Find logs relative to the directory containing the shell script, if r…

…elative paths are used. Closes #1

R/array_submit.R

@@ -103,25 +103,29 @@ array_submit <- function(name, task_ids = NULL, submit = FALSE, restore = TRUE,
         #   Find the log associated with that highest task
         #-----------------------------------------------------------------------
 
-        max_log <- job_original[grep("^#SBATCH -o ", job_original)] |>
-            str_extract("-o (.*)$", group = 1) |>
-            str_replace("%a", max_task)
-
-        #   For jobs created with 'job_loop', the actual log used will be on the
-        #   line where 'log_path' is defined, not '/dev/null'
-        if (!is.na(max_log) && (max_log == "/dev/null")) {
-            max_log <- job_original[grep("^log_path=", job_original)] |>
-                str_extract("^log_path=(.*)/", group = 1) |>
-                list.files(
-                    pattern = sprintf(
-                        "%s.*_%s\\.txt$",
-                        name,
-                        max_task
-                    ),
-                    full.names = TRUE
-                )
+        #   For 'job_loop', use the path in the line starting with 'log_path='.
+        #   Otherwise use the log in the line starting with '#SBATCH -o'.
+        last_occurence = rev(grep("^(#SBATCH -o |log_path=)", job_original))[1]
+        max_log = job_original[last_occurence] |>
+            #   Extract just the path
+            str_replace("^(#SBATCH -o |log_path=)", "") |>
+            #   Set the path for the highest task
+            str_replace("%a|\\$\\{SLURM_ARRAY_TASK_ID\\}", max_task)
+
+        #   If the log is specified with a relative path, make sure it's
+        #   relative to the directory containing the shell script
+        if (!grepl('^/', max_log)) {
+            max_log = file.path(dirname(sh_file), max_log)
         }
 
+        #   Find the precise path of the log in a way that's compatible with
+        #   both 'job_single' and 'job_loop'
+        max_log = list.files(
+            dirname(max_log),
+            pattern = sprintf("^%s.*_%s\\.txt$", name, max_task),
+            full.names = TRUE
+        )
+
         if (verbose) {
             message(
                 sprintf(