tests/testthat/test_carnival_simplest_case.R

In saezlab/CARNIVAL: A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

#TODO 
waitingForFix = TRUE
if(! waitingForFix){
    #library(CARNIVAL)
    
    files.sources = list.files("/Users/olgaivanova/GoogleDrive/_PhD_Heidelberg/playground/carnival_style/carnival/R", full.names=T)
    sapply(files.sources, function(x) {
        print(x)
        source(x)
    })
    
    test_networks_folder <- "../test_networks"
    #TODO 
    test_networks_folder <- "/Users/olgaivanova/GoogleDrive/_PhD_Heidelberg/playground/carnival_style/carnival/tests/test_networks"
    
    simplest_network_file <- file.path(test_networks_folder, "direct_network.sif")
    simplest_network_measurements_files <- file.path(test_networks_folder, "direct_network_measurements.csv")
    simplest_network_perturbations_file <- file.path(test_networks_folder, "direct_network_perturbations.csv")
    
    simplest_network <- read.table(simplest_network_file, header=T)
    simplest_network_measurements <- read.table(simplest_network_measurements_file, header=T)
    simplest_network_perturbations <- read.table(simplest_network_perturbations_file, header=T)
    
    # # get input data
    # load(file = system.file("toy_inputs_ex1.RData",
    #                         package="CARNIVAL"))
    # load(file = system.file("toy_measurements_ex1.RData",
    #                         package="CARNIVAL"))
    # load(file = system.file("toy_network_ex1.RData",
    #                         package="CARNIVAL"))
    
    # get expected result
    load(file = system.file("result_expected.RData",
                            package="CARNIVAL"))
    
    # obtain actual reesult
    result_actual = runCARNIVAL(inputObj = simplest_network, 
                                measObj = simplest_network_measurements, 
                                netObj = simplest_network_perturbations)
    
    #testing
    test_that("Comparison of the results", {
        expect_equal(result_actual, result_expected)
    })
    
    #TODO  for future checkNames tests 
    
    #test_grepl <- c("hel-lo", "hel*lo","hel_lo","hel lo", "hel>lo", "hel<lo", "hel+lo", "hel=lo", "hel/lo", "hello")
    gregexpr(pattern=prepared_pattern, text = test_grepl)
}