\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}{
\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{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}}}
}
}
\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"))
}
}
projects / arvados.git / blobdiff