#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
# probmetab.r version="1.0.0"
# Author: Misharl Monsoor ABIMS TEAM mmonsoor@sb-roscoff.fr


# ----- LOG -----
log_file=file("log.txt", open = "wt")
sink(log_file)
sink(log_file, type = "out")

# ----- PACKAGE -----
cat("\tPACKAGE INFO\n")
pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "igraph", "xcms","snow","CAMERA","batch","ProbMetab")
for(p in pkgs) {
    suppressWarnings( suppressPackageStartupMessages( stopifnot( library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE))))
    cat(p,"\t",as.character(packageVersion(p)),"\n",sep="")
}

source_local <- function(fname){
    argv <- commandArgs(trailingOnly = FALSE)
    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
    source(paste(base_dir, fname, sep="/"))
}

options(bitmapType='cairo')

cat("\n\n")


# ----- ARGUMENTS -----
cat("\tARGUMENTS INFO\n")
listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')



# ----- PROCESSING INFILE -----
cat("\tINFILE PROCESSING INFO\n")

# ----- INFILE PROCESSING -----

if(listArguments[["mode_acquisition"]]=="one") {
    load(listArguments[["image"]])
    cat("\t\tXA OBJECT INFO\n")
    print(xa)

    source_local("lib.r")
    if (!exists("zipfile")) zipfile=NULL
    if (!exists("singlefile")) singlefile=NULL
    rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments)
    zipfile = rawFilePath$zipfile
    singlefile = rawFilePath$singlefile
    retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)

    if (!exists("variableMetadata")) variableMetadata= getVariableMetadata(xa);

} else if(listArguments[["inputs_mode"]]=="two"){

    # POSITIVE
    load(listArguments[["image_pos"]])

    if (!exists("xa")) xaP=xsAnnotate_object
    else xaP=xa
    cat("\t\tXA-POSITIVE OBJECT INFO\n")
    print(xaP)

    if (!exists("variableMetadata")) variableMetadataP = getVariableMetadata(xa)
    else variableMetadataP = variableMetadata

    source_local("lib.r")
    if (!exists("zipfile")) zipfile=NULL
    if (!exists("singlefile")) singlefile=NULL
    rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments)
    zipfilePos = rawFilePath$zipfile
    singlefilePos = rawFilePath$singlefile
    retrieveRawfileInTheWorkingDirectory(singlefilePos, zipfilePos)

    # NEGATIVE
    load(listArguments[["image_neg"]])

    if (!exists("xa"))  xaN=xsAnnotate_object
    else xaN=xa
    cat("\t\tXA-NEGATIVE OBJECT INFO\n")
    print(xaP)

    if (!exists("variableMetadata")) variableMetadataN = getVariableMetadata(xa)
    else variableMetadataN = variableMetadata

    source_local("lib.r")
    if (!exists("zipfile")) zipfile=NULL
    if (!exists("singlefile")) singlefile=NULL
    rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments)
    zipfileNeg = rawFilePath$zipfile
    singlefileNeg = rawFilePath$singlefile
    retrieveRawfileInTheWorkingDirectory(singlefileNeg, zipfileNeg)
}

#Import the different functions
source_local("lib.r")
source_local("export.class.table-color-graph.R")

# ----- PROCESSING INFO -----
cat("\tMAIN PROCESSING INFO\n")

if(listArguments[["mode_acquisition"]]=="one") {
    results=probmetab(xa=xa, variableMetadata=variableMetadata,listArguments=listArguments)
} else if(listArguments[["inputs_mode"]]=="two"){
    results=probmetab(xaP=xaP, xaN=xaN,variableMetadataP=variableMetadataP, variableMetadataN=variableMetadataN, listArguments=listArguments)
}
#delete the parameters to avoid the passage to the next tool in .RData image
#rm(listArguments)
cat("\tDONE\n")
#saving R data in .Rdata file to save the variables used in the present tool
#save.image(paste("probmetab","RData",sep="."))