R/validateBarCodes.R

In mariodejung/samplesubmission: Sample Submission User Web Interface

#' performs a validation check on the barcodes fields
#' @param inputs isolated input list
#' @param pattern regex pattern to be matched the barcodes
#' @return list of validation results
#' @seealso Validated
#' @examples
#' \dontrun{
#' validateBarCodes(isolate(reactiveValuesToList(input)))
#' }
validateBarCodes <- function(inputs, pattern="^IMB_\\w+_\\d{3,5}$") {
  results <- list()

  #barcode_acid
  #barcode_trypsin
  #barcode_protease
  
  if(!inputs$group=="EXT_CF"){
    if(inputs$barcode_trypsin == '' && inputs$barcode_protease == '') {
      results[[length(results) + 1]] <- Validated("barcode_trypsin",
                                                  valid=FALSE,
                                                  message='At least one enzyme needed')
      results[[length(results) + 1]] <- Validated("barcode_protease",
                                                  valid=FALSE,
                                                  message='At least one enzyme needed')
      
    }else{
      barcodes <- grep("barcode", names(inputs), value=TRUE)
      barcodes_filt <- barcodes[inputs[barcodes] != '']
      for(barcode in barcodes_filt){
        if( !grepl(pattern, inputs[barcode])){
          results[[length(results) + 1]] <- Validated(barcode,
                                                      valid=FALSE,
                                                      message='Don\'t meet the required format')
        }
        if(sum(match(inputs[barcodes_filt], inputs[barcode], nomatch=0))>1){
          results[[length(results) + 1]] <- Validated(barcode,
                                                      valid=FALSE,
                                                      message='Barcode used twice')
        }
      }
    }
  }

  return(results)
}