R/getting_started.r

In VertexWiseR: Simplified Vertex-Wise Analyses of Whole-Brain and Hippocampal Surface

#' @title Getting started with tutorials
#'
#' @description Guides the user through the various tutorials and assist with downloading the demo data
#'
#' @param demo_data A boolean object specifying whether to prompt user about downloading the demo data (default is TRUE)
#' @examples
#' getting_started()
#' @importFrom utils menu untar unzip vignette
#' @export
#' 
getting_started=function(demo_data=TRUE)
{
if (interactive()==TRUE) #only works in interactive session
{
  cat("Welcome to VertexWiseR's demo!\n")
  
  if (demo_data==TRUE)
  {
   prompt = utils::menu(title="Before starting, you may want to download the demo_data folder (~218 MB) used by the various tutorials. Would you like to download it now?",
     choices = c(paste0("Yes, in a temporary R directory (default path is tempdir())"),
                 paste0("Yes, in the current working directory (",getwd(),")"),
                 "Yes, let me type a path where it will go", 
                 "No"), 
  )
  if (prompt!=4) 
  {
    if (prompt==1) {out_dir=tempdir()}
    else if (prompt==2){out_dir=getwd()}
    else if (prompt==3)
    {out_dir <- readline("Enter the full path to the directory:")}
    
    demodata=dl_demo(path=out_dir)
  }
  }

  prompt_2 = utils::menu(title="\nAvailable tutorials (will open in Rstudio's Help panel):",
            choices = c("Extracting surface data in VertexWiseR", "Example analyses with VertexWiseR - Example 1", "Example analyses with VertexWiseR - Example 2"))
  if (prompt_2==1) { vignette(package='VertexWiseR', topic='VertexWiseR_surface_extraction')}
  else if (prompt_2==2) { vignette(package='VertexWiseR', topic='VertexWiseR_Example_1')}
  else if (prompt_2==3) { vignette(package='VertexWiseR', topic='VertexWiseR_Example_2')}

}
}

#' @title Demo data downloader
#'
#' @description Downloads all demo data used in the package's examples and vignettes at once.
#' @param path Path to which the demo data folder will be downloaded. Default is tempdir().
#' @param quiet A boolean stating whether to print the progress and outcome of the downloading. Default is FALSE.
#' @author Jörn Alexander Quent
#' @return A string containing the path to the downloaded demo_data folder
#' @examples
#' dl_demo()
#' @importFrom utils menu untar unzip vignette
#' @noRd

dl_demo=function(path=tempdir(), quiet=FALSE){
# Folder name
out_dir <- paste0(path,"/demo_data")

# Create demo_data directory if it doesn't exist
if (!dir.exists(out_dir)) {dir.create(out_dir)}

# GitHub repository URL
base_url <- "https://raw.githubusercontent.com/CogBrainHealthLab/VertexWiseR/refs/heads/main/inst/demo_data/"

files_to_download <- c(
  "FINK_Tv_ses13.rds",
  "FINK_behdata_ses13.rds",
  "SPRENG_CTv_site1.rds",
  "SPRENG_behdata_site1.rds",
  "fink_surf_data_hippunfold.zip",
  "spreng_surf_data_cat12.zip",
  "spreng_surf_data_fmriprep.zip",
  "spreng_surf_data_freesurfer.zip"
)

# Download each file
for (file in files_to_download) {
  if(!file.exists(paste0(out_dir,'/',file)))
  {
    # Construct raw GitHub URL (different from the tree URL)
    raw_url <- paste0(base_url, file)
    
    # Destination path
    dest_path <- file.path(out_dir, file)
    
    tryCatch({
      # Download the file
      if (quiet==FALSE)
      {
        download.file(url = raw_url, destfile = dest_path, mode = "wb")
        cat("Downloaded:", file, "\n")
      } else
      {
        download.file(url = raw_url, destfile = dest_path, mode = "wb",
                      quiet = TRUE)
      }
      
      # Check if file is a zip file and extract it
      if (grepl("\\.zip$", file, ignore.case = TRUE)) {
        #unzip or untar as unzip struggles with long paths
        zip_result <- suppressWarnings(try(unzip(zipfile = dest_path, exdir = out_dir), silent = TRUE))
        if (is.null(zip_result) | inherits(zip_result, "try-error")==TRUE) {untar(tarfile = dest_path, exdir = out_dir)}
        
        if (quiet==FALSE){cat("Unzipped:", file, "\n")}
      }
    }, error = function(e) 
    {
      if (quiet==FALSE){
      cat("Failed to download:", file, "\n");
      cat("Error:", e$message, "\n")}
    })
  }
}

if (quiet==FALSE){
cat("\nDownload and extraction process completed.\n")
cat("\nDemo files were saved in:", normalizePath(out_dir), "\n")
}

return(normalizePath(out_dir))
}