R/Info_manager.R

In raphidoc/lighthouse: Database management and processing workflow for ocean optics science

#' @export
#' @import Cops
#' @import dplyr
#' @import lubridate
#' @import stringr

#library(data.table)

cops_info_manager <- function(project, field= "", to= "", mindate= "yyyy-mm-dd", maxdate="yyyy-mm-dd", Boat=c("")) {

  L2 <- file.path(project, "L2")
  dirs = grep("/COPS(_[[:alpha:]]+)?$",list.dirs(L2), value = T)
  #dirdats <- scan(file = "directories.for.cops.dat", "", sep = "\n", comment.char = "#")

  # create a filter based on date
  #(useful on multi year project where differences occur in data collection)
  mindate <- NULL
  maxdate <- NULL

  # Check field paramter
  field <- as.character(field)
  if (!any(field == c("file", "lon", "lat", "chl", "timwin", "ssrm", "tiltm", "smoo", "b1", "b2", "b3", "b4"))) {
    stop("field does not match any exsisting field.
Only the following are accepted: lat, lon, chl, timwin, ssrm, tiltm, smoo")
  }

  to <- as.character(to)

  if (Sys.getenv("R_COPS_DATA_DIR") == ""){stop("R_COPS_DATA_DIR from package Cops, is not set")}

  header.info.file <- file.path(Sys.getenv("R_COPS_DATA_DIR"), "info.header.dat")

  for(i in dirs) {
    if(!file.exists(i)) {
        cat(i, "does not exist")
        next()
    }
    # message(paste0("PROCESSING DIRECTORY:", dirs))

    #look if absorption file empty, if so go to next iteration
    if(field=="chl" && to == "0"){

      abs <- data.table::fread(file= file.path(i, "absorption.cops.dat"), header= T)

      if(abs[[2]][1] == "a1"){
        message(paste(i, "No absorption values", sep= "   "))
        next()
      }
    }

    info.file <- file.path(i, "info.cops.dat")
    info.tab <- read.table(info.file,
                           colClasses = c(
                             "character", "numeric", "numeric", "numeric",
                             "character", "character", "character", "character",
                             "character", "character", "character", "character"),
                           col.names = c("file", "lon", "lat", "chl", "timwin", "ssrm", "tiltm", "smoo", "b1", "b2", "b3", "b4"),
                           header = FALSE, fill = TRUE, sep = ";")

    info.tab[[field]] <- to
    message(paste(i, "modified", sep = "   "))

    info.tab
    file.copy(from = header.info.file, to = info.file, overwrite = T)
    write.table(info.tab, file = info.file , append = T, quote = F, sep = ";", dec = ".",
                row.names = F, col.names = F)
  }
}