#!/usr/bin/env Rscript

library(batch) ## parseCommandArgs

argVc <- unlist(parseCommandArgs(evaluate=FALSE))

##------------------------------
## Initializing
##------------------------------


## libraries
##----------

suppressMessages(library(proFIA))


## constants
##----------

modNamC <- "proFIA" ## module name


## log file
##---------

sink(argVc["information"])

cat("\nStart of the '", modNamC, "' Galaxy module call: ",
    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")


## arguments
##----------


if("zipfile" %in% names(argVc)) {
    
    zipfile <- argVc["zipfile"]

    ## We unzip automatically the raw files from the zip file
    
    if(exists("zipfile") && (zipfile!="")) {
        if(!file.exists(zipfile)){
            error_message=paste("Cannot access the Zip file:", zipfile)
            print(error_message)
            stop(error_message)
        }

        ## unzip

        suppressWarnings(unzip(zipfile, unzip="unzip"))
        
        ## get the directory name
        
        filesInZip=unzip(zipfile, list=T);
        directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
        directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
        directory = "."
        if (length(directories) == 1) directory = directories
        
        cat("files_root_directory\t",directory,"\n")
        
    }

} else if ("library" %in% names(argVc)) {

    directory <- argVc["library"]
    
    if(!file.exists(directory)) {
        
        error_message=paste("Cannot access the directory:", directory,". Please check that the directory really exists.")
        print(error_message)
        stop(error_message)
        
    }
    
} else {

    error_message <- "No zipfile nor input library available"
    print(error_message)
    stop(error_message)

}

##------------------------------
## Computations
##------------------------------


optWrnN <- options()$warn
options(warn = -1)

stpI <- 1

cat("\n", stpI, ") Peak detection step ('proFIAset'):\n", sep = "")

fiaset <- proFIAset(directory,
                    ppm = as.numeric(argVc["ppmN"]),
                    parallel = TRUE)

stpI <- stpI + 1

cat("\n", stpI, ") Peak alignment ('group.FIA'):\n", sep = "")

fiaset <- group.FIA(fiaset,
                    ppmGroup = as.numeric(argVc["ppmGroupN"]),
                    fracGroup = as.numeric(argVc["fracGroupN"]))

stpI <- stpI + 1

cat("\n", stpI, ") Creating the peak table ('makeDataMatrix'):\n", sep = "")

fiaset <- makeDataMatrix(fiaset,
                         maxo = FALSE)

stpI <- stpI + 1

kI <- as.integer(argVc["kI"])

if(kI > 0) {

    cat("\n", stpI, ") Imputing missing values ('imputeMissingValues.WKNN_TN'):\n", sep = "")

    fiaset <- imputeMissingValues.WKNN_TN(fiaset,
                                          k = kI)

    stpI <- stpI + 1
}

options(warn = optWrnN)


##------------------------------
## Ending
##------------------------------


## Plotting
##---------

cat("\n", stpI, ") Plotting ('plot'):\n", sep = "")

pdf(argVc["figure"])

plot(fiaset)

dev.off()

stpI <- stpI + 1

## Printing
##---------

cat("\n", stpI, ") Printing ('show'):\n", sep = "")

fiaset

stpI <- stpI + 1

## Exporting
##----------

cat("\n", stpI, ") Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'):\n", sep = "")

datMN <- exportDataMatrix(fiaset)
samDF <- exportSampleMetadata(fiaset)
varDF <- exportVariableMetadata(fiaset)

if(nrow(datMN) == nrow(samDF) && ncol(datMN) == nrow(varDF)) {
    datDF <- as.data.frame(t(datMN))
} else {
    datDF <- as.data.frame(datMN)
}
rownames(varDF) <- rownames(datDF)

datDF <- cbind.data.frame(dataMatrix = rownames(datDF),
                          datDF)
write.table(datDF,
            file = argVc["dataMatrix_out"],
            quote = FALSE,
            row.names = FALSE,
            sep = "\t")

samDF <- cbind.data.frame(sampleMetadata = samDF[, "sampleID"],
                          class = samDF[, "class"])
write.table(samDF,
            file = argVc["sampleMetadata_out"],
            quote = FALSE,
            row.names = FALSE,
            sep = "\t")

varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
                          varDF)
write.table(varDF,
            file = argVc["variableMetadata_out"],
            quote = FALSE,
            row.names = FALSE,
            sep = "\t")


## Closing
##--------

cat("\nEnd of '", modNamC, "' Galaxy module call: ",
    as.character(Sys.time()), "\n", sep = "")

sink()

rm(list = ls())