tests/testthat/test-axecute.R

In logrx: A Logging Utility Focus on Clinical Trial Programming Workflows

test_that("axecute will run a file and create the necessary log", {
   options("log.rx" = NULL)
   scriptPath <- tempfile()
   logDir <- tempdir()
   writeLines("print('hello logrx')", con = scriptPath)

   # check no log is currently written out
   expect_warning(expect_error(file(file.path(logDir, "log_out"), "r"), "cannot open the connection"))

   axecute(scriptPath, log_name = "log_out", log_path = logDir)
   con <- file(file.path(logDir, "log_out"), "r")
   flines <- readLines(con)
   close(con)

   # check that the output file is populated
   expect_gt(length(flines), 1)
   # check all the elements are there
   expect_true(grepl(paste(write_log_header("logrx Metadata"), collapse = ','),
                     paste(flines,collapse = ',')))
   expect_true(grepl(paste(write_log_header("User and File Information"), collapse = ','),
                     paste(flines,collapse = ',')))
   expect_true(grepl(paste(write_log_header("Session Information"), collapse = ','),
                     paste(flines,collapse = ',')))
   expect_true(grepl(paste(write_log_header("Masked Functions"), collapse = ','),
                     paste(flines,collapse = ',')))
   expect_true(grepl(paste(write_log_header("Program Run Time Information"), collapse = ','),
                     paste(flines,collapse = ',')))
   expect_true(grepl(paste(write_log_header("Errors and Warnings"), collapse = ','),
                     paste(flines,collapse = ',')))
   expect_true(grepl(paste(write_log_header("Messages, Output, and Result"), collapse = ','),
                     paste(flines,collapse = ',')))
   expect_true(grepl(paste(write_log_header("Log Output File"), collapse = ','),
                     paste(flines,collapse = ',')))

   # remove all the stuff we added
   rm(flines, con, scriptPath, logDir)
   log_remove()
})

test_that("to_report works to control log output elements", {
   options("log.rx" = NULL)
   scriptPath <- tempfile()
   logDir <- tempdir()
   writeLines(
      c("message('hello logrx')",
        "cat('this is output')",
        "data.frame(c(8, 6, 7, 5, 3, 0, 9))"),
      con = scriptPath)

   # check no log is currently written out
   expect_warning(expect_error(file(file.path(logDir, "log_out_report"), "r"), "cannot open the connection"))

   axecute(scriptPath,
           log_name = "log_out_report",
           log_path = logDir,
           to_report = c("messages", "result"))
   con <- file(file.path(logDir, "log_out_report"), "r")
   flines <- readLines(con)
   close(con)

   expect_true(any(grepl("^Messages:", flines) == TRUE))
   expect_true(all(grepl("^Output:", flines) != TRUE))
   expect_true(any(grepl("^Result:", flines) == TRUE))

   rm(flines, con, scriptPath, logDir)
   log_remove()
})

test_that("show_repo_url works to show repo url elements", {
   options("log.rx" = NULL)
   scriptPath <- tempfile()
   logDir <- tempdir()
   writeLines(
      c("message('hello logrx')",
        "cat('this is output')",
        "data.frame(c(8, 6, 7, 5, 3, 0, 9))"),
      con = scriptPath)

   # check no log is currently written out
   expect_warning(expect_error(file(file.path(logDir, "log_out_repo_url"), "r"), "cannot open the connection"))

   axecute(scriptPath, log_name = "log_out_repo_url",
           log_path = logDir,
           show_repo_url = TRUE
   )
   con <- file(file.path(logDir, "log_out_repo_url"), "r")
   flines <- readLines(con)
   close(con)

   expect_true(grepl(paste(write_log_header("Repo URLs"), collapse = ','),
                     paste(flines,collapse = ',')))
   rm(flines, con)
   log_remove()

   axecute(scriptPath, log_name = "log_out_repo_url2",
           log_path = logDir,
           show_repo_url = FALSE
   )
   con <- file(file.path(logDir, "log_out_repo_url2"), "r")
   flines <- readLines(con)
   close(con)

   expect_false(grepl(paste(write_log_header("Repo URLs"), collapse = ','),
                      paste(flines,collapse = ',')))
   rm(flines, con, scriptPath, logDir)
})

test_that("include_rds works to output log as rds", {
   options("log.rx" = NULL)
   scriptPath <- tempfile()
   logDir <- tempdir()
   writeLines(
      c("message('hello logrx')",
        "cat('this is output')",
        "data.frame(c(8, 6, 7, 5, 3, 0, 9))"),
      con = scriptPath)

   # check no log is currently written out
   expect_warning(expect_error(file(file.path(logDir, "log_out_nested"), "r"), "cannot open the connection"))

   axecute(scriptPath,
           log_name = "log_out_nested",
           log_path = logDir,
           include_rds = TRUE,
           to_report = c("messages", "result"))
   con <- file(file.path(logDir, "log_out_nested.Rds"), "r")
   logRDS <- readRDS(file.path(logDir, "log_out_nested.Rds"))

   expect_type(logRDS, "list")
   expect_true("messages" %in% names(logRDS))
   expect_true(all(is.na(logRDS$output)))
   expect_true("result" %in% names(logRDS))
   expect_true("start_time" %in% names(logRDS))

   rm(con, scriptPath, logDir, logRDS)
   log_remove()
})

test_that("axecute will run a markdown file and create the necessary log", {
   options("log.rx" = NULL)

   scriptPath <- test_path("ref", "ex1.Rmd")
   logDir <- tempdir()

   # check no log is currently written out
   expect_warning(expect_error(file(file.path(logDir, "rmd_log_out"), "r"), "cannot open the connection"))

   axecute(scriptPath, log_name = "rmd_log_out", log_path = logDir)
   con <- file(file.path(logDir, "rmd_log_out"), "r")
   flines <- readLines(con)
   close(con)

   # check that the output file is populated
   expect_gt(length(flines), 1)
   # check all the elements are there
   expect_true(grepl(paste(write_log_header("logrx Metadata"), collapse = ','),
      paste(flines,collapse = ',')))
   expect_true(grepl(paste(write_log_header("User and File Information"), collapse = ','),
      paste(flines,collapse = ',')))
   expect_true(grepl(paste(write_log_header("Session Information"), collapse = ','),
      paste(flines,collapse = ',')))
   expect_true(grepl(paste(write_log_header("Masked Functions"), collapse = ','),
      paste(flines,collapse = ',')))
   expect_true(grepl(paste(write_log_header("Program Run Time Information"), collapse = ','),
      paste(flines,collapse = ',')))
   expect_true(grepl(paste(write_log_header("Errors and Warnings"), collapse = ','),
      paste(flines,collapse = ',')))
   expect_true(grepl(paste(write_log_header("Messages, Output, and Result"), collapse = ','),
      paste(flines,collapse = ',')))
   expect_true(grepl(paste(write_log_header("Log Output File"), collapse = ','),
      paste(flines,collapse = ',')))

   # remove all the stuff we added
   rm(flines, con, scriptPath, logDir)
   log_remove()
})