ArvadosR Documentation

Arvados

Description

Arvados class gives users ability to access Arvados REST API.

Usage

arv = Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)

Arguments

authToken

Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.

hostName

Host name. If not specified ARVADOS_API_HOST environment variable will be used.

numRetries

Number which specifies how many times to retry failed service requests.

Methods

api_client_authorizations.create

api_client_authorizations.create_system_auth

api_client_authorizations.current

api_client_authorizations.delete

api_client_authorizations.get

api_client_authorizations.list

api_client_authorizations.update

api_clients.create

api_clients.delete

api_clients.get

api_clients.list

api_clients.update

authorized_keys.create

authorized_keys.delete

authorized_keys.get

authorized_keys.list

authorized_keys.update

collections.create

collections.delete

collections.get

collections.list

collections.provenance

collections.trash

collections.untrash

collections.update

collections.used_by

container_requests.create

container_requests.delete

container_requests.get

container_requests.list

container_requests.update

containers.auth

containers.create

containers.current

containers.delete

containers.get

containers.list

containers.lock

containers.secret_mounts

containers.unlock

containers.update

groups.contents

groups.create

groups.delete

groups.get

groups.list

groups.trash

groups.untrash

groups.update

humans.create

humans.delete

humans.get

humans.list

humans.update

jobs.cancel

jobs.create

jobs.delete

jobs.get

jobs.list

jobs.lock

jobs.queue

jobs.queue_size

jobs.update

job_tasks.create

job_tasks.delete

job_tasks.get

job_tasks.list

job_tasks.update

keep_disks.create

keep_disks.delete

keep_disks.get

keep_disks.list

keep_disks.ping

keep_disks.update

keep_services.accessible

keep_services.create

keep_services.delete

keep_services.get

keep_services.list

keep_services.update

links.create

links.delete

links.get

links.get_permissions

links.list

links.update

logs.create

logs.delete

logs.get

logs.list

logs.update

nodes.create

nodes.delete

nodes.get

nodes.list

nodes.ping

nodes.update

pipeline_instances.cancel

pipeline_instances.create

pipeline_instances.delete

pipeline_instances.get

pipeline_instances.list

pipeline_instances.update

pipeline_templates.create

pipeline_templates.delete

pipeline_templates.get

pipeline_templates.list

pipeline_templates.update

projects.create

projects.delete

projects.get

projects.list

projects.update

repositories.create

repositories.delete

repositories.get

repositories.get_all_permissions

repositories.list

repositories.update

specimens.create

specimens.delete

specimens.get

specimens.list

specimens.update

traits.create

traits.delete

traits.get

traits.list

traits.update

user_agreements.create

user_agreements.delete

user_agreements.get

user_agreements.list

user_agreements.new

user_agreements.sign

user_agreements.signatures

user_agreements.update

users.activate

users.create

users.current

users.delete

users.get

users.list

users.merge

users.setup

users.system

users.unsetup

users.update

users.update_uuid

virtual_machines.create

virtual_machines.delete

virtual_machines.get

virtual_machines.get_all_logins

virtual_machines.list

virtual_machines.logins

virtual_machines.update

workflows.create

workflows.delete

workflows.get

workflows.list

workflows.update

Examples

## Not run: 
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"))

## End(Not run)