avnotebooks: Notebook management
In Bioconductor/AnVIL: Bioconductor on the AnVIL compute environment

avnotebooks

R Documentation

Notebook management

Description

avnotebooks() returns the names of the notebooks associated with the current workspace.

avnotebooks_localize() synchronizes the content of the workspace bucket to the local file system.

avnotebooks_delocalize() synchronizes the content of the notebook location of the local file system to the workspace bucket.

Usage

avnotebooks(
  local = FALSE,
  namespace = avworkspace_namespace(),
  name = avworkspace_name()
)

avnotebooks_localize(
  destination,
  namespace = avworkspace_namespace(),
  name = avworkspace_name(),
  dry = TRUE
)

avnotebooks_delocalize(
  source,
  namespace = avworkspace_namespace(),
  name = avworkspace_name(),
  dry = TRUE
)

Arguments

`local`	= `logical(1)` notebooks located on the workspace (`local = FALSE`, default) or runtime / local instance (`local = TRUE`). When `local = TRUE`, the notebook path is `⁠<avworkspace_name>/notebooks⁠`.
`namespace`	character(1) AnVIL workspace namespace as returned by, e.g., `avworkspace_namespace()`
`name`	character(1) AnVIL workspace name as returned by, eg., `avworkspace_name()`.
`destination`	missing or character(1) file path to the local file system directory for synchronization. The default location is `⁠~/<avworkspace_name>/notebooks⁠`. Out-of-date local files are replaced with the workspace version.
`dry`	`logical(1)`, when `TRUE` (default), return the consequences of the operation without actually performing the operation.
`source`	missing or character(1) file path to the local file system directory for synchronization. The default location is `⁠~/<avworkspace_name>/notebooks⁠`. Out-of-date local files are replaced with the workspace version.

Value

avnotebooks() returns a character vector of buckets / files located in the workspace 'Files/notebooks' bucket path, or on the local file system.

avnotebooks_localize() returns the exit status of gsutil_rsync().

avnotebooks_delocalize() returns the exit status of gsutil_rsync().

Examples

if (gcloud_exists() && nzchar(avworkspace_name()))
    avnotebooks()

if (gcloud_exists() && nzchar(avworkspace_name()))
    avnotebooks_localize()  # dry run

if (gcloud_exists() && nzchar(avworkspace_name()))
    try(avnotebooks_delocalize())  # dry run, fails if no local resource

Bioconductor/AnVIL documentation built on April 12, 2024, 6:41 p.m.