X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/f309b872cc064141d9fbf43a15067998603e2204..3fa6aa4043286ad61e5f29c136d3cc2942e8750d:/sdk/R/man/Arvados.Rd diff --git a/sdk/R/man/Arvados.Rd b/sdk/R/man/Arvados.Rd index 3c66437f04..b55dd00dc5 100644 --- a/sdk/R/man/Arvados.Rd +++ b/sdk/R/man/Arvados.Rd @@ -4,7 +4,7 @@ \alias{Arvados} \title{Arvados} \description{ -Arvados class gives users ability to manipulate collections and projects. +Arvados class gives users ability to access Arvados REST API. } \section{Usage}{ @@ -14,31 +14,175 @@ Arvados class gives users ability to manipulate collections and projects. \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.} + \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{getToken()}{Returns authentification token currently in use.} - \item{getHostName()}{Returns host name currently in use.} - \item{getNumRetries()}{Returns number which specifies how many times to retry failed service requests.} - \item{setNumRetries(newNumOfRetries)}{Sets number which specifies how many times to retry failed service requests.} - \item{getCollection(uuid)}{Get collection with specified UUID.} - \item{listCollections(filters = NULL, limit = 100, offset = 0)}{Returns list of collections based on filters parameter.} - \item{listAllCollections(filters = NULL)}{Lists all collections, based on filters parameter, even if the number of items is greater than maximum API limit.} - \item{deleteCollection(uuid)}{Deletes collection with specified UUID.} - \item{updateCollection(uuid, newContent)}{Updates collection with specified UUID.} - \item{createCollection(content)}{Creates new collection.} - \item{getProject(uuid)}{Get project with specified UUID.} - \item{listProjects(filters = NULL, limit = 100, offset = 0)}{Returns list of projects based on filters parameter.} - \item{listAllProjects(filters = NULL)}{Lists all projects, based on filters parameter, even if the number of items is greater than maximum API limit.} - \item{deleteProject(uuid)}{Deletes project with specified UUID.} - \item{updateProject(uuid, newContent)}{Updates project with specified UUID.} - \item{createProject(content)}{Creates new project.} + \item{}{\code{\link{api_client_authorizations.create}}} + \item{}{\code{\link{api_client_authorizations.create_system_auth}}} + \item{}{\code{\link{api_client_authorizations.current}}} + \item{}{\code{\link{api_client_authorizations.delete}}} + \item{}{\code{\link{api_client_authorizations.get}}} + \item{}{\code{\link{api_client_authorizations.list}}} + \item{}{\code{\link{api_client_authorizations.update}}} + \item{}{\code{\link{api_clients.create}}} + \item{}{\code{\link{api_clients.delete}}} + \item{}{\code{\link{api_clients.get}}} + \item{}{\code{\link{api_clients.list}}} + \item{}{\code{\link{api_clients.update}}} + \item{}{\code{\link{authorized_keys.create}}} + \item{}{\code{\link{authorized_keys.delete}}} + \item{}{\code{\link{authorized_keys.get}}} + \item{}{\code{\link{authorized_keys.list}}} + \item{}{\code{\link{authorized_keys.update}}} + \item{}{\code{\link{collections.create}}} + \item{}{\code{\link{collections.delete}}} + \item{}{\code{\link{collections.get}}} + \item{}{\code{\link{collections.list}}} + \item{}{\code{\link{collections.provenance}}} + \item{}{\code{\link{collections.trash}}} + \item{}{\code{\link{collections.untrash}}} + \item{}{\code{\link{collections.update}}} + \item{}{\code{\link{collections.used_by}}} + \item{}{\code{\link{container_requests.create}}} + \item{}{\code{\link{container_requests.delete}}} + \item{}{\code{\link{container_requests.get}}} + \item{}{\code{\link{container_requests.list}}} + \item{}{\code{\link{container_requests.update}}} + \item{}{\code{\link{containers.auth}}} + \item{}{\code{\link{containers.create}}} + \item{}{\code{\link{containers.current}}} + \item{}{\code{\link{containers.delete}}} + \item{}{\code{\link{containers.get}}} + \item{}{\code{\link{containers.list}}} + \item{}{\code{\link{containers.lock}}} + \item{}{\code{\link{containers.secret_mounts}}} + \item{}{\code{\link{containers.unlock}}} + \item{}{\code{\link{containers.update}}} + \item{}{\code{\link{groups.contents}}} + \item{}{\code{\link{groups.create}}} + \item{}{\code{\link{groups.delete}}} + \item{}{\code{\link{groups.get}}} + \item{}{\code{\link{groups.list}}} + \item{}{\code{\link{groups.trash}}} + \item{}{\code{\link{groups.untrash}}} + \item{}{\code{\link{groups.update}}} + \item{}{\code{\link{humans.create}}} + \item{}{\code{\link{humans.delete}}} + \item{}{\code{\link{humans.get}}} + \item{}{\code{\link{humans.list}}} + \item{}{\code{\link{humans.update}}} + \item{}{\code{\link{jobs.cancel}}} + \item{}{\code{\link{jobs.create}}} + \item{}{\code{\link{jobs.delete}}} + \item{}{\code{\link{jobs.get}}} + \item{}{\code{\link{jobs.list}}} + \item{}{\code{\link{jobs.lock}}} + \item{}{\code{\link{jobs.queue}}} + \item{}{\code{\link{jobs.queue_size}}} + \item{}{\code{\link{jobs.update}}} + \item{}{\code{\link{job_tasks.create}}} + \item{}{\code{\link{job_tasks.delete}}} + \item{}{\code{\link{job_tasks.get}}} + \item{}{\code{\link{job_tasks.list}}} + \item{}{\code{\link{job_tasks.update}}} + \item{}{\code{\link{keep_disks.create}}} + \item{}{\code{\link{keep_disks.delete}}} + \item{}{\code{\link{keep_disks.get}}} + \item{}{\code{\link{keep_disks.list}}} + \item{}{\code{\link{keep_disks.ping}}} + \item{}{\code{\link{keep_disks.update}}} + \item{}{\code{\link{keep_services.accessible}}} + \item{}{\code{\link{keep_services.create}}} + \item{}{\code{\link{keep_services.delete}}} + \item{}{\code{\link{keep_services.get}}} + \item{}{\code{\link{keep_services.list}}} + \item{}{\code{\link{keep_services.update}}} + \item{}{\code{\link{links.create}}} + \item{}{\code{\link{links.delete}}} + \item{}{\code{\link{links.get}}} + \item{}{\code{\link{links.get_permissions}}} + \item{}{\code{\link{links.list}}} + \item{}{\code{\link{links.update}}} + \item{}{\code{\link{logs.create}}} + \item{}{\code{\link{logs.delete}}} + \item{}{\code{\link{logs.get}}} + \item{}{\code{\link{logs.list}}} + \item{}{\code{\link{logs.update}}} + \item{}{\code{\link{nodes.create}}} + \item{}{\code{\link{nodes.delete}}} + \item{}{\code{\link{nodes.get}}} + \item{}{\code{\link{nodes.list}}} + \item{}{\code{\link{nodes.ping}}} + \item{}{\code{\link{nodes.update}}} + \item{}{\code{\link{pipeline_instances.cancel}}} + \item{}{\code{\link{pipeline_instances.create}}} + \item{}{\code{\link{pipeline_instances.delete}}} + \item{}{\code{\link{pipeline_instances.get}}} + \item{}{\code{\link{pipeline_instances.list}}} + \item{}{\code{\link{pipeline_instances.update}}} + \item{}{\code{\link{pipeline_templates.create}}} + \item{}{\code{\link{pipeline_templates.delete}}} + \item{}{\code{\link{pipeline_templates.get}}} + \item{}{\code{\link{pipeline_templates.list}}} + \item{}{\code{\link{pipeline_templates.update}}} + \item{}{\code{\link{projects.create}}} + \item{}{\code{\link{projects.delete}}} + \item{}{\code{\link{projects.get}}} + \item{}{\code{\link{projects.list}}} + \item{}{\code{\link{projects.update}}} + \item{}{\code{\link{repositories.create}}} + \item{}{\code{\link{repositories.delete}}} + \item{}{\code{\link{repositories.get}}} + \item{}{\code{\link{repositories.get_all_permissions}}} + \item{}{\code{\link{repositories.list}}} + \item{}{\code{\link{repositories.update}}} + \item{}{\code{\link{specimens.create}}} + \item{}{\code{\link{specimens.delete}}} + \item{}{\code{\link{specimens.get}}} + \item{}{\code{\link{specimens.list}}} + \item{}{\code{\link{specimens.update}}} + \item{}{\code{\link{traits.create}}} + \item{}{\code{\link{traits.delete}}} + \item{}{\code{\link{traits.get}}} + \item{}{\code{\link{traits.list}}} + \item{}{\code{\link{traits.update}}} + \item{}{\code{\link{user_agreements.create}}} + \item{}{\code{\link{user_agreements.delete}}} + \item{}{\code{\link{user_agreements.get}}} + \item{}{\code{\link{user_agreements.list}}} + \item{}{\code{\link{user_agreements.new}}} + \item{}{\code{\link{user_agreements.sign}}} + \item{}{\code{\link{user_agreements.signatures}}} + \item{}{\code{\link{user_agreements.update}}} + \item{}{\code{\link{users.activate}}} + \item{}{\code{\link{users.create}}} + \item{}{\code{\link{users.current}}} + \item{}{\code{\link{users.delete}}} + \item{}{\code{\link{users.get}}} + \item{}{\code{\link{users.list}}} + \item{}{\code{\link{users.merge}}} + \item{}{\code{\link{users.setup}}} + \item{}{\code{\link{users.system}}} + \item{}{\code{\link{users.unsetup}}} + \item{}{\code{\link{users.update}}} + \item{}{\code{\link{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}}} } } @@ -46,17 +190,17 @@ Arvados class gives users ability to manipulate collections and projects. \dontrun{ arv <- Arvados$new("your Arvados token", "example.arvadosapi.com") -collection <- arv$getCollection("uuid") +collection <- arv$collections.get("uuid") -collectionList <- arv$listCollections(list(list("name", "like", "Test\%"))) -collectionList <- arv$listAllCollections(list(list("name", "like", "Test\%"))) +collectionList <- arv$collections.list(list(list("name", "like", "Test\%"))) +collectionList <- listAll(arv$collections.list, list(list("name", "like", "Test\%"))) -deletedCollection <- arv$deleteCollection("uuid") +deletedCollection <- arv$collections.delete("uuid") -updatedCollection <- arv$updateCollection("uuid", list(name = "New name", - description = "New description")) +updatedCollection <- arv$collections.update(list(name = "New name", description = "New description"), + "uuid") -createdCollection <- arv$createCollection(list(name = "Example", - description = "This is a test collection")) +createdCollection <- arv$collections.create(list(name = "Example", + description = "This is a test collection")) } }