R/cloneWorkspace.R

In shbrief/RunTerraWorkflow: Run workflows implemented in Terra/AnVIL workspace

#' Clone template workspace
#'
#' This function makes your own copy of the existing workspace, selected 
#' through \code{templateName} or \code{analysis}. Your copied/cloned
#' workspace name will be \code{workspaceName} and any computing cost will
#' be charaged to the billing linked to your \code{billingProjectName}.
#' You should provide at least one argument \code{templateName} or
#' \code{analysis}.
#' 
#' @import AnVILGCP
#' @importFrom utils read.table
#'
#' @param workspaceName Name of the workspace you are creating
#' @param templateName Character(1). Name of the template workspace name you 
#' want to clone. You can provide \code{name} or \code{namespace/name}. 
#' @param analysis Character(1). Name of the analysis you want to clone 
#' it's workspace. The list of available analyses can be found using 
#' \code{\link{availableAnalysis}}.
#' @param bucketLocation Character(1). Region in which bucket attached to the
#' workspace should be created. Default is `us-central1`. For multi-region, 
#' enter `US`.
#' @param accountEmail Character(1). Email linked to Terra account
#' @param billingProjectName Character(1). Name of the billing project
#'
#' @return Name of the cloned workspace
#'
#' @examples
#' library(AnVILBase)
#' if (
#'     gcloud_exists() && identical(avplatform_namespace(), "AnVILGCP") &&
#'     nzchar(avworkspace_name())
#' ) {
#' cloneWorkspace(workspaceName = "salmon",
#'                templateName = "Bioconductor-Workflow-DESeq2")
#' }
#'  
#' @export
cloneWorkspace <- function(workspaceName, 
                           templateName = "",
                           analysis = NULL,
                           bucketLocation = "us-central1",
                           accountEmail = gcloud_account(), 
                           billingProjectName = gcloud_project()) {

    setCloudEnv(message = FALSE)
    
    ## Input validity check
    if (all(c(!nzchar(templateName), is.null(analysis)))) { # neither provided
        stop("Provide templateName or analysis arguments.")
    } else if (all(c(nzchar(templateName), !is.null(analysis)))) { # both provided
        stop("Provide only one argument: templateName or analysis") #<<<<< Update this only for conflict
    }
    
    ## Setup gcloud account/project
    setCloudEnv(accountEmail = accountEmail,
                billingProjectName = billingProjectName,
                message = FALSE)
    
    ## Get the WorkspaceNamespace and WorkspaceName of the template
    dir <- system.file("extdata", package = "AnVILWorkflow")
    map <- utils::read.table(file.path(dir, "map.tsv"), header = TRUE)
    
    if (!is.null(analysis)) { # using one of the curated/supported workspaces
        ind <- which(map$analysis == analysis)
        template_ws_namespace <- map$workspaceNamespace[ind]
        template_ws_name <- map$workspaceName[ind]
    } else if (!is.null(templateName)) {
        res <- .get_workspace_fullname(templateName)
        template_ws_namespace <- unlist(strsplit(res, "/"))[1]
        template_ws_name <- unlist(strsplit(res, "/"))[2]
    }

    ## Clone the workspace
    res <- try(avworkspace_clone(namespace = template_ws_namespace,  
                                 name = template_ws_name,  
                                 to_namespace = billingProjectName,
                                 to_name = workspaceName,
                                 bucket_location = bucketLocation),
               silent = TRUE)

    if (methods::is(res, "try-error")) {
        return(message(res))
    } else {
        msg <- paste(res, "is succesfully created.")
        message(msg)
    }
}