#!/usr/bin/env Rscript

## Package
##--------

library(RUnit)

## Constants
##----------

testOutDirC <- "output"
argVc <- commandArgs(trailingOnly = FALSE)
scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)])


## Functions
##-----------

## Reading tables (matrix or data frame)
readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) {

    	file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\"."))

        switch(typeC,
               matrix = return(t(as.matrix(read.table(file = fileC,
                   header = TRUE,
                   row.names = 1,
                   sep = "\t",
                   stringsAsFactors = FALSE)))),
               dataframe = return(read.table(file = fileC,
                   header = TRUE,
                   row.names = 1,
                   sep = "\t",
                   stringsAsFactors = FALSE)))

}

## Call wrapper
wrapperCallF <- function(paramLs) {

    ## Set program path
    wrapperPathC <- file.path(dirname(scriptPathC), "..", "profia_wrapper.R")

    ## Set arguments
    argLs <- NULL
    for (parC in names(paramLs))
        argLs <- c(argLs, parC, paramLs[[parC]])

    ## Call
    wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ")

    print(wrapperCallC)

    if(.Platform$OS.type == "windows")
        wrapperCallC <- paste("Rscript", wrapperCallC)

    wrapperCodeN <- system(wrapperCallC)

    if (wrapperCodeN != 0)
        stop("Error when running profia_wrapper.R.")

    ## Get output
    outLs <- list()
    if ("dataMatrix_out" %in% names(paramLs))
        outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix")
    if ("sampleMetadata_out" %in% names(paramLs))
        outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe")
    if ("variableMetadata_out" %in% names(paramLs))
        outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe")
    if("information" %in% names(paramLs))
        outLs[["infVc"]] <- readLines(paramLs[["information"]])

    return(outLs)
}

## Setting default parameters
defaultArgF <- function(testInDirC) {

    defaultArgLs <- list()
    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")))
        defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")
    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")))
        defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")
    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")))
        defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")

    defaultArgLs[["dataMatrix_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "dataMatrix.tsv")
        defaultArgLs[["sampleMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "sampleMetadata.tsv")
    defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv")
    defaultArgLs[["figure"]] <- file.path(dirname(scriptPathC), testOutDirC, "figure.pdf")
    defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt")

    defaultArgLs

}

## Main
##-----

## Create output folder
file.exists(testOutDirC) || dir.create(testOutDirC)

## Run tests
test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$')
isValidTestSuite(test.suite)
test.results <- runTestSuite(test.suite)
print(test.results)