gadgets: Graphical user interfaces for common AnVIL operations

In Bioconductor/AnVIL: Bioconductor on the AnVIL compute environment

Graphical user interfaces for common AnVIL operations

Description

workspace() allows choice of workspace for subsequent use. It is the equivalent of displaying workspaces with avworkspaces(), and setting the selected workspace with avworkspace().

browse_workspace() uses browseURL() to open a browser window pointing to the Terra workspace.

table() allows choice of table in the current workspace (selected by avworkspace() or workspace()) to be returned as a tibble. It is equivalent to invoking avtables() to show available tables, and avtable() to retrieve the selected table.

workflow() allows choice of workflow for retrieval. It is the equivalent of avworkflows() for listing available workflows, and avworkflow_configuration_get() for retrieving the workflow.

Usage

avworkspace_gadget()

browse_workspace(use_avworkspace = TRUE)

avtable_gadget()

avworkflow_gadget()

Arguments

use_avworkspace

logical(1) when TRUE (default), use the selected workspace (via workspace() or avworkspace() if available. If FALSE or no workspace is currently selected, use workspace() to allow the user to select the workspace.

Value

workspace() returns the selected workspace as a character(1) using the format namespace/name, or character(0) if no workspace is selected.

browse_workspace() returns the status of a system() call to launch the browser, invisibly.

table() returns a tibble representing the selected AnVIL table.

workflow() returns an avworkflow_configuration object representing the inputs and outputs of the selected workflow. This can be edited and updated as described in the "Running an AnVIL workflow within R" vigenette.

Examples

## Not run: 
workspace()
browse_workspace(use_avworkspace = FALSE)
tbl <- table()
wkflw <- avworkflow_gadget()

## End(Not run)

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