Merge pull request #32 from chainsawriot/mattest

Add tests for #23 close #23
gesistsa · Feb 11, 2023 · b242b60 · b242b60
2 parents 83865f2 + 0c3455f
commit b242b60
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Showing 4 changed files with 105 additions and 30 deletions.
diff --git a/R/installation.R b/R/installation.R
@@ -192,10 +192,10 @@
   gran_line <- which(basic_docker == "COPY gran.R ./gran.R")
   c(basic_docker[1:gran_line], 
     "COPY materials/ ./materials/",
-    basic_docker[(gran_line+1):length(basic_docker)])
+    basic_docker[(gran_line + 1):length(basic_docker)])
 }
 
-.generate_pre310_docker <- function(materials_dir,r_version, debian_version = "lenny", lib, sysreqs_cmd, cache) {
+.generate_pre310_docker <- function(r_version, debian_version = "lenny", lib, sysreqs_cmd, cache) {
     basic_docker <- c(
         paste0("FROM debian/eol:", debian_version),
         "ENV TZ UTC",
@@ -283,9 +283,9 @@ export_granlist <- function(granlist, path, granlist_as_comment = TRUE, verbose
 #'
 #' This function exports the result from [resolve()] to a Docker file. For R version >= 3.1.0, the Dockerfile is based on the versioned Rocker image.
 #' For R version < 3.1.0, the Dockerfile is based on Debian and it compiles R from source.
-#' @param output_dir where to put the Docker file
-#' @param materials_dir additional resources (e.g. analysis scripts) to be copied into `output_dir`
-#' @param image character, which versioned Rocker image to use. Can only be "r-ver", "rstudio", "tidyverse", "verse", "geospatial".
+#' @param output_dir character, where to put the Docker file and associated content
+#' @param materials_dir character, path to the directiry containing dditional resources (e.g. analysis scripts) to be copied into `output_dir` and in turn into the Docker container
+#' @param image character, which versioned Rocker image to use. Can only be "r-ver", "rstudio", "tidyverse", "verse", "geospatial"
 #' This applies only to R version <= 3.1
 #' @param cache logical, whether to cache the content from CRAN now. Please note that the system requirements are not cached
 #' @param ... arguments to be passed to `dockerize`
@@ -309,13 +309,16 @@ dockerize <- function(granlist, output_dir, materials_dir = NULL, image = c("r-v
                       granlist_as_comment = TRUE, cache = FALSE, verbose = TRUE, lib = NA,
                       cran_mirror = "https://cran.r-project.org/", check_cran_mirror = TRUE) {
     if (missing(output_dir)) {
-        stop("You must provide `output_dir`.")
+        stop("You must provide `output_dir`.", call. = FALSE)
     }
     if (!grepl("^ubuntu", granlist$os)) {
-        stop("System dependencies of ", granlist$os, " can't be dockerized.")
+        stop("System dependencies of ", granlist$os, " can't be dockerized.", call. = FALSE)
     }
     if (utils::compareVersion(granlist$r_version, "2.1") == -1) {
-        stop("`dockerize` doesn't support this R version (yet).")
+        stop("`dockerize` doesn't support this R version (yet):", granlist$r_version, call. = FALSE)
+    }
+    if (!is.null(materials_dir) && !(dir.exists(materials_dir))) {
+        stop(paste0("The folder ", materials_dir, " does not exist"), call. = FALSE)
     }
     image <- match.arg(image)
     sysreqs_cmd <- .consolidate_sysreqs(granlist)
@@ -350,19 +353,15 @@ dockerize <- function(granlist, output_dir, materials_dir = NULL, image = c("r-v
             basic_docker <- .insert_cache_dir(basic_docker)
         }
     }
-    if(!is.null(materials_dir)){
-      if(!dir.exists(materials_dir)){
-        stop(paste0("The folder ",materials_dir," does not exist"),call. = FALSE)
-      } else{
-        out_mat_dir <- paste0(output_dir,"/materials")
-        if (!dir.exists(out_mat_dir)) {
-          dir.create(out_mat_dir)
+    if (!(is.null(materials_dir))) {
+        out_mat_dir <- file.path(output_dir, "materials")
+        if (isFALSE(dir.exists(out_mat_dir))) {
+            dir.create(out_mat_dir)
         }
         file.copy(list.files(materials_dir, full.names = TRUE), 
                   out_mat_dir, 
                   recursive = TRUE)
         basic_docker <- .insert_materials_dir(basic_docker)
-      }
     }
     writeLines(basic_docker, file.path(output_dir, "Dockerfile"))
     invisible(output_dir)

diff --git a/man/dockerize.Rd b/man/dockerize.Rd
diff --git a/tests/testthat/test_dockerize.R b/tests/testthat/test_dockerize.R
@@ -1,11 +1,15 @@
+.gen_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(dockerize(graph, output_dir = tempdir()))
 })
 
 test_that("integration of #13 in dockerize()", {
     gran_ok <- readRDS("../testdata/gran_ok.RDS")
-    temp_dir <- file.path(tempdir(), sample(1:10000, size = 1))
+    temp_dir <- .gen_temp_dir()
     dockerize(granlist = gran_ok, output_dir = temp_dir) ## granlist_as_comment = TRUE
     x <- readLines(file.path(temp_dir, "gran.R"))
     expect_true(any(grepl("^## ## To reconstruct this file", x)))
@@ -17,7 +21,7 @@ test_that("integration of #13 in dockerize()", {
 test_that("integration of #16 in dockerize()", {
     ## verbose
     gran_ok <- readRDS("../testdata/gran_ok.RDS")
-    temp_dir <- file.path(tempdir(), sample(1:10000, size = 1))
+    temp_dir <- .gen_temp_dir()
     dockerize(granlist = gran_ok, output_dir = temp_dir) ## verbose = TRUE
     x <- readLines(file.path(temp_dir, "gran.R"))
     expect_true(any(grepl("^verbose <- TRUE", x)))
@@ -39,7 +43,7 @@ test_that("integration of #16 in dockerize()", {
 
 test_that("integration of #18 in dockerize()", {
     gran_ok <- readRDS("../testdata/gran_ok.RDS")
-    temp_dir <- file.path(tempdir(), sample(1:10000, size = 1))
+    temp_dir <- .gen_temp_dir()
     dockerize(granlist = gran_ok, output_dir = temp_dir) ## cran_mirror = "https://cran.r-project.org/"
     x <- readLines(file.path(temp_dir, "gran.R"))
     expect_true(any(grepl("^cran_mirror <- \"https://cran\\.r\\-project\\.org/\"", x)))
@@ -58,7 +62,7 @@ test_that("integration of #18 in dockerize()", {
 test_that("integration of #20 to dockerize()", {
     gran_ok <- readRDS("../testdata/gran_ok.RDS")
     expect_equal(gran_ok$r_version, "4.2.2")
-    temp_dir <- file.path(tempdir(), sample(1:10000, size = 1))
+    temp_dir <- .gen_temp_dir()
     dockerize(gran_ok, output_dir = temp_dir) ## cran_mirror = "https://cran.r-project.org/"
     x <- readLines(file.path(temp_dir, "gran.R"))
     expect_true(any(grepl("^cran_mirror <- \"https://cran\\.r\\-project\\.org/\"", x)))
@@ -70,15 +74,15 @@ test_that("integration of #20 to dockerize()", {
     gran_ok <- readRDS("../testdata/gran_ok.RDS")
     gran_ok$r_version <- "3.2.0"
     dockerize(gran_ok, output_dir = temp_dir) ## cran_mirror = "https://cran.r-project.org/"
-    x <- readLines(file.path(temp_dir, "gran.R"))    
+    x <- readLines(file.path(temp_dir, "gran.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("Dockerize R < 3.1 and >= 2.1", {
     gran_rio <- readRDS("../testdata/gran_rio_old.RDS")
     expect_equal(gran_rio$r_version, "3.0.1")
-    temp_dir <- file.path(tempdir(), sample(1:10000, size = 1))
+    temp_dir <- .gen_temp_dir()
     dockerize(gran_rio, output_dir = temp_dir)
     expect_true(file.exists(file.path(temp_dir, "compile_r.sh")))
     Dockerfile <- readLines(file.path(temp_dir, "Dockerfile"))
@@ -92,11 +96,11 @@ test_that("Dockerize R < 3.1 and >= 2.1", {
 test_that("Docker R < 2.1", {
     gran_rio <- readRDS("../testdata/gran_rio_old.RDS")
     gran_rio$r_version <- "2.1.0" ## exactly 2.1.0, no error
-    temp_dir <- file.path(tempdir(), sample(1:10000, size = 1))
+    temp_dir <- .gen_temp_dir()
     expect_error(dockerize(gran_rio, output_dir = temp_dir), NA)
     gran_rio <- readRDS("../testdata/gran_rio_old.RDS")
     gran_rio$r_version <- "2.0.0"
-    expect_error(dockerize(gran_rio, output_dir = temp_dir))    
+    expect_error(dockerize(gran_rio, output_dir = temp_dir))
 })
 
 test_that(".consolidate_sysreqs and issue #21", {
@@ -115,6 +119,74 @@ test_that(".consolidate_sysreqs and issue #21", {
 
 test_that("Dockerize warning, issue #21", {
     graph <- readRDS("../testdata/issue21.RDS")
-    temp_dir <- file.path(tempdir(), sample(1:10000, size = 1))
+    temp_dir <- .gen_temp_dir()
     expect_warning(dockerize(graph, output_dir = temp_dir))
 })
+
+test_that("material_dir, non-existing, #23", {
+    ## normal case
+    gran_rio <- readRDS("../testdata/gran_rio_old.RDS")
+    temp_dir <- .gen_temp_dir()
+    expect_error(dockerize(gran_rio, output_dir = temp_dir, materials_dir = NULL), NA)
+    ## non-existing
+    fake_material_dir <- .gen_temp_dir()
+    expect_false(dir.exists(fake_material_dir))
+    expect_error(dockerize(gran_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
+    gran_rio <- readRDS("../testdata/gran_rio_old.RDS")
+    temp_dir <- .gen_temp_dir()
+    fake_material_dir <- .gen_temp_dir()
+    dir.create(fake_material_dir)
+    dockerize(gran_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, "Dockerfile")) == "COPY materials/ ./materials/"))
+    ## Post R 3.1.0
+    graph <- readRDS("../testdata/graph.RDS")
+    temp_dir <- .gen_temp_dir()
+    fake_material_dir <- .gen_temp_dir()
+    dir.create(fake_material_dir)
+    dockerize(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))
+    expect_true(any(readLines(file.path(temp_dir, "Dockerfile")) == "COPY materials/ ./materials/"))
+    ## Will only test post 3.1.0 from now on
+    ## some files in fake_material_dir
+    temp_dir <- .gen_temp_dir()
+    fake_material_dir <- .gen_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"))
+    dockerize(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, "Dockerfile")) == "COPY 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 <- .gen_temp_dir()
+    fake_material_dir <- .gen_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")
+    dockerize(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, "Dockerfile")) == "COPY 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")
+})
diff --git a/tests/testthat/test_resolve.R b/tests/testthat/test_resolve.R
@@ -1,3 +1,7 @@
+.gen_temp_dir <- function() {
+    file.path(tempdir(), paste(sample(c(LETTERS, letters), 20, replace = TRUE), collapse = ""))
+}
+
 test_that("defensive programming", {
     expect_error(resolve("LDAvis", os = "windows"))
 })
@@ -48,7 +52,7 @@ test_that("cache #17", {
     skip_if_offline()
     skip_on_cran()
     gran_ok <- readRDS("../testdata/gran_ok.RDS")
-    temp_dir <- file.path(tempdir(), sample(1:10000, size = 1))
+    temp_dir <- .gen_temp_dir()
     dockerize(gran_ok, output_dir = temp_dir) ## cache = FALSE
     x <- readLines(file.path(temp_dir, "Dockerfile"))
     expect_false(any(grepl("^COPY cache", x)))
@@ -71,7 +75,7 @@ test_that("cache for R < 3.1 and R >= 2.1", {
     skip_on_cran()
     gran_rio <- readRDS("../testdata/gran_rio_old.RDS")
     expect_equal(gran_rio$r_version, "3.0.1")
-    temp_dir <- file.path(tempdir(), sample(1:10000, size = 1))
+    temp_dir <- .gen_temp_dir()
     dockerize(gran_rio, output_dir = temp_dir, cache = TRUE, verbose = FALSE)
     x <- readLines(file.path(temp_dir, "Dockerfile"))
     expect_true(any(grepl("^COPY cache", x)))