R/wells-parse.R

In jeffrey-stevens/across-the-lot: Across-the-lot testing of an ELISA plate production run

parse_wells_expr <- function(wells) {

  groups <- parse_groups_list(wells)

  # Clean this up a bit

  # Collect together the ungrouped wells
  ungrouped <-
    groups %>%
    plyr::ldply(function(gr) {
      type <- gr$type
      df <- gr$df

      if (is.null(df) || identical(nrow(df), 0L)) {
        return(NULL)
        # Single grouped wells are equivalent to single ungrouped wells
      } else if (identical(type,"Ungrouped") ||
                 identical(nrow(df), 1L)) {
        return(df)
      } else {
        return(NULL)
      }
    })

  ungrouped <-
    if (!identical(nrow(ungrouped), 0L)) {
      ungrouped <-
        ungrouped %>%
        unique() %>%
        arrange(Row, Column)  # Is this desirable?
    } else {
      ungrouped <- NULL
    }


  # Now the grouped wells:
  grouped <-
    lapply(groups,
      function(gr) {
        type <- gr$type
        descr <- gr$descr
        df <- gr$df

        if (is.null(df) || identical(nrow(df), 0L)) {
          return(NULL)
        } else if (identical(type, "Grouped") &&
                    !identical(nrow(df), 1L)) {
          return(list(descr=descr, df=df))
        }
    })

  grouped <- Filter(function(gr) !is.null(gr), grouped)

  return(list(ungrouped=ungrouped, grouped=grouped))
}


parse_groups_list <- function(text) {
  text <- stringr::trim(text)
  pat <- "^((\\(([^\\(\\)]*)\\))|([^,\\(\\)]*))(,(.*))?$"
  mat <- stringr::match(text, pat)

  if (is.na(mat[[1]])) {
    warning("Invalid wells specification.")
    groups_list <- list(NULL)
  }

  paren <- stringr::trim(mat[[3]])
  grouped <- stringr::trim(mat[[4]])
  ungrouped <- stringr::trim(mat[[5]])
  rest <- stringr::trim(mat[[7]])

  if (!identical(ungrouped, "")) {
    # This is an ungrouped item
    group <-
        list(type="Ungrouped",
             descr=ungrouped,
             df=parse_well_range(ungrouped))
  } else if (!identical(grouped, "")) {
    group <-
      list(type="Grouped",
           descr=grouped,
           df=parse_well_range(grouped))
  } else {
    warning("Invalid wells specification.")
    groups_list <- list(NULL)
  }

  if (!identical(rest, "")) {
    groups_list <-
      c(list(group), parse_groups_list(rest))
  } else {
    groups_list <- list(group)
  }

  return(groups_list)
}


parse_well_range <- function(text) {
  rng_df <- select_wells(text)
  return(rng_df)
}


parse_ungrouped_range_list <- function(text) {

  rng_df <- select_wells(text)

  return(rng_df)
}


row_to_int <- function(row) {
  stopifnot(identical(mode(row), "character"),
            identical(nchar(row), 1L),
            row %in% LETTERS[1:8])

  row_int <-
    chartr(paste0(LETTERS[1:8], collapse=""),
         paste0(1:8, collapse=""), row)

  return(as.integer(row_int))
}