R/check_unique_valid_haul.r

In RoME: Multiple Checks on MEDITS Trawl Survey Data

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#   RoME: R code to perform multiple checks on MEDITS Survey data (TA, TB, TC and TE files)                                #
#   Authors: I. Bitetto, W. Zupa, M.T. Spedicato                                                                           #
#   Coispa Tecnologia & Ricerca - Stazione sperimentale per lo Studio delle Risorse del Mare                               #
#   If you have any comments or suggestions please contact the following e-mail address: bitetto@coispa.it, zupa@coispa.it #
#   January 2022                                                                                                           #
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# Among hauls with the same code only one must be valid




check_unique_valid_haul<-function(ResultDataTA,year,wd,suffix){
  Format="from_2012"

  if (!file.exists(file.path(wd, "Logfiles"))){
    dir.create(file.path(wd, "Logfiles"), recursive = TRUE, showWarnings = FALSE)
  }
  if (!file.exists(file.path(wd,"Graphs"))){
    dir.create(file.path(wd, "Graphs"), showWarnings = FALSE)
  }
  if (!exists("suffix")){
    suffix=paste(as.character(Sys.Date()),format(Sys.time(), "_time_h%Hm%Ms%OS0"),sep="")
  }
  numberError = 0
  Errors <- file.path(wd,"Logfiles",paste("Logfile_",suffix,".dat",sep=""))
  if (!file.exists(Errors)){
    file.create(Errors)
  }

  ### FILTERING DATA FOR THE SELECTED YEAR
  arg <- "year"
  if (!exists(arg)) {
    stop(paste0("'", arg, "' argument should be provided"))
  } else if (length(year) != 1) {
    stop(paste0("only one value should be provided for '", arg, "' argument"))
  } else if (is.na(year)) {
    stop(paste0(arg, " argument should be a numeric value"))
  }
  ResultDataTA <- ResultDataTA[ResultDataTA$YEAR == year, ]
  ########################################

  Result = ResultDataTA # read.csv(paste(DataTA,".csv",sep=""), sep=";", header=TRUE)
  write(paste("\n----------- check uniqueness of valid hauls TA - ",Result$YEAR[1]), file = Errors, append = TRUE)


  #channelTA <- odbcConnectExcel(paste(DataTA,".xls", sep = ""))

  #queryHauls= "SELECT HAUL_NUMBER, count(*) as no_hauls from Result where HAUL_NUMBER is not null group by HAUL_NUMBER"

  ResultTA= aggregate(Result$HAUL_NUMBER, by=list(Result$HAUL_NUMBER),FUN="length")
  colnames(ResultTA)=c("HAUL_NUMBER","no_hauls")
  #ResultTA=sqldf(queryHauls)

  moreThanOneHaul = which(ResultTA$no_hauls > 1, arr.ind=TRUE)

  if (length(moreThanOneHaul)>0){
    j=1
    for (j in 1:length(moreThanOneHaul)){
      index= moreThanOneHaul[j]

      ResultCheck=Result[Result$HAUL_NUMBER==ResultTA$HAUL_NUMBER[index] & Result$VALIDITY=="V",]

      if (nrow(ResultCheck)>1)   {
        write(paste("Haul",ResultTA$HAUL_NUMBER[index],": only one row for the haul is allowed to be VALID"), file = Errors, append = TRUE)
        numberError = numberError +1
      }
    }
  }
  #odbcClose(channelTA)

  if (numberError ==0) {
    write(paste("No error occurred"), file = Errors, append = TRUE)
  }
#    if (file.exists(file.path(tempdir(), "Logfiles"))){
#   unlink(file.path(tempdir(),"Logfiles"),recursive=T)
#   }
#   if (file.exists(file.path(tempdir(), "Graphs"))){
#   unlink(file.path(tempdir(),"Graphs"),recursive=T)
#     }
# 	if (file.exists(file.path(tempdir(), "files R-Sufi"))){
#   unlink(file.path(tempdir(),"files R-Sufi"),recursive=T)
#     }
  if (numberError ==0) {
    return(TRUE)
  } else { return(FALSE) }

}

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