context("compression") z <- c("bz2", "bzip2", "gz", "lzma", "xz") e <- c("zip", z, paste("tar", z, sep="."), "tar", "txt", "mzML") f <- paste(letters[1:13], e, sep=".") test_that(".isCompressed", { expect_identical(MALDIquantForeign:::.isCompressed(f), c(rep(TRUE, 11), rep(FALSE, 3))) }) test_that(".isTar", { expect_identical(MALDIquantForeign:::.isTar(f), c(rep(FALSE, 6), rep(TRUE, 6), rep(FALSE, 2))) }) test_that(".isZip", { expect_identical(MALDIquantForeign:::.isZip(f), c(TRUE, rep(FALSE, 13))) }) test_that(".isPackedOrCompressed", { expect_identical(MALDIquantForeign:::.isPackedOrCompressed(f), c(rep(TRUE, 12), rep(FALSE, 2))) }) test_that(".uncompress supports single file compression by gunzip", { u <- MALDIquantForeign:::.uncompress( system.file(file.path("exampledata", "compressed", "csv1.csv.gz"), package="MALDIquantForeign")) f <- system.file(file.path("exampledata", "csv1.csv"), package="MALDIquantForeign") expect_identical(readLines(u), readLines(f)) expect_identical(MALDIquantForeign:::.uncompress("foobar.txt"), "foobar.txt") expect_error(MALDIquantForeign:::.uncompress("foobar.gz"), ".*foobar.gz.* doesn't exist!") }) test_that(".uncompress supports tar compression by untar", { u <- list.files(MALDIquantForeign:::.uncompress( system.file( file.path("exampledata", "compressed", "csv.tar.gz"), package="MALDIquantForeign")), recursive=TRUE, pattern="^.*\\.csv$", full.names=TRUE)[1] f <- system.file(file.path("exampledata", "csv1.csv"), package="MALDIquantForeign") expect_identical(readLines(u), readLines(f)) }) test_that(".uncompress supports zip compression by unzip", { u <- list.files(MALDIquantForeign:::.uncompress( system.file( file.path("exampledata", "compressed", "csv.zip"), package="MALDIquantForeign")), recursive=TRUE, pattern="^.*\\.csv$", full.names=TRUE)[1] f <- system.file(file.path("exampledata", "csv1.csv"), package="MALDIquantForeign") expect_identical(readLines(u), readLines(f)) expect_error(suppressWarnings(MALDIquantForeign:::.uncompress("foobar.zip")), "unzip failed!") }) test_that(".cleanupUncompressedTmpFiles works", { n <- list.files(file.path(tempdir(), "MALDIquantForeign_uncompress"), recursive=TRUE) expect_true(length(n) > 0) MALDIquantForeign:::.cleanupUncompressedTmpFiles() expect_false(file.exists(file.path(tempdir(), "MALDIquantForeign_uncompress"))) }) test_that("typical auto import", { f <- normalizePath(system.file( file.path("exampledata", "compressed", "csv1.csv.gz"), package="MALDIquantForeign")) s <- createMassSpectrum(mass=1:5, intensity=6:10) i <- import(f)[[1]] metaData(i) <- list() expect_identical(i, s) expect_false(file.exists(file.path(tempdir(), "MALDIquantForeign_uncompress"))) })
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