19704: Merge contributed updates to R SDK
authorAnetaSta22 <107112384+AnetaSta22@users.noreply.github.com>
Tue, 16 Aug 2022 10:34:07 +0000 (12:34 +0200)
committerPeter Amstutz <peter.amstutz@curii.com>
Thu, 1 Dec 2022 18:28:31 +0000 (13:28 -0500)
commitde8cd4c6a56cac85dbcf7fe1fcb29abe98fe9f18
treeb57641bcc8562cf5cad2a12e59fa25fdcc039f82
parente5db78600aa8e617ca250c4b15f09e4d05b866cc
19704: Merge contributed updates to R SDK

* Add roxygen documentation
* Add readArvFile() function
* Add files via upload
* New README
* Add parameter relativePath in getCollectionContent()

Contributed by Aneta Stanczyk <aneta.stanczyk@contractors.roche.com>

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
180 files changed:
sdk/R/DESCRIPTION
sdk/R/R/Arvados.R
sdk/R/R/ArvadosFile.R
sdk/R/R/ArvadosR.R [new file with mode: 0644]
sdk/R/R/Collection.R
sdk/R/R/HttpRequest.R
sdk/R/R/RESTService.R
sdk/R/R/Subcollection.R
sdk/R/README.Rmd [deleted file]
sdk/R/README.md [new file with mode: 0644]
sdk/R/man/Arvados.Rd
sdk/R/man/ArvadosFile.Rd
sdk/R/man/ArvadosR.Rd [new file with mode: 0644]
sdk/R/man/Collection.Rd
sdk/R/man/Subcollection.Rd
sdk/R/man/api_client_authorizations.create.Rd [deleted file]
sdk/R/man/api_client_authorizations.create_system_auth.Rd [deleted file]
sdk/R/man/api_client_authorizations.current.Rd [deleted file]
sdk/R/man/api_client_authorizations.delete.Rd [deleted file]
sdk/R/man/api_client_authorizations.get.Rd [deleted file]
sdk/R/man/api_client_authorizations.list.Rd [deleted file]
sdk/R/man/api_client_authorizations.update.Rd [deleted file]
sdk/R/man/api_clients.create.Rd [deleted file]
sdk/R/man/api_clients.delete.Rd [deleted file]
sdk/R/man/api_clients.get.Rd [deleted file]
sdk/R/man/api_clients.list.Rd [deleted file]
sdk/R/man/api_clients.update.Rd [deleted file]
sdk/R/man/authorized_keys.create.Rd [deleted file]
sdk/R/man/authorized_keys.delete.Rd [deleted file]
sdk/R/man/authorized_keys.get.Rd [deleted file]
sdk/R/man/authorized_keys.list.Rd [deleted file]
sdk/R/man/authorized_keys.update.Rd [deleted file]
sdk/R/man/collections.create.Rd [deleted file]
sdk/R/man/collections.delete.Rd [deleted file]
sdk/R/man/collections.get.Rd [deleted file]
sdk/R/man/collections.list.Rd [deleted file]
sdk/R/man/collections.provenance.Rd [deleted file]
sdk/R/man/collections.trash.Rd [deleted file]
sdk/R/man/collections.untrash.Rd [deleted file]
sdk/R/man/collections.update.Rd [deleted file]
sdk/R/man/collections.used_by.Rd [deleted file]
sdk/R/man/container_requests.create.Rd [deleted file]
sdk/R/man/container_requests.delete.Rd [deleted file]
sdk/R/man/container_requests.get.Rd [deleted file]
sdk/R/man/container_requests.list.Rd [deleted file]
sdk/R/man/container_requests.update.Rd [deleted file]
sdk/R/man/containers.auth.Rd [deleted file]
sdk/R/man/containers.create.Rd [deleted file]
sdk/R/man/containers.current.Rd [deleted file]
sdk/R/man/containers.delete.Rd [deleted file]
sdk/R/man/containers.get.Rd [deleted file]
sdk/R/man/containers.list.Rd [deleted file]
sdk/R/man/containers.lock.Rd [deleted file]
sdk/R/man/containers.secret_mounts.Rd [deleted file]
sdk/R/man/containers.unlock.Rd [deleted file]
sdk/R/man/containers.update.Rd [deleted file]
sdk/R/man/figures/dax.png [new file with mode: 0644]
sdk/R/man/groups.contents.Rd [deleted file]
sdk/R/man/groups.create.Rd [deleted file]
sdk/R/man/groups.delete.Rd [deleted file]
sdk/R/man/groups.get.Rd [deleted file]
sdk/R/man/groups.list.Rd [deleted file]
sdk/R/man/groups.trash.Rd [deleted file]
sdk/R/man/groups.untrash.Rd [deleted file]
sdk/R/man/groups.update.Rd [deleted file]
sdk/R/man/humans.create.Rd [deleted file]
sdk/R/man/humans.delete.Rd [deleted file]
sdk/R/man/humans.get.Rd [deleted file]
sdk/R/man/humans.list.Rd [deleted file]
sdk/R/man/humans.update.Rd [deleted file]
sdk/R/man/job_tasks.create.Rd [deleted file]
sdk/R/man/job_tasks.delete.Rd [deleted file]
sdk/R/man/job_tasks.get.Rd [deleted file]
sdk/R/man/job_tasks.list.Rd [deleted file]
sdk/R/man/job_tasks.update.Rd [deleted file]
sdk/R/man/jobs.cancel.Rd [deleted file]
sdk/R/man/jobs.create.Rd [deleted file]
sdk/R/man/jobs.delete.Rd [deleted file]
sdk/R/man/jobs.get.Rd [deleted file]
sdk/R/man/jobs.list.Rd [deleted file]
sdk/R/man/jobs.lock.Rd [deleted file]
sdk/R/man/jobs.queue.Rd [deleted file]
sdk/R/man/jobs.queue_size.Rd [deleted file]
sdk/R/man/jobs.update.Rd [deleted file]
sdk/R/man/keep_disks.create.Rd [deleted file]
sdk/R/man/keep_disks.delete.Rd [deleted file]
sdk/R/man/keep_disks.get.Rd [deleted file]
sdk/R/man/keep_disks.list.Rd [deleted file]
sdk/R/man/keep_disks.ping.Rd [deleted file]
sdk/R/man/keep_disks.update.Rd [deleted file]
sdk/R/man/keep_services.accessible.Rd [deleted file]
sdk/R/man/keep_services.create.Rd [deleted file]
sdk/R/man/keep_services.delete.Rd [deleted file]
sdk/R/man/keep_services.get.Rd [deleted file]
sdk/R/man/keep_services.list.Rd [deleted file]
sdk/R/man/keep_services.update.Rd [deleted file]
sdk/R/man/links.create.Rd [deleted file]
sdk/R/man/links.delete.Rd [deleted file]
sdk/R/man/links.get.Rd [deleted file]
sdk/R/man/links.get_permissions.Rd [deleted file]
sdk/R/man/links.list.Rd [deleted file]
sdk/R/man/links.update.Rd [deleted file]
sdk/R/man/listAll.Rd
sdk/R/man/logs.create.Rd [deleted file]
sdk/R/man/logs.delete.Rd [deleted file]
sdk/R/man/logs.get.Rd [deleted file]
sdk/R/man/logs.list.Rd [deleted file]
sdk/R/man/logs.update.Rd [deleted file]
sdk/R/man/nodes.create.Rd [deleted file]
sdk/R/man/nodes.delete.Rd [deleted file]
sdk/R/man/nodes.get.Rd [deleted file]
sdk/R/man/nodes.list.Rd [deleted file]
sdk/R/man/nodes.ping.Rd [deleted file]
sdk/R/man/nodes.update.Rd [deleted file]
sdk/R/man/pipeline_instances.cancel.Rd [deleted file]
sdk/R/man/pipeline_instances.create.Rd [deleted file]
sdk/R/man/pipeline_instances.delete.Rd [deleted file]
sdk/R/man/pipeline_instances.get.Rd [deleted file]
sdk/R/man/pipeline_instances.list.Rd [deleted file]
sdk/R/man/pipeline_instances.update.Rd [deleted file]
sdk/R/man/pipeline_templates.create.Rd [deleted file]
sdk/R/man/pipeline_templates.delete.Rd [deleted file]
sdk/R/man/pipeline_templates.get.Rd [deleted file]
sdk/R/man/pipeline_templates.list.Rd [deleted file]
sdk/R/man/pipeline_templates.update.Rd [deleted file]
sdk/R/man/print.ArvadosFile.Rd
sdk/R/man/print.Collection.Rd
sdk/R/man/print.Subcollection.Rd
sdk/R/man/projects.create.Rd [deleted file]
sdk/R/man/projects.delete.Rd [deleted file]
sdk/R/man/projects.get.Rd [deleted file]
sdk/R/man/projects.list.Rd [deleted file]
sdk/R/man/projects.update.Rd [deleted file]
sdk/R/man/repositories.create.Rd [deleted file]
sdk/R/man/repositories.delete.Rd [deleted file]
sdk/R/man/repositories.get.Rd [deleted file]
sdk/R/man/repositories.get_all_permissions.Rd [deleted file]
sdk/R/man/repositories.list.Rd [deleted file]
sdk/R/man/repositories.update.Rd [deleted file]
sdk/R/man/specimens.create.Rd [deleted file]
sdk/R/man/specimens.delete.Rd [deleted file]
sdk/R/man/specimens.get.Rd [deleted file]
sdk/R/man/specimens.list.Rd [deleted file]
sdk/R/man/specimens.update.Rd [deleted file]
sdk/R/man/traits.create.Rd [deleted file]
sdk/R/man/traits.delete.Rd [deleted file]
sdk/R/man/traits.get.Rd [deleted file]
sdk/R/man/traits.list.Rd [deleted file]
sdk/R/man/traits.update.Rd [deleted file]
sdk/R/man/user_agreements.create.Rd [deleted file]
sdk/R/man/user_agreements.delete.Rd [deleted file]
sdk/R/man/user_agreements.get.Rd [deleted file]
sdk/R/man/user_agreements.list.Rd [deleted file]
sdk/R/man/user_agreements.new.Rd [deleted file]
sdk/R/man/user_agreements.sign.Rd [deleted file]
sdk/R/man/user_agreements.signatures.Rd [deleted file]
sdk/R/man/user_agreements.update.Rd [deleted file]
sdk/R/man/users.activate.Rd [deleted file]
sdk/R/man/users.create.Rd [deleted file]
sdk/R/man/users.current.Rd [deleted file]
sdk/R/man/users.delete.Rd [deleted file]
sdk/R/man/users.get.Rd [deleted file]
sdk/R/man/users.list.Rd [deleted file]
sdk/R/man/users.merge.Rd [deleted file]
sdk/R/man/users.setup.Rd [deleted file]
sdk/R/man/users.system.Rd [deleted file]
sdk/R/man/users.unsetup.Rd [deleted file]
sdk/R/man/users.update.Rd [deleted file]
sdk/R/man/virtual_machines.create.Rd [deleted file]
sdk/R/man/virtual_machines.delete.Rd [deleted file]
sdk/R/man/virtual_machines.get.Rd [deleted file]
sdk/R/man/virtual_machines.get_all_logins.Rd [deleted file]
sdk/R/man/virtual_machines.list.Rd [deleted file]
sdk/R/man/virtual_machines.logins.Rd [deleted file]
sdk/R/man/virtual_machines.update.Rd [deleted file]
sdk/R/man/workflows.create.Rd [deleted file]
sdk/R/man/workflows.delete.Rd [deleted file]
sdk/R/man/workflows.get.Rd [deleted file]
sdk/R/man/workflows.list.Rd [deleted file]
sdk/R/man/workflows.update.Rd [deleted file]