tests/testthat/test-specs.R

In dbosak01/libr: Libraries, Data Dictionaries, and a Data Step for R

context("Specs Tests")

base_path <- "c:\\packages\\libr\\tests\\testthat\\data"

base_path <- "./data"


test_that("import_spec() function works as expected.", {
  
  is <- import_spec(col1 = "character", col2 = "integer",
                   na = c("NA", ""),
                   trim_ws = FALSE)
  
  expect_equal(is$col_types, list(col1 = "character", col2 = "integer"))
  expect_equal(is$na, c("NA", ""))
  expect_equal(is$trim_ws, FALSE)
  
})

test_that("specs() function works as expected.", {
  
  is1 <- import_spec(col1 = "character", col2 = "integer",
                     na = c("NA", "-"),
                     trim_ws = FALSE)
  
  is2 <- import_spec(col1 = "numeric", col2 = "date:%d%m%Y",
                     na = c(" ", ""),
                     trim_ws = TRUE)
  spcs <- specs(na = c("NA", "-", " ", ""),
               trim_ws = TRUE, AB = is1, AC = is2)
  
  expect_equal(length(spcs$specs), 2)
  expect_equal(spcs$na, c("NA", "-", " ", ""))
  expect_equal(spcs$trim_ws, TRUE)
  expect_equal(spcs$specs$AB$trim_ws, FALSE)
  expect_equal(spcs$specs$AB$col_types[[1]], "character")
  expect_equal(spcs$specs$AC$col_types[[1]], "numeric")
  
  s1 <- capture.output(print(spcs))
  expect_equal(length(s1) > 0, TRUE)
  
  s2 <- capture.output(print(spcs, verbose = TRUE))
  expect_equal(length(s1) > 0, TRUE)
  
})


test_that("write_specs() and read_specs() functions works as expected.", {
  
  is1 <- import_spec(col1 = "character", col2 = "integer",
                     na = c("NA", "-"),
                     trim_ws = FALSE)
  
  is2 <- import_spec(col1 = "numeric", col2 = "date:%d%m%Y",
                     na = c(" ", ""),
                     trim_ws = TRUE)
  spcs <- specs(na = c("NA", "-", " ", ""),
                trim_ws = TRUE, AB = is1, AC = is2)
  
  tmp <- tempdir()
  pth2 <- write.specs(spcs, tmp)
  
  fe <- file.exists(file.path(tmp, "spcs.specs"))
  expect_equal(fe, TRUE)

  
  spcs2 <- read.specs(pth2)
  
  
  expect_equal(length(spcs2$specs), 2)
  expect_equal(spcs2$na, c("NA", "-", " ", ""))
  expect_equal(spcs2$trim_ws, TRUE)
  expect_equal(spcs2$specs$AB$trim_ws, FALSE)
  expect_equal(spcs2$specs$AB$col_types[[1]], "character")
  expect_equal(spcs2$specs$AC$col_types[[1]], "numeric")
  
  spcs3 <- read.specs(tmp)
  expect_equal(length(spcs3$specs), 2)
  
  expect_error(write.specs("fork"))
  expect_error(read.specs("fork"))
  
  if (fe)
    unlink(pth2)
  
})

test_that("get_colspec_xlsx() works as expected.", {
  
  expect_error(get_colspec_xlsx(c(one = "character", 
                       two = "integer", 
                       four = "date:%d%m%y"),
                     5, c("one", "two", "three", "four")))
  
  res <- get_colspec_xlsx(c(one = "character", 
                       two = "integer", 
                       four = "date:%d%m%y"),
                     4, c("one", "two", "three", "four"))

  expect_equal(res[["one"]], "text")
  expect_equal(res[["two"]], "numeric")
  expect_equal(res[["three"]], "guess")
  expect_equal(res[["four"]], "date")
  
})

test_that("get_colspec_csv() works as expected.", {
  
  res <- get_colspec_csv(c(one = "character", 
                       two = "integer", 
                       four = "date=%d%m%y",
                       five = "numeric",
                       six = "guess",
                       seven = "time=%H:%M:%S",
                       eight = "datetime=%d%m%y %H:%M:%S",
                       nine = "logical"))
  
  expect_equal(res$cols[["one"]], col_character())
  expect_equal(res$cols[["two"]], col_integer())
  expect_equal(is.null(res$cols[["three"]]), TRUE)
  expect_equal(res$cols[["four"]], col_date(format = "%d%m%y"))
  expect_equal(res$cols[["five"]], col_double())
  expect_equal(res$cols[["six"]], col_guess())
  expect_equal(res$cols[["seven"]], col_time(format = "%H:%M:%S"))
  expect_equal(res$cols[["eight"]], col_datetime(format = "%d%m%y %H:%M:%S"))
  expect_equal(res$cols[["nine"]], col_logical())
  
})


test_that("libname works on PE data for csv.", {
  
  lst <- specs(PE = import_spec(PESTAT = "character",
                                na = ""))
  
  libname(dat, file.path(base_path, "PE"), "csv", import_specs = lst)
  

  expect_equal(length(dat), 1)
  

})

test_that("libname works on PE data for xlsx.", {
  
  lst <- specs(PE = import_spec(PESTAT = "character",
                                na = "NA"))
  
  
  libname(dat, file.path(base_path, "PE"), "xlsx", import_specs = lst)
  

  expect_equal(length(dat), 1)
  
  
})

test_that("libname works on PE data for xls.", {
  
  lst <- specs(PE = import_spec(PESTAT = "character",
                                na = ""))
  
  
  libname(dat, file.path(base_path, "PE"), "xls", import_specs = lst)
  
  
  expect_equal(length(dat), 1)
  
  
})

test_that("writing xls changes to xlsx.", {
  
  tmp <- tempdir()
  
  libname(dat, tmp, "xls")
  
  lib_add(dat, mtcars)
  
  
  fe <- file.exists(file.path(tmp, "mtcars.xlsx"))
  expect_equal(fe, TRUE)
  
  lib_delete(dat)
  
})

test_that("libname works on SDTM data for csv.", {
  
  lst <- specs(PE = import_spec(PESTAT = "character",
                                na = ""))
  
  
  libname(dat, file.path(base_path, "SDTM"), "csv", import_specs = lst)
  
  expect_equal(length(dat), 13)
  
})

test_that("libname works on SDTM data for sas7bdat.", {
  
  

  libname(dat, file.path(base_path, "SDTM"), "sas7bdat")
  

  expect_equal(length(dat), 13)

})


test_that("import_specs works as expected with dates.", {
  
  library(readr)

  # Create temp path
  tmp <- file.path(tempdir(), "mtcars.csv")

  # Create data for illustration purposes
  df <- data.frame(vehicle = rownames(mtcars), mtcars[c("mpg", "cyl", "disp")], 
                   stringsAsFactors = FALSE)

  # Kill rownames
  rownames(df) <- NULL

  # Add some columns
  df <- df[1:10, ] %>%
    datastep({

      recdt <- "10JUN1974"

      if (mpg >= 20)
        mpgcat <- "High"
      else
        mpgcat <- "Low"

      if (cyl == 8)
        cyl8 <- TRUE

    })

  df

  # Save to temp directory
  write_csv(df, tmp)

  # Create import spec
  spcs <- specs(mtcars = import_spec(vehicle = "character",
                                     cyl = "integer",
                                     recdt = "date=%d%b%Y",
                                     mpgcat = "guess",
                                     cyl8 = "logical"))

  # Create library
  libname(dat, tempdir(), "csv", import_specs = spcs)

  # View data types
  dictionary(dat)
  
  expect_equal(class(dat$mtcars$recdt), "Date")
  
})


test_that("no specs work on CRF data for sas7bdat.", {
  
  
  libname(dat, file.path(base_path, "CRF"), "sas7bdat")
  
  expect_equal(class(dat$dm$VISITREP), "logical")
  expect_equal(class(dat$pe$VISITREP), "logical")
  expect_equal(all(is.na(dat$dm$VISITREP)), TRUE)
  expect_equal(all(is.na(dat$pe$VISITREP)), TRUE)
  
})

test_that("specs na and trim_ws work on CRF data for sas7bdat.", {
  
  lst <- specs(na = c("", "."), trim_ws = TRUE)
                              
  
  libname(dat, file.path(base_path, "CRF"), "sas7bdat", import_specs = lst)
  
  # dat$dm  
  # dat$pe
  
  expect_equal(class(dat$dm$VISITREP), "logical")
  expect_equal(class(dat$dm$VISITREP), "logical")
  
})


test_that("dm import_spec na and trim_ws work on CRF data for sas7bdat.", {
  
  lst <- specs(dm = import_spec(na = c("", "."), trim_ws = TRUE))
  
  
  libname(dat, file.path(base_path, "CRF"), "sas7bdat", import_specs = lst)
  
   # dat$dm  
   # dat$pe
  
  expect_equal(class(dat$dm$VISITREP), "logical")
  expect_equal(class(dat$pe$VISITREP), "character")
  
})


test_that("dm and pe import_spec col_types work on CRF data for sas7bdat.", {
  
  lst <- specs(dm = import_spec(VISITREP = "character", na = c("", ".")),
               pe = import_spec(VISITREP = "character", na = c("", ".")))
  
  
  libname(dat, file.path(base_path, "CRF"), "sas7bdat", import_specs = lst)
  
  # dat$dm  
  # dat$pe
   
  expect_equal(class(dat$dm$VISITREP), "character")
  expect_equal(class(dat$dm$PAGEREP), "logical")
  expect_equal(class(dat$pe$VISITREP), "character")
  expect_equal(class(dat$dm$PAGEREP), "logical")
  
})

test_that("dm and pe multiple import_spec col_types work for sas7bdat.", {
  
  lst <- specs(na = c("", "."), trim_ws = TRUE,
               dm = import_spec(VISITREP = "character",
                                PAGEREP = "character"),
               pe = import_spec(PAGEREP = "character",
                                VISITREP = "numeric",
                                DERMRES = "logical", 
                                CARES = "integer"))
  
  
  libname(dat, file.path(base_path, "CRF"), "sas7bdat", import_specs = lst)
  
  # dat$dm  
  # dat$pe
  # View(dat$pe)

  expect_equal(class(dat$dm$VISITREP), "character")
  expect_equal(class(dat$dm$PAGEREP), "character")
  expect_equal(class(dat$dm$BIRTHDD), "numeric")
  expect_equal(class(dat$pe$VISITREP), "numeric")
  expect_equal(class(dat$pe$PAGEREP), "character")
  expect_equal(class(dat$pe$CARES), "integer")
  expect_equal(class(dat$pe$DERMRES), "logical")
  
})

test_that("lab import_spec with dates works for sas7bdat.", {
  
  
  libname(dat, base_path, "sas7bdat")
  
 # 
 # labels(dat$demo_studya)  
 # unclass(dat$demo_studya)
 # 
 # library(haven)
 # nl <- read_sas(file.path(base_path, "demo_studya.sas7bdat"))
 # labels(nl)
   
  
  expect_equal(attr(dat$demo_studya$screendate, "label"), "Date of Screening")


})

test_that("print function works as expected.", {
  
  is1 <- import_spec(col1 = "character", col2 = "integer",
                     na = c("NA", "-"),
                     trim_ws = FALSE)
  
  is2 <- import_spec(col1 = "numeric", col2 = "date:%d%m%Y",
                     na = c(" ", ""),
                     trim_ws = TRUE)
  spcs <- specs(na = c("NA", "-", " ", ""),
                trim_ws = TRUE, AB = is1, AC = is2)
  
  
  spcs
  
  
  expect_equal(TRUE, TRUE)
  
  
})