tests/testthat/test-log_functions.R

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

context("log functions")

bsp2_log <- system.file("extdata", "logs", "delete_bsp2.txt", package = "sgejobs")
twas_gene_HIPPO <- system.file("extdata", "logs",
    "compute_weights_full_HIPPO_gene.1.txt",
    package = "sgejobs"
)


nas <- as.POSIXlt(c(start = NA, end = NA), tz = "EST")
names(nas) <- c("start", "end")

test_that("log_date", {
    expect_error(log_date(paste0(bsp2_log, "hello")), "does not exist")
    expect_error(log_date(bsp2_log, date_lines = 1), "length 2")
    expect_equal(log_date(bsp2_log, date_lines = c("hello", "bye")), nas)
    expect_equal(date(log_date(bsp2_log))[1], as.Date("2019-09-07"))
    expect_equal(date(log_date(twas_gene_HIPPO))[1], as.Date("2019-08-12"))
})


test_that("log_jobid", {
    expect_error(log_jobid(paste0(bsp2_log, "hello")), "does not exist")
    expect_error(log_jobid(bsp2_log, jobid_header = c("a", "b")), "length 1")
    expect_equal(log_jobid(bsp2_log), "92500")
    expect_equal(log_jobid(twas_gene_HIPPO), "7751602")
})