tests/testthat/test-yspec.R

In metrumresearchgroup/yspec: Data Specification for Pharmacometrics

library(yspec)
library(testthat)

.test_load <- yspec:::.test_load
.test_spec <- yspec:::.test_spec

context("test-yspec")

spec <- load_spec_ex(file = "spec.yml")

test_that("yspec object [YSP-TEST-0134]", {
  expect_is(spec, "yspec")
  expect_true(is.list(spec))
  cl <- purrr::map_chr(spec, class)
  expect_true(all(cl=="ycol"))
})

test_that("yspec methods [YSP-TEST-0135]", {
  expect_is(as.list(spec), "list")
  expect_is(spec$WT, "ycol")
  expect_identical(spec$WT$col, "WT")
  expect_identical(spec$WT,spec[["WT"]])
  expect_equal(spec$EGFR$range, c(10,300))
  expect_is(as.data.frame(spec), "data.frame")
  expect_identical(as.data.frame(spec), summary(spec))
  expect_is(head(spec), "data.frame")
  expect_is(tail(spec), "data.frame")
  pr <- capture.output(print(spec))
  expect_true(grepl("^ STUDY", pr[14]))
})

test_that("misc helpers [YSP-TEST-0136]", {
  expect_equal(yspec:::yml_rm("foo.yml"), "foo")
  expect_equal(yspec:::yml_rm("foo.yaml"), "foo")
  expect_equal(yspec:::yml_rm("foo.txt"), "foo.txt")
})

test_that("ycol accessors [YSP-TEST-0137]", {
  expect_identical("kg", yspec:::unit(spec$WT))
  expect_identical("10 to 300", yspec:::Range(spec$EGFR))
  expect_identical("character", yspec:::type(spec$HAIR))
  expect_identical("dependent variable", yspec:::long(spec$DV))
  expect_identical("Compartment", yspec:::short(spec$CMT))
  expect_identical("per NONMEM specifications", yspec:::comment(spec$EVID))
  expect_identical("C", yspec:::lookup(spec$C))
  expect_identical("<none>", yspec:::lookup(spec$DV))
})

test_that("spec object meta data [YSP-TEST-0138]", {
  meta <- get_meta(spec)
  expect_is(meta[["spec_file"]], "character")
  expect_is(meta[["spec_path"]], "character")
  expect_is(meta$primary_key, "character")
  expect_identical(meta[["spec_path"]], dirname(meta[["spec_file"]]))
  expect_identical(basename(meta[["spec_file"]]), "spec.yml")
})

test_that("testing input data [YSP-TEST-0139]", {
  expect_error(.test_load("foo"),
               regexp = "names not found")
  expect_error(.test_load("foo", 1, 2, 3),
               regexp = "names not found")
  expect_error(.test_load("foo", name = "Kyle"),
               regexp = "invalid column field")
})

test_that("testing input columns [YSP-TEST-0140]", {
  expect_error(.test_load("foo", values = c(1,2,3),
                          range = c(0,100)),
               regexp = "both values and range")
  expect_error(.test_load("foo", values = c(1,2,3),
                          decode = c("a","b")),
               regexp = "the length of values is not equal to the length of decode")
})

file <- system.file("spec", "test_lookup.yml", package = "yspec")

test_that("column data is merged when lookup is true [YSP-TEST-0141]", {
  raw <- yspec:::try_yaml(file)
  mspec <- load_spec_ex(file = "test_lookup.yml")
  look <- yspec:::ys_get_lookup(mspec)
  
  expect_null(raw$BMI$unit)
  expect_identical(mspec$BMI$unit, look$BMI$unit)
})

test_that("column data is not merged when lookup is false [YSP-TEST-0142]", {
  raw <- yspec:::try_yaml(file)
  mspec <- load_spec_ex(file = "test_lookup.yml")
  look <- yspec:::ys_get_lookup(mspec)
  expect_null(raw$ALB$unit)
  expect_identical(mspec$BMI$unit, look$BMI$unit)
})

test_that("combine two specs [YSP-TEST-0143]", {
  dat <- ys_help$spec()
  intn <- system.file("internal", "post.yml", package = "yspec")
  post <- ys_load(intn)
  spec <- c(dat,post)
  expect_identical(names(spec), c(names(dat),names(post)))
})

test_that("add column labels [YSP-TEST-0144]", {
  spec <- ys_help$spec()
  data <- ys_help$data()
  
  data2 <- ys_add_labels(data,spec)
  labs2 <- purrr::map(data2, attr, "label")
  expect_identical(labs2$WT,yspec:::label.ycol(spec$WT))
  expect_identical(labs2$STUDY,yspec:::label.ycol(spec$STUDY))
  
  data3 <- ys_add_labels(data,spec,function(x) x$short)
  labs3 <- purrr::map(data3, attr, "label")
  
  expect_identical(labs3$HT,spec$HT$short)
  expect_error(ys_add_labels(spec,data), "data does not inherit from class")
  expect_error(ys_add_labels(data,"A"), "spec does not inherit from class")
  datamix <- data[,sample(names(data))]
  expect_error(ys_add_labels(datamix,spec), "names\\(data\\) not identical to")
})