tests/testthat/test-array_submit.R

In LieberInstitute/sgejobs: Helper functions for SGE jobs at JHPCE

## Choose a script name
job_name <- paste0("array_submit_test_", Sys.Date())


run_test <- function(restore) {
    ## Delete it in case it exists
    unlink(file.path(tempdir(), paste0(job_name, ".sh")))

    ## 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
        )

        original <- readLines(paste0(job_name, ".sh"))

        ## 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 = !restore,
            restore = restore
        )

        final <- readLines(paste0(job_name, ".sh"))
        NULL
    })

    return(list("original" = original, "final" = final))
}

test1 <- run_test(restore = TRUE)
test2 <- run_test(restore = FALSE)
t_line <- which(grepl("#\\$ -t ", test2$original))


run_test_break <- function(restore) {
    ## Delete it in case it exists
    unlink(file.path(tempdir(), paste0(job_name, ".sh")))

    ## 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
        )

        original <- readLines(paste0(job_name, ".sh"))
        ## Break the original script
        writeLines(original[-grep("#$ -t", original)], paste0(job_name, ".sh"))

        ## 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 = !restore,
            restore = restore
        )
    })
}

test_that("array_submit", {
    expect_equal(test1$original, test1$final)
    expect_equal(test2$original[-t_line], test2$final[-t_line])
    expect_equal(test2$final[t_line], "#$ -t 225043-225043")
    expect_error(
        array_submit(file.path(tempdir(), paste0(job_name, ".sh")), "1"),
        "script has to exist in the current working directory"
    )
    expect_error(
        run_test_break(FALSE),
        "Could not find the line that specifies that this is an array job"
    )
})