_task_uuid = resource$created_by_job_task_uuid, - qsequence = resource$qsequence, started_at = resource$started_at, - finished_at = resource$finished_at) - }, - - job_tasks.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("job_tasks") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - JobTaskList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) - }, - - job_tasks.create = function(job_task, ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("job_tasks") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- job_task$toJSON() - - 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$errors) - - JobTask$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, job_uuid = resource$job_uuid, - sequence = resource$sequence, parameters = resource$parameters, - output = resource$output, progress = resource$progress, - success = resource$success, created_at = resource$created_at, - updated_at = resource$updated_at, created_by_job_task_uuid = resource$created_by_job_task_uuid, - qsequence = resource$qsequence, started_at = resource$started_at, - finished_at = resource$finished_at) - }, - - job_tasks.update = function(job_task, uuid) - { - endPoint <- stringr::str_interp("job_tasks/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- job_task$toJSON() - - 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$errors) - - JobTask$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, job_uuid = resource$job_uuid, - sequence = resource$sequence, parameters = resource$parameters, - output = resource$output, progress = resource$progress, - success = resource$success, created_at = resource$created_at, - updated_at = resource$updated_at, created_by_job_task_uuid = resource$created_by_job_task_uuid, - qsequence = resource$qsequence, started_at = resource$started_at, - finished_at = resource$finished_at) - }, - - job_tasks.delete = function(uuid) - { - endPoint <- stringr::str_interp("job_tasks/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - JobTask$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, job_uuid = resource$job_uuid, - sequence = resource$sequence, parameters = resource$parameters, - output = resource$output, progress = resource$progress, - success = resource$success, created_at = resource$created_at, - updated_at = resource$updated_at, created_by_job_task_uuid = resource$created_by_job_task_uuid, - qsequence = resource$qsequence, started_at = resource$started_at, - finished_at = resource$finished_at) - }, - - job_tasks.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("job_tasks") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - JobTaskList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) - }, - - job_tasks.show = function(uuid) - { - endPoint <- stringr::str_interp("job_tasks/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- 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$errors) - - JobTask$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, job_uuid = resource$job_uuid, - sequence = resource$sequence, parameters = resource$parameters, - output = resource$output, progress = resource$progress, - success = resource$success, created_at = resource$created_at, - updated_at = resource$updated_at, created_by_job_task_uuid = resource$created_by_job_task_uuid, - qsequence = resource$qsequence, started_at = resource$started_at, - finished_at = resource$finished_at) - }, - - job_tasks.destroy = function(uuid) - { - endPoint <- stringr::str_interp("job_tasks/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - JobTask$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, job_uuid = resource$job_uuid, - sequence = resource$sequence, parameters = resource$parameters, - output = resource$output, progress = resource$progress, - success = resource$success, created_at = resource$created_at, - updated_at = resource$updated_at, created_by_job_task_uuid = resource$created_by_job_task_uuid, - qsequence = resource$qsequence, started_at = resource$started_at, - finished_at = resource$finished_at) - }, - - links.get = function(uuid) - { - endPoint <- stringr::str_interp("links/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - 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$errors) - - Link$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, tail_uuid = resource$tail_uuid, - link_class = resource$link_class, name = resource$name, - head_uuid = resource$head_uuid, properties = resource$properties, - updated_at = resource$updated_at) - }, - - links.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("links") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - LinkList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) - }, - - links.create = function(link, ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("links") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- link$toJSON() - - 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$errors) - - Link$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, tail_uuid = resource$tail_uuid, - link_class = resource$link_class, name = resource$name, - head_uuid = resource$head_uuid, properties = resource$properties, - updated_at = resource$updated_at) - }, - - links.update = function(link, uuid) - { - endPoint <- stringr::str_interp("links/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- link$toJSON() - - response <- private$REST$http$exec("PUT", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - Link$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, tail_uuid = resource$tail_uuid, - link_class = resource$link_class, name = resource$name, - head_uuid = resource$head_uuid, properties = resource$properties, - updated_at = resource$updated_at) - }, - - links.delete = function(uuid) - { - endPoint <- stringr::str_interp("links/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - Link$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, tail_uuid = resource$tail_uuid, - link_class = resource$link_class, name = resource$name, - head_uuid = resource$head_uuid, properties = resource$properties, - updated_at = resource$updated_at) - }, - - links.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("links") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - 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$errors) - - LinkList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) - }, - - links.show = function(uuid) - { - endPoint <- stringr::str_interp("links/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - Link$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, tail_uuid = resource$tail_uuid, - link_class = resource$link_class, name = resource$name, - head_uuid = resource$head_uuid, properties = resource$properties, - updated_at = resource$updated_at) - }, - - links.destroy = function(uuid) - { - endPoint <- stringr::str_interp("links/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - Link$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, tail_uuid = resource$tail_uuid, - link_class = resource$link_class, name = resource$name, - head_uuid = resource$head_uuid, properties = resource$properties, - updated_at = resource$updated_at) - }, - - links.get_permissions = function(uuid) - { - endPoint <- stringr::str_interp("permissions/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - Link$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, tail_uuid = resource$tail_uuid, - link_class = resource$link_class, name = resource$name, - head_uuid = resource$head_uuid, properties = resource$properties, - updated_at = resource$updated_at) - }, - - jobs.get = function(uuid) - { - endPoint <- stringr::str_interp("jobs/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) - }, - - jobs.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("jobs") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - JobList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) - }, - - jobs.create = function( - job, ensure_unique_name = "false", find_or_create = "false", - filters = NULL, minimum_script_version = NULL, - exclude_script_versions = NULL) - { - endPoint <- stringr::str_interp("jobs") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - ensure_unique_name = ensure_unique_name, - find_or_create = find_or_create, filters = filters, - minimum_script_version = minimum_script_version, - exclude_script_versions = exclude_script_versions) - body <- job$toJSON() - - 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$errors) - - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) - }, - - jobs.update = function(job, uuid) - { - endPoint <- stringr::str_interp("jobs/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- job$toJSON() - - 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$errors) - - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) - }, - - jobs.delete = function(uuid) - { - endPoint <- stringr::str_interp("jobs/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) - }, - - jobs.queue = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("jobs/queue") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) - }, - - jobs.queue_size = function() - { - endPoint <- stringr::str_interp("jobs/queue_size") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) - }, - - jobs.cancel = function(uuid) - { - endPoint <- stringr::str_interp("jobs/${uuid}/cancel") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = 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$errors) - - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) - }, - - jobs.lock = function(uuid) - { - endPoint <- stringr::str_interp("jobs/${uuid}/lock") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) - }, - - jobs.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("jobs") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - JobList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) - }, - - jobs.show = function(uuid) - { - endPoint <- stringr::str_interp("jobs/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - 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$errors) - - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) - }, - - jobs.destroy = function(uuid) - { - endPoint <- stringr::str_interp("jobs/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) - }, - - keep_disks.get = function(uuid) - { - endPoint <- stringr::str_interp("keep_disks/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- 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$errors) - - KeepDisk$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, ping_secret = resource$ping_secret, - node_uuid = resource$node_uuid, filesystem_uuid = resource$filesystem_uuid, - bytes_total = resource$bytes_total, bytes_free = resource$bytes_free, - is_readable = resource$is_readable, is_writable = resource$is_writable, - last_read_at = resource$last_read_at, last_write_at = resource$last_write_at, - last_ping_at = resource$last_ping_at, created_at = resource$created_at, - updated_at = resource$updated_at, keep_service_uuid = resource$keep_service_uuid) - }, - - keep_disks.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("keep_disks") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - KeepDiskList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) - }, - - keep_disks.create = function(keep_disk, ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("keep_disks") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- keep_disk$toJSON() - - 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$errors) - - KeepDisk$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, ping_secret = resource$ping_secret, - node_uuid = resource$node_uuid, filesystem_uuid = resource$filesystem_uuid, - bytes_total = resource$bytes_total, bytes_free = resource$bytes_free, - is_readable = resource$is_readable, is_writable = resource$is_writable, - last_read_at = resource$last_read_at, last_write_at = resource$last_write_at, - last_ping_at = resource$last_ping_at, created_at = resource$created_at, - updated_at = resource$updated_at, keep_service_uuid = resource$keep_service_uuid) - }, - - keep_disks.update = function(keep_disk, uuid) - { - endPoint <- stringr::str_interp("keep_disks/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- keep_disk$toJSON() - - response <- private$REST$http$exec("PUT", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - KeepDisk$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, ping_secret = resource$ping_secret, - node_uuid = resource$node_uuid, filesystem_uuid = resource$filesystem_uuid, - bytes_total = resource$bytes_total, bytes_free = resource$bytes_free, - is_readable = resource$is_readable, is_writable = resource$is_writable, - last_read_at = resource$last_read_at, last_write_at = resource$last_write_at, - last_ping_at = resource$last_ping_at, created_at = resource$created_at, - updated_at = resource$updated_at, keep_service_uuid = resource$keep_service_uuid) - }, - - keep_disks.delete = function(uuid) - { - endPoint <- stringr::str_interp("keep_disks/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - KeepDisk$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, ping_secret = resource$ping_secret, - node_uuid = resource$node_uuid, filesystem_uuid = resource$filesystem_uuid, - bytes_total = resource$bytes_total, bytes_free = resource$bytes_free, - is_readable = resource$is_readable, is_writable = resource$is_writable, - last_read_at = resource$last_read_at, last_write_at = resource$last_write_at, - last_ping_at = resource$last_ping_at, created_at = resource$created_at, - updated_at = resource$updated_at, keep_service_uuid = resource$keep_service_uuid) - }, - - keep_disks.ping = function( - uuid = NULL, ping_secret, node_uuid = NULL, - filesystem_uuid = NULL, service_host = NULL, - service_port, service_ssl_flag) - { - endPoint <- stringr::str_interp("keep_disks/ping") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - uuid = uuid, ping_secret = ping_secret, node_uuid = node_uuid, - filesystem_uuid = filesystem_uuid, service_host = service_host, - service_port = service_port, service_ssl_flag = service_ssl_flag) - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - KeepDisk$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, ping_secret = resource$ping_secret, - node_uuid = resource$node_uuid, filesystem_uuid = resource$filesystem_uuid, - bytes_total = resource$bytes_total, bytes_free = resource$bytes_free, - is_readable = resource$is_readable, is_writable = resource$is_writable, - last_read_at = resource$last_read_at, last_write_at = resource$last_write_at, - last_ping_at = resource$last_ping_at, created_at = resource$created_at, - updated_at = resource$updated_at, keep_service_uuid = resource$keep_service_uuid) - }, - - keep_disks.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("keep_disks") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - KeepDiskList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) - }, - - keep_disks.show = function(uuid) - { - endPoint <- stringr::str_interp("keep_disks/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- 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$errors) - - KeepDisk$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, ping_secret = resource$ping_secret, - node_uuid = resource$node_uuid, filesystem_uuid = resource$filesystem_uuid, - bytes_total = resource$bytes_total, bytes_free = resource$bytes_free, - is_readable = resource$is_readable, is_writable = resource$is_writable, - last_read_at = resource$last_read_at, last_write_at = resource$last_write_at, - last_ping_at = resource$last_ping_at, created_at = resource$created_at, - updated_at = resource$updated_at, keep_service_uuid = resource$keep_service_uuid) - }, - - keep_disks.destroy = function(uuid) - { - endPoint <- stringr::str_interp("keep_disks/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- 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$errors) - - KeepDisk$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, ping_secret = resource$ping_secret, - node_uuid = resource$node_uuid, filesystem_uuid = resource$filesystem_uuid, - bytes_total = resource$bytes_total, bytes_free = resource$bytes_free, - is_readable = resource$is_readable, is_writable = resource$is_writable, - last_read_at = resource$last_read_at, last_write_at = resource$last_write_at, - last_ping_at = resource$last_ping_at, created_at = resource$created_at, - updated_at = resource$updated_at, keep_service_uuid = resource$keep_service_uuid) - }, - - keep_services.get = function(uuid) - { - endPoint <- stringr::str_interp("keep_services/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- 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$errors) - - KeepService$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, service_host = resource$service_host, - service_port = resource$service_port, service_ssl_flag = resource$service_ssl_flag, - service_type = resource$service_type, created_at = resource$created_at, - updated_at = resource$updated_at, read_only = resource$read_only) - }, - - keep_services.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("keep_services") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - KeepServiceList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) - }, - - keep_services.create = function( - keep_service, ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("keep_services") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- keep_service$toJSON() - - 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$errors) - - KeepService$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, service_host = resource$service_host, - service_port = resource$service_port, service_ssl_flag = resource$service_ssl_flag, - service_type = resource$service_type, created_at = resource$created_at, - updated_at = resource$updated_at, read_only = resource$read_only) - }, - - keep_services.update = function(keep_service, uuid) - { - endPoint <- stringr::str_interp("keep_services/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- keep_service$toJSON() - - response <- private$REST$http$exec("PUT", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - KeepService$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, service_host = resource$service_host, - service_port = resource$service_port, service_ssl_flag = resource$service_ssl_flag, - service_type = resource$service_type, created_at = resource$created_at, - updated_at = resource$updated_at, read_only = resource$read_only) - }, - - keep_services.delete = function(uuid) - { - endPoint <- stringr::str_interp("keep_services/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - KeepService$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, service_host = resource$service_host, - service_port = resource$service_port, service_ssl_flag = resource$service_ssl_flag, - service_type = resource$service_type, created_at = resource$created_at, - updated_at = resource$updated_at, read_only = resource$read_only) - }, - - keep_services.accessible = function() - { - endPoint <- stringr::str_interp("keep_services/accessible") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - KeepService$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, service_host = resource$service_host, - service_port = resource$service_port, service_ssl_flag = resource$service_ssl_flag, - service_type = resource$service_type, created_at = resource$created_at, - updated_at = resource$updated_at, read_only = resource$read_only) - }, - - keep_services.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("keep_services") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - KeepServiceList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) - }, - - keep_services.show = function(uuid) - { - endPoint <- stringr::str_interp("keep_services/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- 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$errors) - - KeepService$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, service_host = resource$service_host, - service_port = resource$service_port, service_ssl_flag = resource$service_ssl_flag, - service_type = resource$service_type, created_at = resource$created_at, - updated_at = resource$updated_at, read_only = resource$read_only) - }, - - keep_services.destroy = function(uuid) - { - endPoint <- stringr::str_interp("keep_services/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- 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$errors) - - KeepService$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, service_host = resource$service_host, - service_port = resource$service_port, service_ssl_flag = resource$service_ssl_flag, - service_type = resource$service_type, created_at = resource$created_at, - updated_at = resource$updated_at, read_only = resource$read_only) - }, - - pipeline_templates.get = function(uuid) - { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- 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$errors) - - PipelineTemplate$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - components = resource$components, updated_at = resource$updated_at, - description = resource$description) - }, - - pipeline_templates.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("pipeline_templates") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - PipelineTemplateList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) - }, - - pipeline_templates.create = function( - pipeline_template, ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("pipeline_templates") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- pipeline_template$toJSON() - - 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$errors) - - PipelineTemplate$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - components = resource$components, updated_at = resource$updated_at, - description = resource$description) - }, - - pipeline_templates.update = function(pipeline_template, uuid) - { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- pipeline_template$toJSON() - - response <- private$REST$http$exec("PUT", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - PipelineTemplate$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - components = resource$components, updated_at = resource$updated_at, - description = resource$description) - }, - - pipeline_templates.delete = function(uuid) - { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - PipelineTemplate$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - components = resource$components, updated_at = resource$updated_at, - description = resource$description) - }, - - pipeline_templates.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("pipeline_templates") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - 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$errors) - - PipelineTemplateList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) - }, - - pipeline_templates.show = function(uuid) - { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - PipelineTemplate$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - components = resource$components, updated_at = resource$updated_at, - description = resource$description) - }, - - pipeline_templates.destroy = function(uuid) - { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - PipelineTemplate$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - components = resource$components, updated_at = resource$updated_at, - description = resource$description) - }, - - pipeline_instances.get = function(uuid) - { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - PipelineInstance$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, pipeline_template_uuid = resource$pipeline_template_uuid, - name = resource$name, components = resource$components, - updated_at = resource$updated_at, properties = resource$properties, - state = resource$state, components_summary = resource$components_summary, - started_at = resource$started_at, finished_at = resource$finished_at, - description = resource$description) - }, - - pipeline_instances.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("pipeline_instances") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - 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$errors) - - PipelineInstanceList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) - }, - - pipeline_instances.create = function( - pipeline_instance, ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("pipeline_instances") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- pipeline_instance$toJSON() - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - PipelineInstance$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, pipeline_template_uuid = resource$pipeline_template_uuid, - name = resource$name, components = resource$components, - updated_at = resource$updated_at, properties = resource$properties, - state = resource$state, components_summary = resource$components_summary, - started_at = resource$started_at, finished_at = resource$finished_at, - description = resource$description) - }, - - pipeline_instances.update = function(pipeline_instance, uuid) - { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") + endPoint <- stringr::str_interp("jobs/queue_size") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- pipeline_instance$toJSON() + queryArgs <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - PipelineInstance$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, pipeline_template_uuid = resource$pipeline_template_uuid, - name = resource$name, components = resource$components, - updated_at = resource$updated_at, properties = resource$properties, - state = resource$state, components_summary = resource$components_summary, - started_at = resource$started_at, finished_at = resource$finished_at, - description = resource$description) + resource }, - pipeline_instances.delete = function(uuid) + jobs.cancel = function(uuid) { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") + endPoint <- stringr::str_interp("jobs/${uuid}/cancel") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - PipelineInstance$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, pipeline_template_uuid = resource$pipeline_template_uuid, - name = resource$name, components = resource$components, - updated_at = resource$updated_at, properties = resource$properties, - state = resource$state, components_summary = resource$components_summary, - started_at = resource$started_at, finished_at = resource$finished_at, - description = resource$description) + resource }, - pipeline_instances.cancel = function(uuid) + jobs.lock = function(uuid) { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}/cancel") + endPoint <- stringr::str_interp("jobs/${uuid}/lock") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -4260,32 +3524,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineInstance$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, pipeline_template_uuid = resource$pipeline_template_uuid, - name = resource$name, components = resource$components, - updated_at = resource$updated_at, properties = resource$properties, - state = resource$state, components_summary = resource$components_summary, - started_at = resource$started_at, finished_at = resource$finished_at, - description = resource$description) + resource }, - pipeline_instances.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + jobs.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("pipeline_instances") + endPoint <- stringr::str_interp("jobs") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4295,20 +3548,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineInstanceList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - pipeline_instances.show = function(uuid) + keep_disks.get = function(uuid) { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") + endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4318,117 +3568,91 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineInstance$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, pipeline_template_uuid = resource$pipeline_template_uuid, - name = resource$name, components = resource$components, - updated_at = resource$updated_at, properties = resource$properties, - state = resource$state, components_summary = resource$components_summary, - started_at = resource$started_at, finished_at = resource$finished_at, - description = resource$description) + resource }, - pipeline_instances.destroy = function(uuid) + keep_disks.create = function(keepdisk, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") + endPoint <- stringr::str_interp("keep_disks") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - response <- private$REST$http$exec("DELETE", url, headers, body, + if(length(keepdisk) > 0) + body <- jsonlite::toJSON(list(keepdisk = keepdisk), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - PipelineInstance$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, pipeline_template_uuid = resource$pipeline_template_uuid, - name = resource$name, components = resource$components, - updated_at = resource$updated_at, properties = resource$properties, - state = resource$state, components_summary = resource$components_summary, - started_at = resource$started_at, finished_at = resource$finished_at, - description = resource$description) + resource }, - nodes.get = function(uuid) + keep_disks.update = function(keepdisk, uuid) { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + if(length(keepdisk) > 0) + body <- jsonlite::toJSON(list(keepdisk = keepdisk), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Node$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, slot_number = resource$slot_number, - hostname = resource$hostname, domain = resource$domain, - ip_address = resource$ip_address, first_ping_at = resource$first_ping_at, - last_ping_at = resource$last_ping_at, info = resource$info, - updated_at = resource$updated_at, properties = resource$properties, - job_uuid = resource$job_uuid) + resource }, - nodes.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + keep_disks.delete = function(uuid) { - endPoint <- stringr::str_interp("nodes") + endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - NodeList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - nodes.create = function( - node, ensure_unique_name = "false", assign_slot = NULL) + keep_disks.ping = function(uuid = NULL, ping_secret, + node_uuid = NULL, filesystem_uuid = NULL, + service_host = NULL, service_port, service_ssl_flag) { - endPoint <- stringr::str_interp("nodes") + endPoint <- stringr::str_interp("keep_disks/ping") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - ensure_unique_name = ensure_unique_name, - assign_slot = assign_slot) - body <- node$toJSON() + 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) @@ -4437,85 +3661,68 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Node$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, slot_number = resource$slot_number, - hostname = resource$hostname, domain = resource$domain, - ip_address = resource$ip_address, first_ping_at = resource$first_ping_at, - last_ping_at = resource$last_ping_at, info = resource$info, - updated_at = resource$updated_at, properties = resource$properties, - job_uuid = resource$job_uuid) + resource }, - nodes.update = function(node, uuid, assign_slot = NULL) + keep_disks.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("keep_disks") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid, assign_slot = assign_slot) - body <- node$toJSON() + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - response <- private$REST$http$exec("PUT", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Node$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, slot_number = resource$slot_number, - hostname = resource$hostname, domain = resource$domain, - ip_address = resource$ip_address, first_ping_at = resource$first_ping_at, - last_ping_at = resource$last_ping_at, info = resource$info, - updated_at = resource$updated_at, properties = resource$properties, - job_uuid = resource$job_uuid) + resource }, - nodes.delete = function(uuid) + keep_services.get = function(uuid) { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Node$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, slot_number = resource$slot_number, - hostname = resource$hostname, domain = resource$domain, - ip_address = resource$ip_address, first_ping_at = resource$first_ping_at, - last_ping_at = resource$last_ping_at, info = resource$info, - updated_at = resource$updated_at, properties = resource$properties, - job_uuid = resource$job_uuid) + resource }, - nodes.ping = function(uuid, ping_secret) + keep_services.create = function(keepservice, + ensure_unique_name = "false") { - endPoint <- stringr::str_interp("nodes/${uuid}/ping") + endPoint <- stringr::str_interp("keep_services") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid, ping_secret = ping_secret) - body <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) + + if(length(keepservice) > 0) + body <- jsonlite::toJSON(list(keepservice = keepservice), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -4524,113 +3731,86 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Node$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, slot_number = resource$slot_number, - hostname = resource$hostname, domain = resource$domain, - ip_address = resource$ip_address, first_ping_at = resource$first_ping_at, - last_ping_at = resource$last_ping_at, info = resource$info, - updated_at = resource$updated_at, properties = resource$properties, - job_uuid = resource$job_uuid) + resource }, - nodes.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + keep_services.update = function(keepservice, uuid) { - endPoint <- stringr::str_interp("nodes") + endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL + queryArgs <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + if(length(keepservice) > 0) + body <- jsonlite::toJSON(list(keepservice = keepservice), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - NodeList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - nodes.show = function(uuid) + keep_services.delete = function(uuid) { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Node$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, slot_number = resource$slot_number, - hostname = resource$hostname, domain = resource$domain, - ip_address = resource$ip_address, first_ping_at = resource$first_ping_at, - last_ping_at = resource$last_ping_at, info = resource$info, - updated_at = resource$updated_at, properties = resource$properties, - job_uuid = resource$job_uuid) + resource }, - nodes.destroy = function(uuid) + keep_services.accessible = function() { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("keep_services/accessible") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Node$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, slot_number = resource$slot_number, - hostname = resource$hostname, domain = resource$domain, - ip_address = resource$ip_address, first_ping_at = resource$first_ping_at, - last_ping_at = resource$last_ping_at, info = resource$info, - updated_at = resource$updated_at, properties = resource$properties, - job_uuid = resource$job_uuid) + resource }, - repositories.get = function(uuid) + keep_services.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("repositories/${uuid}") + endPoint <- stringr::str_interp("keep_services") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4640,27 +3820,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Repository$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - repositories.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + pipeline_templates.get = function(uuid) { - endPoint <- stringr::str_interp("repositories") + endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4670,21 +3840,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - RepositoryList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - repositories.create = function(repository, ensure_unique_name = "false") + pipeline_templates.create = function(pipelinetemplate, + ensure_unique_name = "false") { - endPoint <- stringr::str_interp("repositories") + endPoint <- stringr::str_interp("pipeline_templates") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- repository$toJSON() + + if(length(pipelinetemplate) > 0) + body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -4693,22 +3865,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Repository$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - repositories.update = function(repository, uuid) + pipeline_templates.update = function(pipelinetemplate, uuid) { - endPoint <- stringr::str_interp("repositories/${uuid}") + endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- repository$toJSON() + queryArgs <- NULL + + if(length(pipelinetemplate) > 0) + body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -4717,21 +3889,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Repository$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - repositories.delete = function(uuid) + pipeline_templates.delete = function(uuid) { - endPoint <- stringr::str_interp("repositories/${uuid}") + endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -4741,21 +3909,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Repository$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - repositories.get_all_permissions = function() + pipeline_templates.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("repositories/get_all_permissions") + endPoint <- stringr::str_interp("pipeline_templates") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4765,27 +3934,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Repository$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - repositories.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + pipeline_instances.get = function(uuid) { - endPoint <- stringr::str_interp("repositories") + endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4795,276 +3954,245 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - RepositoryList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - repositories.show = function(uuid) + pipeline_instances.create = function(pipelineinstance, + ensure_unique_name = "false") { - endPoint <- stringr::str_interp("repositories/${uuid}") + endPoint <- stringr::str_interp("pipeline_instances") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - response <- private$REST$http$exec("GET", url, headers, body, + if(length(pipelineinstance) > 0) + body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Repository$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - repositories.destroy = function(uuid) + pipeline_instances.update = function(pipelineinstance, uuid) { - endPoint <- stringr::str_interp("repositories/${uuid}") + endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + if(length(pipelineinstance) > 0) + body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Repository$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - specimens.get = function(uuid) + pipeline_instances.delete = function(uuid) { - endPoint <- stringr::str_interp("specimens/${uuid}") + endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Specimen$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, material = resource$material, - updated_at = resource$updated_at, properties = resource$properties) + resource }, - specimens.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + pipeline_instances.cancel = function(uuid) { - endPoint <- stringr::str_interp("specimens") + endPoint <- stringr::str_interp("pipeline_instances/${uuid}/cancel") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - SpecimenList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - specimens.create = function(specimen, ensure_unique_name = "false") + pipeline_instances.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("specimens") + endPoint <- stringr::str_interp("pipeline_instances") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- specimen$toJSON() + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - response <- private$REST$http$exec("POST", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Specimen$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, material = resource$material, - updated_at = resource$updated_at, properties = resource$properties) + resource }, - specimens.update = function(specimen, uuid) + nodes.get = function(uuid) { - endPoint <- stringr::str_interp("specimens/${uuid}") + endPoint <- stringr::str_interp("nodes/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- specimen$toJSON() + queryArgs <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Specimen$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, material = resource$material, - updated_at = resource$updated_at, properties = resource$properties) + resource }, - specimens.delete = function(uuid) + nodes.create = function(node, ensure_unique_name = "false", + assign_slot = NULL) { - endPoint <- stringr::str_interp("specimens/${uuid}") + endPoint <- stringr::str_interp("nodes") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name, + assign_slot = assign_slot) - response <- private$REST$http$exec("DELETE", url, headers, body, + if(length(node) > 0) + body <- jsonlite::toJSON(list(node = node), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Specimen$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, material = resource$material, - updated_at = resource$updated_at, properties = resource$properties) + resource }, - specimens.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + nodes.update = function(node, uuid, assign_slot = NULL) { - endPoint <- stringr::str_interp("specimens") + endPoint <- stringr::str_interp("nodes/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL + queryArgs <- list(assign_slot = assign_slot) - response <- private$REST$http$exec("GET", url, headers, body, + if(length(node) > 0) + body <- jsonlite::toJSON(list(node = node), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - SpecimenList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - specimens.show = function(uuid) + nodes.delete = function(uuid) { - endPoint <- stringr::str_interp("specimens/${uuid}") + endPoint <- stringr::str_interp("nodes/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Specimen$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, material = resource$material, - updated_at = resource$updated_at, properties = resource$properties) + resource }, - specimens.destroy = function(uuid) + nodes.ping = function(uuid, ping_secret) { - endPoint <- stringr::str_interp("specimens/${uuid}") + endPoint <- stringr::str_interp("nodes/${uuid}/ping") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(ping_secret = ping_secret) + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Specimen$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, material = resource$material, - updated_at = resource$updated_at, properties = resource$properties) + resource }, - logs.get = function(uuid) + nodes.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("logs/${uuid}") + endPoint <- stringr::str_interp("nodes") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5074,30 +4202,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Log$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - object_uuid = resource$object_uuid, event_at = resource$event_at, - event_type = resource$event_type, summary = resource$summary, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at, modified_at = resource$modified_at, - object_owner_uuid = resource$object_owner_uuid) + resource }, - logs.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + repositories.get = function(uuid) { - endPoint <- stringr::str_interp("logs") + endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5107,21 +4222,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - LogList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - logs.create = function(log, ensure_unique_name = "false") + repositories.create = function(repository, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("logs") + endPoint <- stringr::str_interp("repositories") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- log$toJSON() + + if(length(repository) > 0) + body <- jsonlite::toJSON(list(repository = repository), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -5130,25 +4246,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Log$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - object_uuid = resource$object_uuid, event_at = resource$event_at, - event_type = resource$event_type, summary = resource$summary, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at, modified_at = resource$modified_at, - object_owner_uuid = resource$object_owner_uuid) + resource }, - logs.update = function(log, uuid) + repositories.update = function(repository, uuid) { - endPoint <- stringr::str_interp("logs/${uuid}") + endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- log$toJSON() + queryArgs <- NULL + + if(length(repository) > 0) + body <- jsonlite::toJSON(list(repository = repository), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -5157,24 +4270,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Log$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - object_uuid = resource$object_uuid, event_at = resource$event_at, - event_type = resource$event_type, summary = resource$summary, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at, modified_at = resource$modified_at, - object_owner_uuid = resource$object_owner_uuid) + resource }, - logs.delete = function(uuid) + repositories.delete = function(uuid) { - endPoint <- stringr::str_interp("logs/${uuid}") + endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -5184,30 +4290,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Log$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - object_uuid = resource$object_uuid, event_at = resource$event_at, - event_type = resource$event_type, summary = resource$summary, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at, modified_at = resource$modified_at, - object_owner_uuid = resource$object_owner_uuid) + resource }, - logs.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + repositories.get_all_permissions = function() { - endPoint <- stringr::str_interp("logs") + endPoint <- stringr::str_interp("repositories/get_all_permissions") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5217,20 +4310,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - LogList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - logs.show = function(uuid) + repositories.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("logs/${uuid}") + endPoint <- stringr::str_interp("repositories") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5240,234 +4335,198 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Log$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - object_uuid = resource$object_uuid, event_at = resource$event_at, - event_type = resource$event_type, summary = resource$summary, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at, modified_at = resource$modified_at, - object_owner_uuid = resource$object_owner_uuid) + resource }, - logs.destroy = function(uuid) + specimens.get = function(uuid) { - endPoint <- stringr::str_interp("logs/${uuid}") + endPoint <- stringr::str_interp("specimens/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Log$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - object_uuid = resource$object_uuid, event_at = resource$event_at, - event_type = resource$event_type, summary = resource$summary, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at, modified_at = resource$modified_at, - object_owner_uuid = resource$object_owner_uuid) + resource }, - traits.get = function(uuid) + specimens.create = function(specimen, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("traits/${uuid}") + endPoint <- stringr::str_interp("specimens") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - response <- private$REST$http$exec("GET", url, headers, body, + if(length(specimen) > 0) + body <- jsonlite::toJSON(list(specimen = specimen), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Trait$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at) + resource }, - traits.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + specimens.update = function(specimen, uuid) { - endPoint <- stringr::str_interp("traits") + endPoint <- stringr::str_interp("specimens/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL + queryArgs <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + if(length(specimen) > 0) + body <- jsonlite::toJSON(list(specimen = specimen), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - TraitList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - traits.create = function(trait, ensure_unique_name = "false") + specimens.delete = function(uuid) { - endPoint <- stringr::str_interp("traits") + endPoint <- stringr::str_interp("specimens/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- trait$toJSON() + queryArgs <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Trait$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at) + resource }, - traits.update = function(trait, uuid) + specimens.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("traits/${uuid}") + endPoint <- stringr::str_interp("specimens") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- trait$toJSON() + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - response <- private$REST$http$exec("PUT", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Trait$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at) + resource }, - traits.delete = function(uuid) + logs.get = function(uuid) { - endPoint <- stringr::str_interp("traits/${uuid}") + endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Trait$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at) + resource }, - traits.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + logs.create = function(log, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("traits") + endPoint <- stringr::str_interp("logs") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - response <- private$REST$http$exec("GET", url, headers, body, + if(length(log) > 0) + body <- jsonlite::toJSON(list(log = log), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - TraitList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - traits.show = function(uuid) + logs.update = function(log, uuid) { - endPoint <- stringr::str_interp("traits/${uuid}") + endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + if(length(log) > 0) + body <- jsonlite::toJSON(list(log = log), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Trait$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at) + resource }, - traits.destroy = function(uuid) + logs.delete = function(uuid) { - endPoint <- stringr::str_interp("traits/${uuid}") + endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -5477,22 +4536,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Trait$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at) + resource }, - virtual_machines.get = function(uuid) + logs.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("virtual_machines/${uuid}") + endPoint <- stringr::str_interp("logs") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5502,27 +4560,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - virtual_machines.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + traits.get = function(uuid) { - endPoint <- stringr::str_interp("virtual_machines") + endPoint <- stringr::str_interp("traits/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5532,22 +4580,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachineList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - virtual_machines.create = function( - virtual_machine, ensure_unique_name = "false") + traits.create = function(trait, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("virtual_machines") + endPoint <- stringr::str_interp("traits") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- virtual_machine$toJSON() + + if(length(trait) > 0) + body <- jsonlite::toJSON(list(trait = trait), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -5556,22 +4604,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - virtual_machines.update = function(virtual_machine, uuid) + traits.update = function(trait, uuid) { - endPoint <- stringr::str_interp("virtual_machines/${uuid}") + endPoint <- stringr::str_interp("traits/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- virtual_machine$toJSON() + queryArgs <- NULL + + if(length(trait) > 0) + body <- jsonlite::toJSON(list(trait = trait), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -5580,21 +4628,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - virtual_machines.delete = function(uuid) + traits.delete = function(uuid) { - endPoint <- stringr::str_interp("virtual_machines/${uuid}") + endPoint <- stringr::str_interp("traits/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -5604,21 +4648,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - virtual_machines.logins = function(uuid) + traits.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("virtual_machines/${uuid}/logins") + endPoint <- stringr::str_interp("traits") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5628,21 +4672,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - virtual_machines.get_all_logins = function() + virtual_machines.get = function(uuid) { - endPoint <- stringr::str_interp("virtual_machines/get_all_logins") + endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5652,74 +4692,66 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - virtual_machines.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + virtual_machines.create = function(virtualmachine, + ensure_unique_name = "false") { endPoint <- stringr::str_interp("virtual_machines") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - response <- private$REST$http$exec("GET", url, headers, body, + if(length(virtualmachine) > 0) + body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachineList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - virtual_machines.show = function(uuid) + virtual_machines.update = function(virtualmachine, uuid) { endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + if(length(virtualmachine) > 0) + body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - virtual_machines.destroy = function(uuid) + virtual_machines.delete = function(uuid) { endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -5729,21 +4761,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - workflows.get = function(uuid) + virtual_machines.logins = function(uuid) { - endPoint <- stringr::str_interp("workflows/${uuid}") + endPoint <- stringr::str_interp("virtual_machines/${uuid}/logins") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5753,28 +4781,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Workflow$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - definition = resource$definition, updated_at = resource$updated_at) + resource }, - workflows.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + virtual_machines.get_all_logins = function() { - endPoint <- stringr::str_interp("workflows") + endPoint <- stringr::str_interp("virtual_machines/get_all_logins") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5784,149 +4801,110 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - WorkflowList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - workflows.create = function(workflow, ensure_unique_name = "false") + virtual_machines.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("workflows") + endPoint <- stringr::str_interp("virtual_machines") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- workflow$toJSON() + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - Workflow$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - definition = resource$definition, updated_at = resource$updated_at) - }, - - workflows.update = function(workflow, uuid) - { - endPoint <- stringr::str_interp("workflows/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- workflow$toJSON() + body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Workflow$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - definition = resource$definition, updated_at = resource$updated_at) + resource }, - workflows.delete = function(uuid) + workflows.get = function(uuid) { endPoint <- stringr::str_interp("workflows/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Workflow$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - definition = resource$definition, updated_at = resource$updated_at) + resource }, - workflows.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + workflows.create = function(workflow, ensure_unique_name = "false") { endPoint <- stringr::str_interp("workflows") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) - body <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - response <- private$REST$http$exec("GET", url, headers, body, + if(length(workflow) > 0) + body <- jsonlite::toJSON(list(workflow = workflow), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - WorkflowList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - workflows.show = function(uuid) + workflows.update = function(workflow, uuid) { endPoint <- stringr::str_interp("workflows/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + if(length(workflow) > 0) + body <- jsonlite::toJSON(list(workflow = workflow), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Workflow$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - definition = resource$definition, updated_at = resource$updated_at) + resource }, - workflows.destroy = function(uuid) + workflows.delete = function(uuid) { endPoint <- stringr::str_interp("workflows/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -5936,22 +4914,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Workflow$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - definition = resource$definition, updated_at = resource$updated_at) + resource }, - groups.get = function(uuid) + workflows.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("groups/${uuid}") + endPoint <- stringr::str_interp("workflows") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5961,30 +4939,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, - groups.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact", include_trash = NULL) + groups.get = function(uuid) { - endPoint <- stringr::str_interp("groups") + endPoint <- stringr::str_interp("groups/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count, include_trash = include_trash) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5994,11 +4959,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - GroupList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, groups.create = function(group, ensure_unique_name = "false") @@ -6008,7 +4969,12 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- group$toJSON() + + if(length(group) > 0) + body <- jsonlite::toJSON(list(group = group), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -6017,15 +4983,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, groups.update = function(group, uuid) @@ -6034,8 +4992,13 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- group$toJSON() + queryArgs <- NULL + + if(length(group) > 0) + body <- jsonlite::toJSON(list(group = group), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -6044,15 +5007,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, groups.delete = function(uuid) @@ -6061,7 +5016,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -6071,32 +5027,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, - groups.contents = function( - filters = NULL, where = NULL, order = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact", include_trash = NULL, uuid = NULL, - recursive = NULL) + groups.contents = function(filters = NULL, + where = NULL, order = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact", + include_trash = NULL, uuid = NULL, recursive = NULL) { endPoint <- stringr::str_interp("groups/contents") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - distinct = distinct, limit = limit, offset = offset, - count = count, include_trash = include_trash, - uuid = uuid, recursive = recursive) + queryArgs <- list(filters = filters, where = where, + order = order, distinct = distinct, limit = limit, + offset = offset, count = count, include_trash = include_trash, + uuid = uuid, recursive = recursive) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -6106,15 +5053,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, groups.trash = function(uuid) @@ -6123,7 +5062,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -6133,15 +5073,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, groups.untrash = function(uuid) @@ -6150,7 +5082,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -6160,53 +5093,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, - groups.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact", include_trash = NULL) + groups.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact", + include_trash = NULL) { endPoint <- stringr::str_interp("groups") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count, include_trash = include_trash) - 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$errors) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count, + include_trash = include_trash) - GroupList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) - }, - - groups.show = function(uuid) - { - endPoint <- stringr::str_interp("groups/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -6216,42 +5119,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) - }, - - groups.destroy = function(uuid) - { - endPoint <- stringr::str_interp("groups/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - 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$errors) - - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, user_agreements.get = function(uuid) @@ -6260,45 +5128,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - 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$errors) + queryArgs <- NULL - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - }, - - user_agreements.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("user_agreements") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -6308,22 +5139,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreementList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - user_agreements.create = function( - user_agreement, ensure_unique_name = "false") + user_agreements.create = function(useragreement, + ensure_unique_name = "false") { endPoint <- stringr::str_interp("user_agreements") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- user_agreement$toJSON() + + if(length(useragreement) > 0) + body <- jsonlite::toJSON(list(useragreement = useragreement), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -6332,30 +5164,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + resource }, - user_agreements.update = function(user_agreement, uuid) + user_agreements.update = function(useragreement, uuid) { endPoint <- stringr::str_interp("user_agreements/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- user_agreement$toJSON() + queryArgs <- NULL + + if(length(useragreement) > 0) + body <- jsonlite::toJSON(list(useragreement = useragreement), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -6364,20 +5188,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + resource }, user_agreements.delete = function(uuid) @@ -6386,7 +5197,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -6396,20 +5208,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + resource }, user_agreements.signatures = function() @@ -6419,6 +5218,7 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -6428,20 +5228,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + resource }, user_agreements.sign = function() @@ -6451,6 +5238,7 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -6460,35 +5248,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + resource }, - user_agreements.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + user_agreements.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("user_agreements") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -6498,11 +5273,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreementList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, user_agreements.new = function() @@ -6512,38 +5283,7 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - }, - - user_agreements.show = function(uuid) - { - endPoint <- stringr::str_interp("user_agreements/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -6553,57 +5293,13 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - }, - - user_agreements.destroy = function(uuid) - { - endPoint <- stringr::str_interp("user_agreements/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- 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$errors) - - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + resource }, getHostName = function() private$host, getToken = function() private$token, - setRESTService = function(newREST) private$REST <- newREST + setRESTService = function(newREST) private$REST <- newREST, + getRESTService = function() private$REST ), private = list(