tests/testthat/test_apptainerize.R

In rang: Reconstructing Reproducible R Computational Environments

.generate_temp_dir <- function() {
    file.path(tempdir(), paste(sample(c(LETTERS, letters), 20, replace = TRUE), collapse = ""))
}

test_that("defensive programming", {
    graph <- readRDS("../testdata/sle_graph.RDS")
    expect_error(apptainerize(graph, output_dir = tempdir()))
    expect_error(apptainerize(graph))
})

test_that("empty rang apptainerize #75", {
    graph <- readRDS("../testdata/rang_ok.RDS")
    graph$ranglets <- list()
    expect_warning(x <- apptainerize(graph, output_dir = .generate_temp_dir()))
    expect_equal(x, NULL)
})

test_that("integration of #13 in apptainerize()", {
    rang_ok <- readRDS("../testdata/rang_ok.RDS")
    temp_dir <- .generate_temp_dir()
    apptainerize(rang = rang_ok, output_dir = temp_dir) ## rang_as_comment = TRUE
    x <- readLines(file.path(temp_dir, "rang.R"))
    expect_true(any(grepl("^## ## To reconstruct this file", x)))
    expect_false(any(grepl("^## ## WARNING", x)))
    apptainerize(rang = rang_ok, output_dir = temp_dir, rang_as_comment = FALSE)
    x <- readLines(file.path(temp_dir, "rang.R"))
    expect_false(any(grepl("^## ## To reconstruct this file", x)))
})

test_that("integration of #16 in apptainerize()", {
    ## verbose
    rang_ok <- readRDS("../testdata/rang_ok.RDS")
    temp_dir <- .generate_temp_dir()
    apptainerize(rang = rang_ok, output_dir = temp_dir) ## verbose = TRUE
    x <- readLines(file.path(temp_dir, "rang.R"))
    expect_true(any(grepl("^verbose <- TRUE", x)))
    apptainerize(rang = rang_ok, output_dir = temp_dir, verbose = FALSE)
    x <- readLines(file.path(temp_dir, "rang.R"))
    expect_true(any(grepl("^verbose <- FALSE", x)))
    container_file <- readLines(file.path(temp_dir, "container.def"))
    expect_true(any(grepl("Rscript \\$RANG_PATH", container_file)))
    ## lib
    apptainerize(rang = rang_ok, output_dir = temp_dir) ## lib = NA
    x <- readLines(file.path(temp_dir, "rang.R"))
    expect_true(any(grepl("^lib <- NA", x)))
    container_file <- readLines(file.path(temp_dir, "container.def"))
    expect_false(any(grepl("mkdir", container_file)))
    apptainerize(rang = rang_ok, output_dir = temp_dir, lib = "abc") ## lib = NA
    x <- readLines(file.path(temp_dir, "rang.R"))
    expect_true(any(grepl("^lib <- \"abc\"", x)))
    container_file <- readLines(file.path(temp_dir, "container.def"))
    expect_true(any(grepl("mkdir", container_file)))
    expect_false(any(grepl("^Rscript \\$RANG_PATH", container_file)))
    ## #123
    expect_equal(tail(container_file, 1), "exec R \"${@}\"")
    ## post
    apptainerize(rang = rang_ok, output_dir = temp_dir, post_installation_steps = "date")
    container_file <- readLines(file.path(temp_dir, "container.def"))
    last_post_line_before_start_script <- which(grepl("\\%startscript", container_file)) -2
    expect_equal(container_file[last_post_line_before_start_script], "date")
})

test_that("integration of #18 in apptainerize()", {
    rang_ok <- readRDS("../testdata/rang_ok.RDS")
    temp_dir <- .generate_temp_dir()
    apptainerize(rang = rang_ok, output_dir = temp_dir) ## cran_mirror = "https://cran.r-project.org/"
    x <- readLines(file.path(temp_dir, "rang.R"))
    expect_true(any(grepl("^cran.mirror <- \"https://cran\\.r\\-project\\.org/\"", x)))
    apptainerize(rang = rang_ok, output_dir = temp_dir, cran_mirror = "cran.r-project.org")
    x <- readLines(file.path(temp_dir, "rang.R"))
    expect_true(any(grepl("^cran.mirror <- \"https://cran\\.r\\-project\\.org/\"", x)))
    apptainerize(rang = rang_ok, output_dir = temp_dir, cran_mirror = "https://cloud.r-project.org/")
    x <- readLines(file.path(temp_dir, "rang.R"))
    expect_true(any(grepl("^cran.mirror <- \"https://cloud\\.r\\-project\\.org/\"", x)))
    expect_error(apptainerize(rang = rang_ok, output_dir = temp_dir, cran_mirror = "https://www.chainsawriot.com/"))
    expect_error(apptainerize(rang = rang_ok, output_dir = temp_dir, cran_mirror = "https://www.chainsawriot.com/", check_cran_mirror = FALSE), NA)
    x <- readLines(file.path(temp_dir, "rang.R"))
    expect_true(any(grepl("^cran.mirror <- \"https://www\\.chainsawriot\\.com/\"", x)))
})

test_that("integration of #20 to apptainerize()", {
    rang_ok <- readRDS("../testdata/rang_ok.RDS")
    expect_equal(rang_ok$r_version, "4.2.2")
    temp_dir <- .generate_temp_dir()
    apptainerize(rang_ok, output_dir = temp_dir) ## cran_mirror = "https://cran.r-project.org/"
    x <- readLines(file.path(temp_dir, "rang.R"))
    expect_true(any(grepl("^cran.mirror <- \"https://cran\\.r\\-project\\.org/\"", x)))
    rang_ok <- readRDS("../testdata/rang_ok.RDS")
    rang_ok$r_version <- "3.3.0"
    apptainerize(rang_ok, output_dir = temp_dir) ## cran_mirror = "https://cran.r-project.org/"
    x <- readLines(file.path(temp_dir, "rang.R"))
    expect_true(any(grepl("^cran.mirror <- \"https://cran\\.r\\-project\\.org/\"", x)))
    rang_ok <- readRDS("../testdata/rang_ok.RDS")
    rang_ok$r_version <- "3.2.0"
    apptainerize(rang_ok, output_dir = temp_dir) ## cran_mirror = "https://cran.r-project.org/"
    x <- readLines(file.path(temp_dir, "rang.R"))
    expect_false(any(grepl("^cran.mirror <- \"https://cran\\.r\\-project\\.org/\"", x)))
    expect_true(any(grepl("^cran.mirror <- \"http://cran\\.r\\-project\\.org/\"", x)))
})

test_that("sugars", {
    rang_ok <- readRDS("../testdata/rang_ok.RDS")
    expect_equal(rang_ok$r_version, "4.2.2")
    temp_dir1 <- .generate_temp_dir()
    expect_error(apptainerize(rang_ok, output_dir = temp_dir1), NA)
    temp_dir2 <- .generate_temp_dir()
    expect_error(apptainerize(rang_ok, output_dir = temp_dir2), NA)
    temp_dir3 <- .generate_temp_dir()
    expect_error(apptainerize(rang_ok, output_dir = temp_dir3), NA)
    temp_dir4 <- .generate_temp_dir()
    expect_error(apptainerize(rang_ok, output_dir = temp_dir4), NA)
    for (tdir in c(temp_dir1, temp_dir2, temp_dir3, temp_dir4)) {
        expect_true(file.exists(file.path(tdir, "rang.R")))
        expect_true(file.exists(file.path(tdir, "container.def")))
    }
})

test_that("copy_all", {
    rang_ok <- readRDS("../testdata/rang_ok.RDS")
    expect_equal(rang_ok$r_version, "4.2.2")
    temp_dir <- .generate_temp_dir()
    apptainerize(rang_ok, output_dir = temp_dir) ## copy_all = FALSE
    container_file <- readLines(file.path(temp_dir, "container.def"))
    expect_false(any(container_file == ". /"))
    temp_dir <- .generate_temp_dir()
    apptainerize(rang_ok, output_dir = temp_dir, copy_all = TRUE)
    container_file <- readLines(file.path(temp_dir, "container.def"))
    expect_true(any(container_file == ". /"))
})

test_that("apptainerize R < 3.1 and >= 2.1", {
    rang_rio <- readRDS("../testdata/rang_rio_old.RDS")
    expect_equal(rang_rio$r_version, "3.0.1")
    temp_dir <- .generate_temp_dir()
    apptainerize(rang_rio, output_dir = temp_dir)
    expect_true(file.exists(file.path(temp_dir, "compile_r.sh")))
    container_file <- readLines(file.path(temp_dir, "container.def"))
    expect_true(any(grepl("^bash \\$COMPILE_PATH 3.0.1", container_file)))
    expect_equal(tail(container_file, 1), "exec R \"${@}\"")
    ## lib
    apptainerize(rang_rio, output_dir = temp_dir, lib = "abc")
    container_file <- readLines(file.path(temp_dir, "container.def"))
    expect_true(any(grepl("^mkdir", container_file)))
    expect_equal(tail(container_file, 1), "exec R \"${@}\"")
    apptainerize(rang_rio, output_dir = temp_dir, lib = "abc", post_installation_step = "date")
    container_file <- readLines(file.path(temp_dir, "container.def"))
    last_post_line_before_start_script <- which(grepl("\\%startscript", container_file)) -2
    expect_equal(container_file[last_post_line_before_start_script], "date")
})

test_that("Docker R < 1.3.1", {
    rang_rio <- readRDS("../testdata/rang_rio_old.RDS")
    rang_rio$r_version <- "1.3.1" ## exactly 1.3.1, no error
    temp_dir <- .generate_temp_dir()
    expect_error(apptainerize(rang_rio, output_dir = temp_dir)) ## no cache
    ##expect_error(apptainerize(rang_rio, output_dir = temp_dir, cache = TRUE, verbose = FALSE), NA)
    rang_rio <- readRDS("../testdata/rang_rio_old.RDS")
    rang_rio$r_version <- "1.3.0"
    expect_error(apptainerize(rang_rio, output_dir = temp_dir))
})


test_that("apptainerize warning, issue #21", {
    graph <- readRDS("../testdata/issue21.RDS")
    temp_dir <- .generate_temp_dir()
    expect_warning(apptainerize(graph, output_dir = temp_dir))
})

test_that("material_dir, non-existing, #23", {
    ## normal case
    rang_rio <- readRDS("../testdata/rang_rio_old.RDS")
    temp_dir <- .generate_temp_dir()
    expect_error(apptainerize(rang_rio, output_dir = temp_dir, materials_dir = NULL), NA)
    ## non-existing
    fake_material_dir <- .generate_temp_dir()
    expect_false(dir.exists(fake_material_dir))
    expect_error(apptainerize(rang_rio, output_dir = temp_dir, materials_dir = fake_material_dir))
})

test_that("material_dir, existing, no subdir, #23", {
    ## exist, but empty dir
    ## Pre R 3.1.0
    rang_rio <- readRDS("../testdata/rang_rio_old.RDS")
    temp_dir <- .generate_temp_dir()
    fake_material_dir <- .generate_temp_dir()
    dir.create(fake_material_dir)
    apptainerize(rang_rio, output_dir = temp_dir, materials_dir = fake_material_dir)
    expect_true(dir.exists(file.path(temp_dir, "materials")))
    expect_equal(list.files(file.path(temp_dir, "materials")), character(0))
    expect_true(any(readLines(file.path(temp_dir, "container.def")) == "materials/ ./materials/"))
    ## Post R 3.1.0
    graph <- readRDS("../testdata/graph.RDS")
    temp_dir <- .generate_temp_dir()
    fake_material_dir <- .generate_temp_dir()
    dir.create(fake_material_dir)
    apptainerize(graph, output_dir = temp_dir, materials_dir = fake_material_dir)
    expect_true(dir.exists(file.path(temp_dir, "materials")))
    expect_equal(list.files(file.path(temp_dir, "materials")), character(0))
    container_file <- readLines(file.path(temp_dir, "container.def"))
    expect_true(any(container_file == "materials/ ./materials/"))
    expect_equal(tail(container_file, 1), "exec R \"${@}\"")
    ## Will only test post 3.1.0 from now on
    ## some files in fake_material_dir
    temp_dir <- .generate_temp_dir()
    fake_material_dir <- .generate_temp_dir()
    dir.create(fake_material_dir)
    file.copy("../testdata/graph.RDS", file.path(fake_material_dir, "graph.RDS"))
    writeLines(c("831721", "GESIS"), file.path(fake_material_dir, "test.R"))
    apptainerize(graph, output_dir = temp_dir, materials_dir = fake_material_dir)
    expect_true(dir.exists(file.path(temp_dir, "materials")))
    expect_equal(list.files(file.path(temp_dir, "materials")), c("graph.RDS", "test.R"))
    expect_true(any(readLines(file.path(temp_dir, "container.def")) == "materials/ ./materials/"))
    expect_true(file.exists(file.path(temp_dir, "materials", "graph.RDS")))
    expect_true(file.exists(file.path(temp_dir, "materials", "test.R")))
    content <- readLines(file.path(temp_dir, "materials", "test.R"))
    expect_equal(content[1], "831721")
    expect_equal(content[2], "GESIS")
})

test_that("material_dir, existing, with 1 subdir, #23", {
    temp_dir <- .generate_temp_dir()
    fake_material_dir <- .generate_temp_dir()
    dir.create(fake_material_dir)
    dir.create(file.path(fake_material_dir, "data"))
    file.copy("../testdata/graph.RDS", file.path(fake_material_dir, "data", "graph.RDS"))
    writeLines(c("831721", "GESIS"), file.path(fake_material_dir, "test.R"))
    graph <- readRDS("../testdata/graph.RDS")
    apptainerize(graph, output_dir = temp_dir, materials_dir = fake_material_dir)
    expect_true(dir.exists(file.path(temp_dir, "materials")))
    expect_true(any(readLines(file.path(temp_dir, "container.def")) == "materials/ ./materials/"))
    expect_true(dir.exists(file.path(temp_dir, "materials", "data")))
    expect_true(file.exists(file.path(temp_dir, "materials", "data", "graph.RDS")))
    expect_true(file.exists(file.path(temp_dir, "materials", "test.R")))
    content <- readLines(file.path(temp_dir, "materials", "test.R"))
    expect_equal(content[1], "831721")
    expect_equal(content[2], "GESIS")
})

test_that("readme issue #50", {
    skip_on_os("windows", arch = NULL)
    skip_on_cran()
    rang_ok <- readRDS("../testdata/rang_ok.RDS")
    expect_equal(rang_ok$r_version, "4.2.2")
    temp_dir <- .generate_temp_dir()
    apptainerize(rang_ok, output_dir = temp_dir)
    expect_true(file.exists(file.path(temp_dir, "README")))
    content <- readLines(file.path(temp_dir, "README"))
    expect_true(any(grepl(temp_dir, content)))
})

test_that("#123 rstudio", {
    graph <- readRDS("../testdata/graph.RDS")
    temp_dir <- .generate_temp_dir()
    apptainerize(graph, output_dir = temp_dir, image = "rstudio")
    container_file <- readLines(file.path(temp_dir, "container.def"))
    first_startscript_line <- which(grepl("\\%startscript", container_file)) + 2
    expect_true(all(grepl("exec /usr/lib/rstudio-server/bin/rserver", container_file[first_startscript_line])))
})

test_that("apptainerize with bioc #58", {
    rang_bioc <- readRDS("../testdata/rang_bioc.RDS")
    temp_dir <- .generate_temp_dir()
    apptainerize(rang = rang_bioc, output_dir = temp_dir) ## verbose = TRUE
    x <- readLines(file.path(temp_dir, "rang.R"))
    expect_true(any(grepl("bioc.mirror",x)))
})

test_that("no_rocker #67", {
    rang_ok <- readRDS("../testdata/rang_ok.RDS")
    temp_dir <- .generate_temp_dir()
    apptainerize(rang = rang_ok, output_dir = temp_dir) ## no_rocker = FALSE
    expect_false(file.exists(file.path(temp_dir, "compile_r.sh")))
    expect_false(any(readLines(file.path(temp_dir, "container.def")) == "From: debian/eol:lenny"))
    temp_dir <- .generate_temp_dir()
    apptainerize(rang = rang_ok, output_dir = temp_dir, no_rocker = TRUE) ## debian_version = lenny
    expect_true(file.exists(file.path(temp_dir, "compile_r.sh")))
    expect_true(any(readLines(file.path(temp_dir, "container.def")) == "From: debian/eol:lenny"))
    temp_dir <- .generate_temp_dir()
    apptainerize(rang = rang_ok, output_dir = temp_dir, no_rocker = TRUE,
              debian_version = "jessie")
    expect_true(file.exists(file.path(temp_dir, "compile_r.sh")))
    expect_true(any(readLines(file.path(temp_dir, "container.def")) == "From: debian/eol:jessie"))
    temp_dir <- .generate_temp_dir()
    expect_error(apptainerize(rang = rang_ok, output_dir = temp_dir, no_rocker = TRUE,
              debian_version = "3.11"))
})

test_that("apptainerize with inst/rang", {
    rang_ok <- readRDS("../testdata/rang_ok.RDS")
    temp_dir <- .generate_temp_dir()
    dir.create(temp_dir)
    use_rang(temp_dir, verbose = FALSE)
    apptainerize(rang_ok, output_dir = temp_dir, verbose = FALSE)
    expect_true("inst/rang/rang.R" %in% list.files(temp_dir, recursive = TRUE))
    expect_false("rang.R" %in% list.files(temp_dir, recursive = TRUE))
    expect_true("container.def" %in% list.files(temp_dir, recursive = TRUE))
    container_file <- readLines(file.path(temp_dir, "container.def"))
    expect_true(". /" %in% container_file) ## coerced
    expect_true("export RANG_PATH=inst/rang/rang.R" %in% container_file)
})

test_that(".insert_materials_dir with actual outcome", {
    container_content <- list()
    container_content$COPY <- "COPY rang.R /rang.R"
    expect_identical(names(.insert_materials_dir(container_content, verb = "dockerize")), "COPY")
    expect_false(names(.insert_materials_dir(container_content, verb = "dockerize")) %in% "FILES")
    container_content <- list()
    container_content$FILES <- "rang.R /rang.R"
    expect_identical(names(.insert_materials_dir(container_content, verb = "apptainerize/singularize")), "FILES")
    expect_false(names(.insert_materials_dir(container_content, verb = "apptainerize/singularize")) %in% "COPY")
})

test_that("No .normalize_docker_steps integration in apptainerize", {
    graph <- readRDS("../testdata/graph.RDS")
    temp_dir <- .generate_temp_dir()
    apptainerize(graph, output_dir = temp_dir, post_installation_steps = c(recipes[["texlive"]], "RUN apt-get install -y make"))
    def_file <- readLines(file.path(temp_dir, "container.def"))
    expect_true("RUN apt-get install -y make" %in% def_file) ## you ask for it
    expect_false("RUN apt-get install -y pandoc pandoc-citeproc texlive" %in% def_file)
})