R/parseErrors.R

In metadevpro/traitbaser: R package providing API access to Traitbase https://www.traitbase.info

#' @name parseErrors
#'
#' @title Helper function to parse errors from validateDataset().
#'
#' @description Transform the hard to read output of validateDataset() in
#' a useful format.
#'
#' @param errors Output of validateDataset()
#'
#' @return list of errors (err) and lines where encountered (tax).
#'
#' @examples
#' # not run
#'
#' @export
parseErrors <- function(errors) {
    if (errors$valid) {
        message("This dataset is valid")
    } else {
        message("This dataset is NOT valid")
    }
    if (length(errors$warnings) > 0) {
        temp <- unlist(errors$warnings, use.names = FALSE)
        message(temp[seq(2, length(temp), 2)])
    }
    if (length(errors$errors) > 0) {
        temp <- unlist(errors$errors, use.names = FALSE)
        err <- temp[seq(2, length(temp), 2)]
        cod <- temp[seq(1, length(temp), 2)]
        taxonomy <- err[which(cod == "402")]
        tax <- as.numeric(substr(taxonomy, regexpr("at line", taxonomy) +
            7, nchar(taxonomy))) - 1  #to remove header, which is line 1
        ambigous <- err[which(cod == "401")]
        amb <- as.numeric(substr(ambigous, regexpr("at line", ambigous) +
                                     7, nchar(ambigous))) - 1  #to remove header, which is line 1
        list(errors = err, lines_unrecognized_taxa = tax, lines_ambigous_taxa = amb)
    }
}


# #two functions we may not need once in a proper server.
# validate_sliced <- function(cnx, d){ if(length(unique(d$species)) >
# 50){ errors <- list() cuts <- seq(1,nrow(d),50) cuts[length(cuts)+1]
# <- nrow(d) for(i in 1:(length(cuts)-1)){ insert <-
# d[cuts[i]:cuts[i+1],] errors[[i]] <- validateDataset(cnx, insert)
# #awefull format.  } } else { errors <- validateDataset(cnx, d) }
# errors } import_sliced <- function(cnx, d){
# if(length(unique(d$species)) > 50){ errors <- list() cuts <-
# seq(1,nrow(d),50) cuts[length(cuts)+1] <- nrow(d) for(i in
# 1:(length(cuts)-1)){ insert <- d[cuts[i]:cuts[i+1],] errors[[i]] <-
# importDataset(cnx, insert) #not working because name gets duplicated
# } } else { errors <- importDataset(cnx, d) } errors }