From ab2b67fae9156169269bd08d23ee55a1f6d904ee Mon Sep 17 00:00:00 2001
From: Nick-Eagles <nick.eagles@libd.org>
Date: Thu, 28 Sep 2023 13:49:30 -0400
Subject: [PATCH] Remove array_submit.R, which isn't ready for testing (or even
 SLURM)

---
 R/array_submit.R | 101 -----------------------------------------------
 1 file changed, 101 deletions(-)
 delete mode 100644 R/array_submit.R

diff --git a/R/array_submit.R b/R/array_submit.R
deleted file mode 100644
index 305c13c..0000000
--- a/R/array_submit.R
+++ /dev/null
@@ -1,101 +0,0 @@
-#' Submit an array job with a specified set of task IDs
-#'
-#' Given a bash script that specifies the SGE option -t (that is, an array job),
-#' this function submits that job using `qsub` for a given list of task
-#' IDs. This function is useful in case some tasks for a given job failed which
-#' you can find using `qstat | grep Eqw` or other options.
-#'
-#' @param job_bash A `character(1)` vector with the name of a bash script
-#' in the current working directory.
-#' @param task_ids A set of task ids that will get parsed by [parse_task_ids].
-#' @param submit A `logical(1)` vector determining whether to actually submit
-#' the tasks or not using `qsub`.
-#' @param restore A `logical(1)` vector determining whether to restore the
-#' script to the original state.
-#'
-#' @return The path to `job_bash`.
-#' @export
-#' @author Leonardo Collado-Torres
-#' @import purrr glue
-#'
-#' @examples
-#'
-#' ## Choose a script name
-#' job_name <- paste0("array_submit_example_", Sys.Date())
-#'
-#' ## Create an array job on the temporary directory
-#' with_wd(tempdir(), {
-#'     ## Create an array job script to use for this example
-#'     job_single(
-#'         name = job_name,
-#'         create_shell = TRUE,
-#'         task_num = 100
-#'     )
-#'
-#'     ## Now we can submit the SGE job for a set of task IDs
-#'     array_submit(
-#'         job_bash = paste0(job_name, ".sh"),
-#'         task_ids = "225019-225038:1,225040,225043",
-#'         submit = FALSE
-#'     )
-#' })
-#'
-array_submit <- function(job_bash, task_ids, submit = file.exists("/cm/shared/apps/sge/sge-8.1.9/default/common/accounting_20191007_0300.txt"),
-    restore = TRUE) {
-    ## Check that the script is local, in case the script uses -cwd
-    if (basename(job_bash) != job_bash) {
-        stop(
-            "The 'job_bash' script has to exist in the current working directory.\n",
-            "This protects the user from the case where the script uses -cwd.",
-            call. = FALSE
-        )
-    }
-
-    task_ids <- parse_task_ids(task_ids)
-    job_original <- readLines(job_bash)
-    t_line <- which(grepl("#\\$ -t ", job_original))
-    if (length(t_line) != 1) {
-        stop("Could not find the line that specifies that this is an array job,\n",
-            "that is, the line that starts with: #$ -t ",
-            call. = FALSE
-        )
-    }
-
-    ## Loop through the task ids and re-submit
-    purrr::walk(task_ids, function(task) {
-        ## Replace the script with the current task ID
-        job_new <- job_original
-        job_new[t_line] <- glue::glue("#$ -t {task}")
-        writeLines(job_new, con = job_bash)
-
-
-        ## If you wanted to see the files use:
-        # cat(job_new)
-
-        ## Show how to re-submit or actually re-submit:
-        message(paste(Sys.time(), "resubmitting the SGE job for task", task))
-        cmd <- paste("qsub", job_bash)
-        message(cmd)
-        if (submit) {
-            ## Check if qstat can run
-            qstat_status <- suppressWarnings(
-                system("qstat", ignore.stdout = TRUE, ignore.stderr = TRUE)
-            )
-            if (qstat_status == 127) {
-                system(cmd)
-            } else {
-                cmd_msg <- system(cmd, intern = TRUE)
-                message(cmd_msg)
-            }
-        }
-
-        ## Done
-        return(cmd)
-    })
-
-    ## Restore the original script
-    if (restore) writeLines(job_original, con = job_bash)
-
-    ## Return the path
-    return(invisible(job_bash))
-}