Add a check for memory-request validity

LieberInstitute · Sep 28, 2023 · 5597cd7 · 5597cd7
1 parent 2c29601
commit 5597cd7
Show file tree

Hide file tree

Showing 2 changed files with 10 additions and 2 deletions.
diff --git a/R/job_single.R b/R/job_single.R
@@ -82,11 +82,19 @@ job_single <- function(name, create_shell = FALSE, partition = "shared", memory
         stop("'logdir' has to be a relative path.")
     }
 
+    ## Check the validity of core and memory requests
     if (cores < 1) {
         stop("'cores' should be at least 1", call. = FALSE)
     }
     cores <- as.integer(cores)
 
+    if (!grepl('^[1-9][0-9]*[KMGT]$', memory)) {
+        stop(
+            "Could not parse memory request. Must be a character containing a positive integer and units 'K', 'M', 'G', or 'T'.",
+            call. = FALSE
+        )
+    }
+
     ## Specify the array options if a task number was specified
     array_spec <- if (!is.null(task_num)) {
         paste0("#SBATCH --array=1-", task_num, "%", tc, "\n")

diff --git a/tests/testthat/test-job_single.R b/tests/testthat/test-job_single.R
@@ -20,8 +20,8 @@ test_that("job_single", {
     expect_error(run_test(email = "hello"), "'email' should be one of")
     expect_error(run_test(logdir = "/logs"), "relative path")
     expect_error(run_test(cores = 0.5), "should be at least 1")
-    expect_error(run_test(memory = 10), "invalid memory request")
-    expect_error(run_test(memory = "5GB"), "invalid memory request")
+    expect_error(run_test(memory = 10), "Could not parse memory request")
+    expect_error(run_test(memory = "5GB"), "Could not parse memory request")
     run_test()
     expect_error(run_test(delete = FALSE, create_shell = TRUE), "already exists!")
 })