R/DBnormStations.R

In nicolasfstgelais/dbExtract:

#' @export
DBnormStations<- function(inputFile = "dbInputStations.csv")
{

  # inputs----

  # input
  input = LtoC(read.csv(paste0("raw/inputs/",inputFile),na.strings = ""))

  for(i in 1:nrow(input)){


    #if(file.exists(paste0(input$name[i],"_norm.csv"))){next}


    sheetTemp = do.call(rbind, strsplit(LtoC(input[i, "sheet"]), ";"))
    if(!is.na(sheetTemp)){if(sheetTemp=="NA"){sheetTemp=NA}}
    lineSkip=input[i, "lineSkip"]
    fileType=input[i, "type"]

    if(length(grep("csv",LtoC(input[i, "path"])))!=0){fileType="csv"}
    if(length(grep("xl",LtoC(input[i, "path"])))!=0){fileType="xls"}

    # For xlsx if multiple sheets need to be rbind, sep = ';' and the
    # columns of the first sheet are used in the rbind
    # time the loop

    #log input
    fileName=paste0("logs/",as.character(Sys.Date()),".log")
    cat(as.character(Sys.time()), file=fileName, append=T, sep = "\n")


    time=gsub(" EDT","",gsub(" ","_",Sys.time()))

    if (fileType == "xls") {
      first = T
      for (w in sheetTemp) {
        if (!is.na(w)) {
          sheet = w
        } else {
          sheet = 1
        }
        if (first)
        {

          db = readxl::read_excel(paste( LtoC(input[i, "path"]),sep=""), sheet = sheet,skip = input$lineSkip[i])}
        if (!first)
        {db = rbind(db, readxl::read_excel(paste( LtoC(input[i, "path"]), sep = ""), sheet = sheet,skip = input$lineSkip[i])[, colnames(db)])}
        first = F
      }
    }

    if (fileType == "csv")
    {db = read.csv(paste( LtoC(input[i, "path"]), sep = ""),
                   1 ,skip = input$lineSkip[i],na.strings = c("", "NA"),stringsAsFactors = F)}

    db=as.data.frame(db)




    # this is for db with only one
    if (is.na(input[i, "stationID"]) | input[i, "stationID"] == "NA") {
      db$stationId = "A"
      stationId = "stationId"
    } else {
      stationId = LtoC(input[i, "stationID"])
    }

    dateId=input$dateID[i]


    #norm colnames
    colnames(db)[which(colnames(db)==input$stationID[i])]="station"
    colnames(db)[which(colnames(db)==input$latitude[i])]="latitude"
    colnames(db)[which(colnames(db)==input$longitude[i])]="longitude"



    if(i==1)dbMerged=db[,c("station","latitude","longitude")]
    if(i!=1)dbMerged=rbind(dbMerged,db[,c("station","latitude","longitude")])

  }
  write.csv(x = dbMerged,paste0("data/stations_norm.csv"),row.names = F)
}