R/runBenchmark.R

In psolaimani/benchmaRk: Benchmark/Profiling for R Scripts

#' runBenchmark
#' @description This function extracts benchmark information, and downloads the necessary data/packages. 
#' @usage runBenchmark(runs, loc.src, dcf, timedFunFile, bench_log, warn_log)
#' @usage runBenchmark()
#' @param runs number of runs for warming up. After warmup runs the workflow
#' will be runned one more time for timing perpose. Default is 0.
#' @param loc.src location of CRAN like repository containing the source code
#' of used package versions. Default is NULL.
#' @param dcf information about workflows name and description and 
#' datafile name, download location, md5hash in Debian Control Format. Default
#' is BENCHMARK.dcf
#' @param timedFunFile file with functions to be profiled. Default is
#' FUNCTION.PROFILE
#' @param bench_log filename to use to store message/warning/errors.
#' Default is "benchmark.log"
#' @param warn_log level of logging to use (choose from -1, "INFO", "WARN", 
#' "STOP". Default value is -1.
#' @import rlogging
#' @export
runBenchmark <- function(        runs = 0, 
                              loc.src = NULL, 
                                  dcf = "BENCHMARK.dcf",
                         timedFunFile = "FUNCTION.PROFILE", 
                            bench_log = "benchmark.log",
                             warn_log = c(-1,"INFO","WARN","STOP")){
  
  # configure logging of the benchmark progress
  wd <- normalizePath("./")
  SetLogFile(base.file = bench_log, folder = wd)
  log_arg <- match.arg(warn_log)
  switch(log_arg,
         "-1" = options(warn = -1),
         "INFO" = options(warn = "INFO"),
         "WARN" = options(warn = "WARN"),
         "STOP" = options(warn = "STOP"),
         options(warn = -1)
         )
  
  # check if correct datasets are present and otherwise download
  isPresent <- function(Name, Hash, Source){
    File <- file.path(Name)
    message(sprintf("processing: %s", File))
    if (file.exists(File) == FALSE) {
      warning(sprintf("%s doesn't exist.\n", Name ))
      n = 1
      Try = TRUE
      while (n < 4 & Try == TRUE){
        message(sprintf("Downloading file. Try %i out of 3...", n))
        try(download.file(Source, File), TRUE)
        n <- n + 1
        if (file.exists(File) == TRUE){ 
          fHash <- tools::md5sum(File)
          if(fHash == Hash) { 
            Try <- FALSE 
          }
        }
      }
      
      if (file.exists(File) == FALSE) {
        warning(sprintf("Couldn't download %s.\n", Name))
        return("ERROR")
      }
      
      fHash <- tools::md5sum(File)
      if ( fHash != Hash ){
        warning(sprintf("%s md5sum is still incorrect\nPlease correct dcf info.\n", Name))
        return("ERROR")
      } else {
        return("READY")
      }
      
    } else {
      fHash <- tools::md5sum(File)
      if (fHash != Hash){
        warning(sprintf("%s has incorrect md5sum!\n", File))
        try(file.remove(File),TRUE)
        n=1
        Try=TRUE
        while (n < 4 & Try == TRUE){
          message( sprintf("Downloading and overwriting file. Try %i out of 3...", n) )
          try(download.file(Source, File), TRUE)
          n <- n + 1
          if (file.exists(File) == TRUE){ 
            fHash <- tools::md5sum(File)
            if(fHash == Hash) { 
              Try <- FALSE 
              message(sprintf("Download %s completed.", Name))
            }
          }
        }
        fHash <- tools::md5sum(File)
        if (fHash != Hash){
          warning(sprintf("%s md5sum is still incorrect\nPlease correct dcf info.\n", Name))
          return("ERROR")
        } else {
          return("READY")
        }
      } else {
        message(sprintf("md5sum data file is correct.", Name))
        return("READY")
      }
    }
  }
  
  Name        <- na.omit(read.dcf(dcf, fields = c('Name')))[1]
  Description <- na.omit(read.dcf(dcf, fields = c('Description')))[1]
  File        <- na.omit(read.dcf(dcf, fields = c('File')))
  Source      <- na.omit(read.dcf(dcf, fields = c('Source')))
  Hash        <- na.omit(read.dcf(dcf, fields = c('Hash')))
  
    
  if (length(File) > 0) {
    Prepare_data <- mapply(isPresent, File, Hash, Source)
    if (any(as.vector(Prepare_data) == "ERROR")){
      warning("\nCheck data: datasets not correct/complete!\n")
    } else {
      message("\nCheck data: correct datasets available.")
    }
  } else {
    message("\nBenchmark doesn't contain datasets.")
  }
  
  # Get R script filename
  file_name  <- paste0(tail(strsplit(wd,"/")[[1]],n=1),".R")
  bench_file <- file.path(wd, file_name)
  
  # Read profiling information if available
  if (file.exists(timedFunFile)) {
    timed_fun <- read.table(timedFunFile, stringsAsFactors = FALSE)
  } else {
    timed_fun <- NULL
  }
  
  # benchmark R script with/without profiler
  benchmarkSource(file = bench_file, timed_fun = timed_fun, runs = runs, loc.src = loc.src)
  
}