context("importTab") test_that("importTab", { ## suppress warnings to avoid creation of Rplots.pdf expect_error(suppressWarnings(MALDIquantForeign:::.importTab("tmp.tmp"))) path <- normalizePath(system.file(file.path("exampledata", "ascii.txt"), package="MALDIquantForeign")) s <- MALDIquantForeign:::.importTab(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importTxt(path, verbose=FALSE)) expect_equal(s, import(path, type="txt", verbose=FALSE)) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "ascii.txt") ## issue 29, double skip expect_equal( as.matrix(MALDIquantForeign:::.importTab(path, skip=2L, verbose=FALSE)[[1L]]), matrix(c(3:5, 8:10), ncol=2L, dimnames=list(c(), c("mass", "intensity"))) ) }) test_that("importCsv", { ## suppress warnings to avoid creation of Rplots.pdf expect_error(suppressWarnings(MALDIquantForeign:::.importCsv("tmp.tmp"))) path <- normalizePath(system.file(file.path("exampledata", "csv1.csv"), package="MALDIquantForeign")) s <- MALDIquantForeign:::.importCsv(path, sep=",", header=TRUE, verbose=FALSE) expect_equal(s, import(path, sep=",", header=TRUE, verbose=FALSE)) expect_equal(s, importCsv(path, sep=",", header=TRUE, verbose=FALSE)) expect_equal(s, import(path, type="csv", sep=",", header=TRUE, verbose=FALSE)) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "csv1.csv") ## auto header s <- MALDIquantForeign:::.importCsv(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importCsv(path, verbose=FALSE)) expect_equal(s, import(path, type="csv", verbose=FALSE)) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "csv1.csv") s <- MALDIquantForeign:::.importCsv(system.file( file.path("exampledata", "csv2.csv"), package="MALDIquantForeign"), sep=";", header=FALSE) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "csv2.csv") ## auto header s <- MALDIquantForeign:::.importCsv(file.path(dirname(path), "csv2.csv"), sep=";") expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "csv2.csv") }) x <- c("10, 30", "\"foo\", \"bar\"", "foo; bar", "foo\tbar", "1\t 2") sep <- c(",", ",", ";", "\t", "\t") test_that("autoHeader", { result <- c(FALSE, TRUE, TRUE, TRUE, FALSE) for (i in seq(along=x)) { expect_identical(MALDIquantForeign:::.autoHeader(x[i], sep=sep[i]), result[i]) } }) test_that("autoSep", { for (i in seq(along=x)) { expect_identical(MALDIquantForeign:::.autoSep(x[i]), sep[i]) } })
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