Allow to specify temp filenames in 'mhcnuggetsr_self_test'

R/install_pip.R

@@ -1,22 +1,37 @@
 #' Install pip.
+#' @param python_script_filename name of a temporary Python
+#' script file. Will be deleted at the end of the function
 #' @return Nothing
 #' @examples
 #' \dontrun{
 #'   install_pip()
 #' }
 #' @author Richèl J.C. Bilderbeek
 #' @export
-install_pip <- function() {
-  script_filename <- tempfile()
+install_pip <- function(
+  python_script_filename = file.path(
+    tmpdir = rappdirs::user_cache_dir(),
+    "temp_install_pip.py"
+  )
+) {
+  dir.create(
+    dirname(python_script_filename),
+    showWarnings = FALSE,
+    recursive = TRUE
+  )
 
   utils::download.file(
     url = "https://bootstrap.pypa.io/get-pip.py",
-    destfile = script_filename,
+    destfile = python_script_filename,
     quiet = TRUE
   )
-  system2(
+  error_code <- system2(
     reticulate::py_config()$python,
-    args = c(script_filename, "--user"),
+    args = c(python_script_filename, "--user"),
     stdout = FALSE
   )
+
+  file.remove(python_script_filename)
+
+  error_code
 }

R/mhcnuggetsr_self_test.R

@@ -7,11 +7,19 @@
 #' @author Richèl J.C. Bilderbeek
 #' @export
 mhcnuggetsr_self_test <- function(
-  mhcnuggets_options = create_test_mhcnuggets_options()
+  mhcnuggets_options = create_test_mhcnuggets_options(),
+  peptides_path = create_temp_peptides_path(),
+  mhcnuggets_output_filename = mhcnuggetsr::create_temp_peptides_path(
+    fileext = ".csv"
+  ),
+  verbose = FALSE
 ) {
   df <- mhcnuggetsr::predict_ic50(
     peptides = "AIAACAMLLV",
-    mhcnuggets_options = mhcnuggets_options
+    mhcnuggets_options = mhcnuggets_options,
+    peptides_path = peptides_path,
+    mhcnuggets_output_filename = mhcnuggets_output_filename,
+    verbose = verbose
   )
   testthat::expect_equal(df$ic50, 5578.77)
 }

R/predict_ic50.R

@@ -31,19 +31,34 @@
 predict_ic50 <- function(
   mhcnuggets_options,
   peptides,
-  peptides_path = create_temp_peptides_path()
+  peptides_path = create_temp_peptides_path(),
+  mhcnuggets_output_filename = mhcnuggetsr::create_temp_peptides_path(
+    fileext = ".csv"
+  ),
+  verbose = FALSE
 ) {
   if (any(nchar(peptides) > 15)) {
     stop(
       "'peptides' must have lengths of at most 15 amino acids. \n",
       "Tip: use 'predict_ic50s' to get the IC50s for longer peptides"
     )
   }
+  dir.create(
+    path = dirname(peptides_path),
+    showWarnings = FALSE,
+    recursive = TRUE
+  )
+
+  # Write the peptides to file
   writeLines(text = peptides, con = peptides_path)
+  testthat::expect_true(file.exists(peptides_path))
   ic50 <- mhcnuggetsr::predict_ic50_from_file(
     mhcnuggets_options = mhcnuggets_options,
-    peptides_path = peptides_path
+    peptides_path = peptides_path,
+    mhcnuggets_output_filename = mhcnuggets_output_filename,
+    verbose = verbose
   )
+  testthat::expect_true(file.exists(peptides_path))
   file.remove(peptides_path)
   ic50
 }

R/predict_ic50_from_file.R

@@ -27,7 +27,8 @@ predict_ic50_from_file <- function(
   peptides_path,
   mhcnuggets_output_filename = mhcnuggetsr::create_temp_peptides_path(
     fileext = ".csv"
-  )
+  ),
+  verbose = FALSE
 ) {
   if (!file.exists(peptides_path)) {
     stop(
@@ -39,6 +40,14 @@ predict_ic50_from_file <- function(
     stop("'peptides' must have lengths of at most 15")
   }
   mhcnuggetsr::check_mhcnuggets_options(mhcnuggets_options)
+  if (peptides_path == mhcnuggets_output_filename) {
+    stop(
+      "'peptides_path' and 'mhcnuggets_output_filename' must be different, \n",
+      "because 'mhcnuggets_output_filename' is a temporary file that will \n",
+      "be deleted. \n",
+      "peptides_path: ", peptides_path
+    )
+  }
 
   if (is.na(mhcnuggets_options$mhc_class)) {
     if (mhcnuggets_options$mhc %in% mhcnuggetsr::get_mhc_1_haplotypes()) {
@@ -52,21 +61,62 @@ predict_ic50_from_file <- function(
   }
   testthat::expect_true(mhcnuggets_options$mhc_class %in% c("I", "II"))
 
+  dir.create(
+    path = dirname(mhcnuggets_output_filename),
+    showWarnings = FALSE,
+    recursive = TRUE
+  )
+
+  # Up to full path
+  peptides_path <- normalizePath(peptides_path)
+  testthat::expect_true(file.exists(peptides_path))
+  mhcnuggets_output_filename <- normalizePath(
+    mhcnuggets_output_filename,
+    mustWork = FALSE
+  )
+  testthat::expect_true(peptides_path != mhcnuggets_output_filename)
+
+  if (verbose) {
+    message(
+      "Calling MHCnuggets, with:\n",
+      "class: ", mhcnuggets_options$mhc_class,"\n",
+      "peptides_path: ", peptides_path,"\n",
+      "mhc: ", mhcnuggets_options$mhc,"\n",
+      "ba_models: ", mhcnuggets_options$ba_models,"\n",
+      "output: ", mhcnuggets_output_filename,"\n"
+    )
+  }
+
   module <- reticulate::import_from_path(module = "mhcnuggets")
-  suppressMessages(
+  if (verbose) {
     module$src$predict$predict(
       class_ = mhcnuggets_options$mhc_class,
       peptides_path = peptides_path,
       mhc = mhcnuggets_options$mhc,
       ba_models = mhcnuggets_options$ba_models,
       output = mhcnuggets_output_filename
     )
-  )
+  } else {
+    suppressWarnings(
+      suppressMessages(
+        module$src$predict$predict(
+          class_ = mhcnuggets_options$mhc_class,
+          peptides_path = peptides_path,
+          mhc = mhcnuggets_options$mhc,
+          ba_models = mhcnuggets_options$ba_models,
+          output = mhcnuggets_output_filename
+        )
+      )
+    )
+  }
+  testthat::expect_true(file.exists(peptides_path))
 
   df <- tibble::as_tibble(utils::read.csv(mhcnuggets_output_filename))
   df$peptide <- as.character(df$peptide)
 
   file.remove(mhcnuggets_output_filename)
 
+  testthat::expect_true(file.exists(peptides_path))
+
   df
 }

tests/testthat/test-mhcnuggetsr_self_test.R

@@ -1,7 +1,33 @@
-test_that("use", {
+test_that("default use", {
   if (is_mhcnuggets_installed()) {
     expect_silent(mhcnuggetsr_self_test())
   } else {
     expect_error(mhcnuggetsr_self_test())
   }
 })
+
+test_that("verbosity", {
+  if (is_mhcnuggets_installed()) {
+    expect_message(mhcnuggetsr_self_test(verbose = TRUE))
+  } else {
+    expect_message(mhcnuggetsr_self_test(verbose = TRUE))
+  }
+})
+
+test_that("detailed use", {
+  if (!is_mhcnuggets_installed()) return()
+
+  mhcnuggets_options <- create_test_mhcnuggets_options()
+  peptides_path <- create_temp_peptides_path()
+  mhcnuggets_output_filename = mhcnuggetsr::create_temp_peptides_path(
+    fileext = ".csv"
+  )
+  expect_silent(
+    mhcnuggetsr_self_test(
+      mhcnuggets_options = mhcnuggets_options,
+      peptides_path = peptides_path,
+      mhcnuggets_output_filename = mhcnuggets_output_filename,
+      verbose = FALSE
+    )
+  )
+})

tests/testthat/test-predict_ic50_from_file.R

@@ -161,3 +161,17 @@ test_that("abuse, too long peptide", {
     "'peptides' must have lengths of at most 15"
   )
 })
+
+test_that("abuse, too long peptide", {
+  peptides_path <- tempfile()
+  writeLines(text = "CCCCCCCCCCCCCCC", con = peptides_path)
+  expect_error(
+    predict_ic50_from_file(
+      peptides_path = peptides_path,
+      mhcnuggets_options = create_test_mhcnuggets_options(),
+      mhcnuggets_output_filename = peptides_path
+    ),
+    "'peptides_path' and 'mhcnuggets_output_filename' must be different"
+  )
+  file.remove(peptides_path)
+})