tests/testthat/test_summary.nprcgenekeeprErr.R

In rmsharp/nprcmanager: Genetic Tools for Colony Management

#' Copyright(c) 2017-2020 R. Mark Sharp
# This file is part of nprcgenekeepr
context("summary.nprcgenekeeprErr")
library(testthat)
library(stringi)

pedOne <- nprcgenekeepr::pedOne
test_that("summary.nprcgenekeeprErr provides expected classes of output", {
  expect_equal(class(summary(qcStudbook(pedOne, reportErrors = TRUE))$txt),
               "character")
  expect_equal(class(summary(qcStudbook(pedOne, reportErrors = TRUE))$sp),
               "data.frame")
})
test_that("summary.nprcgenekeeprErr provides expected output", {
  expect_equal(length(summary(qcStudbook(pedOne, reportErrors = TRUE))$txt), 1)
  expect_equal(nrow(summary(qcStudbook(pedOne, reportErrors = TRUE))$sp), 3)
  expect_equal(stri_count_regex(
    summary(qcStudbook(pedOne, reportChanges = TRUE, reportErrors = TRUE))$txt,
    "\\n"), 9)
  pedTwo <- pedOne
  pedTwo$sex <- NULL
  expect_true(stri_detect_regex(
    summary(qcStudbook(pedTwo, reportChanges = TRUE, reportErrors = TRUE))$txt,
    pattern =
      "sex.\\n The required columns are: id, sire, dam, sex, and birth"))
  pedTwo <- pedOne
  pedTwo$birth_date <- "badDate"
  expect_true(stri_detect_regex(
    summary(qcStudbook(pedTwo, reportChanges = TRUE, reportErrors = TRUE))$txt,
    pattern = stri_c("There are 8 rows having an invalid date. ",
                     "The first five records having bad dates are ",
                     "on rows 1, 2, 3, 4, and 5.")))
})
test_that(
  "summary.nprcgenekeeprErr identifies individual bad dates in date columns", {
  birth <- as.character(pedOne$birth_date, format = "%Y-%m-%d")
  birth[5] <- "04-02-2015"
  birth[6] <- "03-17-2009"
  pedEight <- pedOne
  pedEight$birth_date <- NULL
  pedEight$birth <- birth
  ped8 <- qcStudbook(pedEight, minParentAge = NULL, reportErrors = TRUE)
  summary(ped8)
  expect_true(stri_detect_fixed(summary(ped8)$txt,
                                "rows having an invalid date are: 5 and 6"))
})
test_that("summary.nprcgenekeeprErr identifies bad database connection", {
  birth <- as.character(pedOne$birth_date, format = "%Y-%m-%d")
  birth[5] <- "04-02-2015"
  birth[6] <- "03-17-2009"
  pedEight <- pedOne
  pedEight$birth_date <- NULL
  pedEight$birth <- birth
  ped8 <- qcStudbook(pedEight, minParentAge = NULL, reportErrors = TRUE)
  ped8$failedDatabaseConnection <-
    "Database connection failed: configuration or permissions are invalid."
  summary(ped8)
  expect_true(stri_detect_fixed(summary(ped8)$txt,
                                "Database connection failed"))
})