#!/usr/bin/env Rscript

# ----- PACKAGE -----
cat("\tSESSION INFO\n")

#Import the different functions
source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
source_local("lib.r")

pkgs=c("CAMERA","multtest","batch")
loadAndDisplayPackages(pkgs)
cat("\n\n");

# ----- ARGUMENTS -----
cat("\tARGUMENTS INFO\n")

args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
write.table(as.matrix(args), col.names=F, quote=F, sep='\t')

cat("\n\n");


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

#image is an .RData file necessary to use xset variable given by previous tools
load(args$image); args$image=NULL

cat("\n\n")


# ----- ARGUMENTS PROCESSING -----
cat("\tARGUMENTS PROCESSING INFO\n")

# Save arguments to generate a report
if (!exists("listOFargs")) listOFargs=list()
listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_annotatediff")]] = args

# We unzip automatically the chromatograms from the zip files.
if (!exists("zipfile")) zipfile=NULL
if (!exists("singlefile")) singlefile=NULL
rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, args)
zipfile = rawFilePath$zipfile
singlefile = rawFilePath$singlefile
args = rawFilePath$args
directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)


# Because so far CAMERA isn't compatible with the new XCMSnExp object
if (exists("xdata")){
    xset <- getxcmsSetObject(xdata)
}

cat("\n\n")


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

results_list=annotatediff(xset=xset,args=args,variableMetadataOutput="variableMetadata.tsv")
xa=results_list$xa
diffrep=results_list$diffrep
variableMetadata=results_list$variableMetadata

cat("\n\n")

# ----- EXPORT -----

cat("\tXSET OBJECT INFO\n")
print(xa)
cat("\n\n")

#saving R data in .Rdata file to save the variables used in the present tool
objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFargs","zipfile","singlefile")
save(list=objects2save[objects2save %in% ls()], file="annotatediff.RData")

cat("\n\n")

cat("\tDONE\n")