R.Version()$version.string 

librariesVersion <- c()

for(i in 1:length(libraries))
    librariesVersion <- c(librariesVersion, paste(packageVersion(libraries[i] )))

librariesLoaded <- lapply(libraries, require, character.only = TRUE) 

timeNeeded <- (proc.time()[3] -  source.starting.time);

sourceTimeNeeded <- c( sourceTimeNeeded, timeNeeded)


source.starting.time <- proc.time()[3]


## Base functions

# @authors kp@eworx.gr ako@eworx.gr
repository <- "/data/generic/"

getSourcePath <- function(filename, baseFolder = repository){
    return(paste(baseFolder, filename, sep = ""))
}

readData <- function(filename, colClasses = c(), baseFolder = repository, header = TRUE, sep = "\t", encoding = "UTF-8", stringsAsFactors = TRUE, na.strings = c("", "NULL"), verbose = FALSE){
    if(length(colClasses) == 0)
        return (data.table::fread(input = getSourcePath(filename, baseFolder), header = header, sep = sep, encoding = encoding, stringsAsFactors = stringsAsFactors, verbose = verbose, showProgress = TRUE, na.strings = na.strings ) )
    return (data.table::fread(input = getSourcePath(filename, baseFolder), colClasses = colClasses, header = header, sep = sep, encoding = encoding, verbose = verbose, showProgress = TRUE,   na.strings = na.strings )  )
}

#rds for small disk space & fst for fast load
saveBinary <- function(data, filename = filename, baseFolder = repository, format = "rds"){
  if(format == "rds"){saveRDS(data, getSourcePath(filename, baseFolder))}
  if(format == "fst"){fst::write_fst(data, getSourcePath(filename, baseFolder))}
}

#rds for small disk space & fst for fast load
loadBinary <- function(filename, baseFolder = repository, format = "rds", as.data.table = TRUE){
  if(format == "rds"){return(readRDS(getSourcePath(filename, baseFolder)))}
  if(format == "fst"){return(fst::read_fst(getSourcePath(filename, baseFolder), as.data.table = as.data.table))}
}

rowColumns <- function(data){
    return(paste( format(nrow(data),  big.mark=","), "Rows X ", ncol(data), "Columns"))
}

publishIncludeCss <- function(){
    sourceFile <- "/data/jobs/wp41.analysis/000.core/include.css"
    destinatinoFile <- "/data/tmpfs/results/include.css"
    if (!file.exists(destinatinoFile)) {
        return (file.copy(sourceFile, destinatinoFile))
    }else{
        return(TRUE);
    }

}
#as the mountstorage is on memory make sure the asset include.css is there.

summariseTable <- function(data){
    return(data.frame(unclass(summary(data)), check.names = FALSE, stringsAsFactors = FALSE))
    #return(do.call(cbind, lapply(data, summary)))
}

factoriseCharacterColumns <- function(data){
    for(name in names(data)){
        if( class(data[[name]]) =="character"){
            data[[name]] <- as.factor(data[[name]])
        }
    }
    return(data) 
}

############################
# https://rstudio.github.io/DT/010-style.html
#https://rpubs.com/marschmi/RMarkdown

capitalise <- function(x) paste0(toupper(substring(x, 1, 1)), substring(x, 2, nchar(x)))


styliseDTNumericalColumn <- function(data, result, columnName, color, columnsName_original ){

    if(columnName%in% columnsName_original){
        result <- result %>%   formatStyle(
            columnName,
            background = styleColorBar(data[[columnName]], color),
            backgroundSize = '100% 90%',
            backgroundRepeat = 'no-repeat',
            backgroundPosition = 'center'
        )
    }
    return(result)

}


reportTabularData <- function(data){
    
    columnsName <- names(data)
    #columnsName <- lapply(columnsName, capitalise)
    columnsName_original <- names(data)

    result <-
        DT::datatable(
            data,
            class = 'cell-border stripe',
            filter = 'top',
            rownames = FALSE,
            colnames = columnsName,
            extensions = 'Buttons',
            options = list(
                pageLength = 20,
                columnDefs = list(list(className = 'dt-left', targets = "_all")),
                dom = 'Bfrtip',
                buttons = c('copy', 'csv', 'excel', 'pdf'),
                searchHighlight = TRUE,
                initComplete = JS(
                    "function(settings, json) {",
                        "$(this.api().table().header()).css({'border': '1px solid'});",
                    "}"
                )
            )

        )


    result <- styliseDTNumericalColumn(data,result, "Count", 'steelblue', columnsName_original)
    result <- styliseDTNumericalColumn(data,result, "sourceTimeNeeded", '#808080', columnsName_original)
    result <- styliseDTNumericalColumn(data,result, "timeNeeded", '#808080', columnsName_original)
    result <- styliseDTNumericalColumn(data,result, "percentMatch", '#4682b4', columnsName_original)

    return(result)
}

fonts <- list(
 sans = "DejaVu Serif",
  mono = "DejaVu Serif",
  `Times New Roman` = "DejaVu Serif"
)

cleanJsonId <- function(txt){
    txt <- gsub("\\.json", "", txt)
    gsub(".*/", "", txt)
}

embed_data <- function(x= mtcars, filename= "file.csv", label= "Get data"){

  # Create encoded Base64 datastream 
  encode_data= function(x){
    saveMe <- getSourcePath("file.csv")
    write.csv2(x, saveMe)
    enc= sprintf('data:text/csv;base64,%s', openssl::base64_encode(paste0(readLines(saveMe), collapse="\n")) )
    unlink(saveMe)
    return(enc)
  }

  # String result ready to be placed in rmarkdown
  paste0("<a download='", filename, "' href=", encode_data(x), ">", label, "</a>")

}

###########################################################################################################

if(exists("libraries")){
    data.table(library = libraries, version = librariesVersion)
}

includeCssPublished <- publishIncludeCss()

sessionInfo()

timeNeeded <- (proc.time()[3] -  source.starting.time);

sourceTimeNeeded <- c( sourceTimeNeeded, timeNeeded)


source.starting.time <- proc.time()[3]

reportTabularData(source.blocks);