test: add basic tests for run & main.R

.github/workflows/tests.yml

@@ -0,0 +1,32 @@
+name: tests
+
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+    branches: [main, dev]
+
+permissions:
+  contents: read
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Parse environment.json and set Docker image
+        id: docker_image
+        run: |
+          IMAGE=$(jq -r '.base_image' .codeocean/environment.json)
+          IMAGE=${IMAGE//codeocean/nciccbr}
+          echo "image=$IMAGE" >> $GITHUB_OUTPUT
+          echo "Using Docker image: $IMAGE"
+
+      - name: Run tests in Docker
+        run: |
+          docker run --rm \
+            -v ${{ github.workspace }}:/workspace \
+            -w /workspace \
+            ${{ steps.docker_image.outputs.image }} \
+            Rscript tests/testthat.R

README.md

@@ -2,5 +2,7 @@
 
 Code Ocean capsule: MOSuite - plot expression heatmap
 
+[![tests](https://github.com/NIDAP-Community/MOSuite-plot-expr-heatmap/actions/workflows/tests.yml/badge.svg)](https://github.com/NIDAP-Community/MOSuite-plot-expr-heatmap/actions/workflows/tests.yml)
+
 - [Code Ocean Capsule](https://poc-nci.codeocean.io/capsule/6385174/tree) | [Latest Release](https://poc-nci.codeocean.io/capsule/0936928/tree/latest)
 - [MOSuite R package docs](https://ccbr.github.io/MOSuite/)

tests/test-setup.R

@@ -0,0 +1,28 @@
+testthat::test_that("basic test setup is valid", {
+  cwd <- getwd()
+  repo_root_script <- normalizePath(dirname(cwd))
+
+  fixture_file <- file.path(
+    repo_root_script,
+    "..",
+    "code",
+    "MOSuite",
+    "tests",
+    "testthat",
+    "data",
+    "moo.rds"
+  )
+
+  code_main <- file.path(repo_root_script, "..", "code", "main.R")
+  code_run <- file.path(repo_root_script, "..", "code", "run")
+
+  testthat::expect_true(file.exists(fixture_file))
+  testthat::expect_true(file.exists(code_main))
+  testthat::expect_true(file.exists(code_run))
+
+  testthat::skip_if_not_installed("readr")
+  testthat::expect_no_error({
+    moo <- readr::read_rds(fixture_file)
+    testthat::expect_gt(length(class(moo)), 0)
+  })
+})

tests/testthat.R

@@ -0,0 +1,2 @@
+library(testthat)
+test_dir(here::here('tests/testthat/'))

tests/testthat/helper-cli.R

@@ -0,0 +1,75 @@
+setup_cli_workspace <- function(prefix = "mosuite_plot_expr_heatmap_test_") {
+  workspace <- tempfile(prefix)
+  dir.create(workspace)
+
+  code_dir <- file.path(workspace, "code")
+  data_dir <- file.path(workspace, "data")
+  results_dir <- file.path(workspace, "results")
+  dir.create(code_dir, recursive = TRUE)
+  dir.create(data_dir, recursive = TRUE)
+  dir.create(file.path(results_dir, "figures"), recursive = TRUE)
+  dir.create(file.path(results_dir, "moo"), recursive = TRUE)
+
+  repo_root <- normalizePath(
+    file.path(testthat::test_path(), "..", ".."),
+    mustWork = TRUE
+  )
+
+  test_data_file <- file.path(
+    repo_root,
+    "code",
+    "MOSuite",
+    "tests",
+    "testthat",
+    "data",
+    "moo.rds"
+  )
+
+  expect_true(
+    file.exists(test_data_file),
+    info = paste("Test data file should exist at", test_data_file)
+  )
+  file.copy(test_data_file, file.path(data_dir, "moo.rds"), overwrite = TRUE)
+
+  file.copy(
+    file.path(repo_root, "code", "main.R"),
+    file.path(code_dir, "main.R"),
+    overwrite = TRUE
+  )
+
+  # Keep main.R behavior the same while pointing to this checkout's MOSuite package.
+  main_copy <- file.path(code_dir, "main.R")
+  main_lines <- readLines(main_copy)
+  main_lines <- gsub(
+    'devtools::load_all("/code/MOSuite")',
+    sprintf(
+      'devtools::load_all("%s")',
+      file.path(repo_root, "code", "MOSuite")
+    ),
+    main_lines,
+    fixed = TRUE
+  )
+  writeLines(main_lines, main_copy)
+
+  list(
+    workspace = workspace,
+    code_dir = code_dir,
+    results_dir = results_dir,
+    repo_root = repo_root
+  )
+}
+
+expect_plot_created <- function(results_dir) {
+  plot_path <- file.path(results_dir, "figures", "heatmap", "expr_heatmap.png")
+  expect_true(file.exists(plot_path), info = "Heatmap plot should be created")
+  expect_true(
+    file.info(plot_path)$size > 0,
+    info = "Heatmap plot should be non-empty"
+  )
+}
+
+common_cli_args <- c(
+  "--count_type=clean",
+  "--display_gene_names=FALSE",
+  "--display_sample_names=TRUE"
+)

tests/testthat/test-main.R

@@ -0,0 +1,33 @@
+test_that("main.R CLI creates expression heatmap plot", {
+  setup <- setup_cli_workspace("mosuite_plot_expr_heatmap_test_")
+  on.exit(unlink(setup$workspace, recursive = TRUE), add = TRUE)
+
+  old_wd <- getwd()
+  setwd(setup$code_dir)
+  on.exit(setwd(old_wd), add = TRUE)
+
+  exit_code <- system2("Rscript", args = c("main.R", common_cli_args))
+  expect_equal(exit_code, 0, info = "main.R should execute without error")
+
+  expect_plot_created(setup$results_dir)
+})
+
+test_that("run wrapper executes and creates expression heatmap plot", {
+  setup <- setup_cli_workspace("mosuite_plot_expr_heatmap_run_test_")
+  on.exit(unlink(setup$workspace, recursive = TRUE), add = TRUE)
+
+  file.copy(
+    file.path(setup$repo_root, "code", "run"),
+    file.path(setup$code_dir, "run"),
+    overwrite = TRUE
+  )
+
+  old_wd <- getwd()
+  setwd(setup$code_dir)
+  on.exit(setwd(old_wd), add = TRUE)
+
+  exit_code <- system2("bash", args = c("run", common_cli_args))
+  expect_equal(exit_code, 0, info = "run script should execute without error")
+
+  expect_plot_created(setup$results_dir)
+})