Add .normalize_docker_steps ref #133

gesistsa · Apr 18, 2023 · ac8ca2e · ac8ca2e
1 parent e83008e
commit ac8ca2e
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Showing 5 changed files with 63 additions and 25 deletions.
diff --git a/R/dockerfile.R b/R/dockerfile.R
@@ -1,3 +1,15 @@
+## for normalizing post_installation_steps
+.normalize_docker_steps <- function(steps) {
+    fx <- function(step) {
+        docker_regex <- "^#|^ADD |^COPY |^ENV |^EXPOSE |^FROM |^LABEL |^STOPSIGNAL |^USER |^VOLUME |^WORKDIR |^ONBUILD |^RUN |^CMD |^ENTRYPOINT |^ARG |^HEALTHCHECK |^SHELL "
+        splitted_step <- strsplit(step, "\n")[[1]]
+        docker_line_lgl <- grepl(docker_regex, splitted_step)
+        splitted_step[!docker_line_lgl] <- paste0("RUN ", splitted_step[!docker_line_lgl])
+        paste0(splitted_step, collapse = "\n")
+    }
+    vapply(steps, fx, character(1), USE.NAMES = FALSE)
+}
+
 .generate_debian_eol_dockerfile_content <- function(r_version, lib, sysreqs_cmd, cache, debian_version = "lenny",
                                                     post_installation_steps = NULL,
                                                     rel_dir = "",
@@ -24,7 +36,7 @@
         containerfile_content$FROM <- c("FROM scratch", paste0("ADD ", file.path(rel_dir, "cache/debian/rootfs.tar.xz"), " /"))
         containerfile_content$ENV <- append(containerfile_content$ENV, paste0("ENV CACHE_PATH ", cache_path))
     }
-    containerfile_content$RUN <- append(containerfile_content$RUN, post_installation_steps)
+    containerfile_content$RUN <- append(containerfile_content$RUN, .normalize_docker_steps(post_installation_steps))
     if (isTRUE(copy_all)) {
         containerfile_content$COPY <- c("COPY . /")
     }
@@ -55,7 +67,7 @@
     if (image == "rstudio") {
         containerfile_content$CMD <- c("EXPOSE 8787", "CMD [\"/init\"]")
     }
-    containerfile_content$RUN <- append(containerfile_content$RUN, post_installation_steps)
+    containerfile_content$RUN <- append(containerfile_content$RUN, .normalize_docker_steps(post_installation_steps))
     if (isTRUE(copy_all)) {
         containerfile_content$COPY <- c("COPY . /")
     }

diff --git a/R/memo_misc.R b/R/memo_misc.R
@@ -64,11 +64,11 @@ NULL
 ## data generation
 ## ---
 ## recipes <- list()
-## recipes["texlive"] <- "## install texlive\nRUN apt-get install -y pandoc pandoc-citeproc texlive"
-## recipes["texlivefull"] <- "## install texlive-full\nRUN apt-get install -y pandoc pandoc-citeproc texlive-full"
-## recipes["quarto"] <- "## install quarto (latest)\nRUN apt-get install -y curl git && curl -LO https://quarto.org/download/latest/quarto-linux-amd64.deb && dpkg -i quarto-linux-amd64.deb && quarto install tool tinytex && rm quarto-linux-amd64.deb"
-## recipes["clean"] <- "## Clean up caches\nRUN rm -rf /var/lib/apt/lists/* && if [ -d \"$CACHE_PATH\" ]; then rm -rf $CACHE_PATH; fi"
-## recipes["make"] <- "## install GNU make\nRUN apt-get -y install make"
+## recipes["texlive"] <- "## install texlive\napt-get install -y pandoc pandoc-citeproc texlive"
+## recipes["texlivefull"] <- "## install texlive-full\napt-get install -y pandoc pandoc-citeproc texlive-full"
+## recipes["quarto"] <- "## install quarto (latest)\napt-get install -y curl git && curl -LO https://quarto.org/download/latest/quarto-linux-amd64.deb && dpkg -i quarto-linux-amd64.deb && quarto install tool tinytex && rm quarto-linux-amd64.deb"
+## recipes["clean"] <- "## Clean up caches\nrm -rf /var/lib/apt/lists/* && if [ -d \"$CACHE_PATH\" ]; then rm -rf $CACHE_PATH; fi"
+## recipes["make"] <- "## install GNU make\napt-get -y install make"
 ## usethis::use_data(recipes, overwrite = TRUE)
 
 #' Recipes for Building Container Images

diff --git a/data/recipes.rda b/data/recipes.rda
diff --git a/tests/testthat/test_apptainerize.R b/tests/testthat/test_apptainerize.R
@@ -309,3 +309,12 @@ test_that(".insert_materials_dir with actual outcome", {
     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)
+})
diff --git a/tests/testthat/test_dockerize.R b/tests/testthat/test_dockerize.R
@@ -317,25 +317,42 @@ test_that("dockerize with inst/rang", {
     expect_true("ENV RANG_PATH inst/rang/rang.R" %in% dockerfile)
 })
 
+test_that(".normalize_docker_steps", {
+    expect_equal(.normalize_docker_steps("RUN apt-get install -y pandoc"), "RUN apt-get install -y pandoc")
+    expect_equal(.normalize_docker_steps("apt-get install -y pandoc"), "RUN apt-get install -y pandoc")
+    expect_equal(.normalize_docker_steps(c("apt-get install -y pandoc", "RUN apt-get install -y pandoc")),
+                 rep("RUN apt-get install -y pandoc", 2))
+    expect_equal(.normalize_docker_steps(recipes[["quarto"]]), "## install quarto (latest)\nRUN apt-get install -y curl git && curl -LO https://quarto.org/download/latest/quarto-linux-amd64.deb && dpkg -i quarto-linux-amd64.deb && quarto install tool tinytex && rm quarto-linux-amd64.deb")
+})
+
+test_that(".normalize_docker_steps integration", {
+    graph <- readRDS("../testdata/graph.RDS")
+    temp_dir <- .generate_temp_dir()
+    dockerize(graph, output_dir = temp_dir, post_installation_steps = c(recipes[["texlive"]], "RUN apt-get install -y make"))
+    dockerfile <- readLines(file.path(temp_dir, "Dockerfile"))
+    expect_true("RUN apt-get install -y make" %in% dockerfile)
+    expect_true("RUN apt-get install -y pandoc pandoc-citeproc texlive" %in% dockerfile)
+})
+
 test_that(".generate_wrapped_line", {
-  graph <- readRDS("../testdata/graph.RDS")
-  temp_dir <- .generate_temp_dir()
-  dockerize(graph, output_dir = temp_dir)
-  Dockerfile <- readLines(file.path(temp_dir, "Dockerfile"))
-  expect_equal(max(lengths(regmatches(Dockerfile, gregexpr("&&", Dockerfile)))), 1)
-  expect_true(all(grepl("^\t&&", Dockerfile[grepl("&&", Dockerfile)])))
-  graph <- readRDS("../testdata/rang_bioc.RDS")
-  temp_dir <- .generate_temp_dir()
-  dockerize(graph, output_dir = temp_dir)
-  Dockerfile <- readLines(file.path(temp_dir, "Dockerfile"))
-  expect_equal(max(lengths(regmatches(Dockerfile, gregexpr("&&", Dockerfile)))), 1)
-  expect_true(all(grepl("^\t&&", Dockerfile[grepl("&&", Dockerfile)])))
-  graph <- readRDS("../testdata/rang_rio_old.RDS")
-  temp_dir <- .generate_temp_dir()
-  dockerize(graph, output_dir = temp_dir)
-  Dockerfile <- readLines(file.path(temp_dir, "Dockerfile"))
-  expect_equal(max(lengths(regmatches(Dockerfile, gregexpr("&&", Dockerfile)))), 1)
-  expect_true(all(grepl("^\t&&", Dockerfile[grepl("&&", Dockerfile)])))
+    graph <- readRDS("../testdata/graph.RDS")
+    temp_dir <- .generate_temp_dir()
+    dockerize(graph, output_dir = temp_dir)
+    Dockerfile <- readLines(file.path(temp_dir, "Dockerfile"))
+    expect_equal(max(lengths(regmatches(Dockerfile, gregexpr("&&", Dockerfile)))), 1)
+    expect_true(all(grepl("^\t&&", Dockerfile[grepl("&&", Dockerfile)])))
+    graph <- readRDS("../testdata/rang_bioc.RDS")
+    temp_dir <- .generate_temp_dir()
+    dockerize(graph, output_dir = temp_dir)
+    Dockerfile <- readLines(file.path(temp_dir, "Dockerfile"))
+    expect_equal(max(lengths(regmatches(Dockerfile, gregexpr("&&", Dockerfile)))), 1)
+    expect_true(all(grepl("^\t&&", Dockerfile[grepl("&&", Dockerfile)])))
+    graph <- readRDS("../testdata/rang_rio_old.RDS")
+    temp_dir <- .generate_temp_dir()
+    dockerize(graph, output_dir = temp_dir)
+    Dockerfile <- readLines(file.path(temp_dir, "Dockerfile"))
+    expect_equal(max(lengths(regmatches(Dockerfile, gregexpr("&&", Dockerfile)))), 1)
+    expect_true(all(grepl("^\t&&", Dockerfile[grepl("&&", Dockerfile)])))
 })
 
 test_that(".generate_wrapped_line with actual outcome", {