HARD/Validate/vaidate.R

In AshwinAgrawal16/BiodiversityGSoC17: Integrating biodiversity data curation functionality.

#Here config data contains all the Darwin core fields

validate <- function(data, config) {

  errors <- data.frame(id = character(), column = character(), message = character())

  # iterate over column names in configuration
  for (column in names(config)) {

    # check if dataset has column as in Darwin Core
    if (column %in% names(data)) {

      # iterate over tests for found column
      for (test in names(config[[column]])) {

        if (test != "if") {
          allowed_errors <- validate_any(data[[column]], test, config[[column]][[test]], data$occurrenceID)
          allowed_errors$column = column
          errors <- rbind(errors, allowed_errors)
        } else {
          # todo: conditional tests these include all the checks which acn be implemented by extending other packages.
         
        }

      }
    }
  }

  return(errors)
}



validate_any <- function(values, test, criteria, ids) {

  if (test == "allowed") {
    return(validate_allowed(values, criteria, ids))
  }

}





validate_allowed <- function(values, allowed, ids) {
  errors <- NULL

  for (i in 1:length(values)) {
    if (!values[i] %in% allowed) {
      errors <- rbind(errors, data.frame(id = ids[i], message = paste0("unallowed value ", values[i])))
    }
  }

  return(errors);
}



validate_type <- function(values, type, ids) {
  errors <- NULL

#Below to check the integer field
  if (type == "integer") {
    for (i in 1:length(values)) {
      if (!grepl("^[-]?[0-9]+$", as.character(values[i]))) {
        errors <- rbind(errors, data.frame(id = ids[i], message = paste0(values[i], " is not an integer")))
      }
    }
  } else if (type == "url") {
    for (i in 1:length(values)) {
      if (!grepl("^(http|https|ftp)://(?:[a-zA-Z]|[0-9]|[$-_@.&+]|[!*\\(\\),]|(?:%[0-9a-fA-F][0-9a-fA-F]))+$", as.character(values[i]))) {
        errors <- rbind(errors, data.frame(id = ids[i], message = paste0(values[i], " is not a url")))
      }
    }
  }
#Above to check the url field

  return(errors);
}