tests/testthat/test_GEO.R

In oganm/ogbox: Stuff and things

context('GEO error check')

if (Sys.getenv("USER") != "travis"){
    test_that('gsmDown', {
        temp = tempfile()
        temp2 = tempfile()
        expect_that(a<-gsmDown('GSM1026376',temp),gives_warning('has mutliple files'))
        expect_that(a,testthat::equals(F))
        expect_that(a<-gsmDown('GSM1539691',temp),gives_warning("doesn't have a file attached"))
        expect_that(a,testthat::equals(F))
        expect_that(gsmDown('GSM86787',temp2),testthat::equals(T))
    })
    
    test_that('gsmFind >500',{
        cores = parallel::detectCores()
        if(is.na(cores)){
            cores = 1
        }
        expect_equal(gsmFind('GSE14468',regex = '6455',cores = cores),'GSM361359')
        # if(cores > 1){
        #     expect_equal(gsmFind('GSE14468',regex = '6455',cores = 1),'GSM361359')
        #     
        # }
    })
    
    test_that('gsmFind with regex merge',{
        expect_that(gsmFind('GSE29949','Brain mic'), testthat::equals(c( "GSM741192", "GSM741193", "GSM741194")))
        expect_equal(gsmFind('GSE69340',regex = regexMerge(c('OLIG2','NEK7'))),
                     c("GSM1698231", "GSM1698232", "GSM1698233", "GSM1698237", "GSM1698238" ,"GSM1698239"))
        expect_equal(gsmFind('GSE42021', regex = regexMerge(c('04_(+) 24hi', '22_(-) 24hi'), exact = T)),
                     c("GSM1030712", "GSM1030715"))
    })
    
    test_that('whichGSE', {
        expect_equal(whichGSE('GSM874480'), c("GSE35758", "GSE35766"))
        expect_equal(whichGSE('GSM63015'), 'GSE2882')
    })
    
    test_that('softDown and softParser',{
        tmp = tempfile()
        softDown('GSE28642',tmp)
        
        expect_equal(suppressWarnings(softDown('GSE28642',tmp)), FALSE)
        
        softDataWithExp = softParser(tmp, expression = TRUE)
        softData = softParser(tmp)
        expect_that(softData, is_a('data.frame'))
        expect_equal(nrow(softData),4)
        expect_that(softDataWithExp, is_a('list'))
    })
    
    
    
}