test.chunkR.R
In chunkR: Read Tables in Chunks

context("test_chunkR.R")

data(iris)
tmp_csv <- tempfile()
write.table(iris, tmp_csv, quote = FALSE, sep = ",")
tmp_txt <- tempfile()
write.table(iris, tmp_txt, quote = FALSE)
tmp_txt_q <- tempfile()
write.table(iris, tmp_txt_q, quote = TRUE)
tmp_txt_nrnc <- tempfile()
write.table(iris, tmp_txt_nrnc, quote = FALSE, row.names = FALSE, col.names = FALSE)


test_that("chunkR data.frame autodetection works", {
 
 # test object creation
 my_chunker_object <- chunker(tmp_txt, chunksize = 30, scan_rows = 20)
 expect_that(my_chunker_object, is_a("chunker"))
 
 # test read_chunk
 expect_true(next_chunk(my_chunker_object))
 expect_true(next_chunk(my_chunker_object))
 
 # test get_table
 this_data <- get_table(my_chunker_object)
 expect_that(this_data, is_a("data.frame"))
 expect_that(length(grep("\r|\n",as.matrix(this_data))), equals(0)) # no \r and \n
 
 # test get_completed
 expect_that(get_completed(my_chunker_object), is_a("numeric"))

})


test_that("chunkR data.frame custom detection works", {
 
  # test object creation
  my_chunker_object <- chunker(tmp_txt, chunksize = 120, 
                             columns_classes = c("numeric", "numeric", "numeric","numeric", "character"))

  # test object creation
  expect_that(my_chunker_object, is_a("chunker"))
  
  # test next_chunk
  expect_true(next_chunk(my_chunker_object))
  expect_true(next_chunk(my_chunker_object))
  
  # test get_table
  this_data <- get_table(my_chunker_object)
  expect_that(this_data, is_a("data.frame"))
  expect_that(length(grep("\r|\n",as.matrix(this_data))), equals(0)) # no \r and \n  
  
  # test get_completed
  expect_that(get_completed(my_chunker_object), is_a("numeric"))

})


test_that("chunkR removes quotes in data frames", {

  # test object creation
  my_chunker_object <- chunker(tmp_txt_q, chunksize = 120, quote = TRUE)

  # test object creation
  expect_that(my_chunker_object, is_a("chunker"))

  # test next_chunk
  expect_true(next_chunk(my_chunker_object))

  # test get_table
  this_data <- get_table(my_chunker_object)
  expect_that(this_data, is_a("data.frame"))
  expect_true(this_data[, 5][1] == "setosa")
  expect_that(length(grep("\r|\n",as.matrix(this_data))), equals(0)) # no \r and \n

})

test_that("chunkR removes quotes in matrices", {

  # test object creation
  my_chunker_object <- chunker(tmp_txt_q, chunksize = 120, quote = TRUE, data_format = "matrix")

  # test object creation
  expect_that(my_chunker_object, is_a("chunker"))

  # test next_chunk
  expect_true(next_chunk(my_chunker_object))

  # test get_table
  this_data <- get_table(my_chunker_object)
  expect_that(this_data, is_a("matrix"))
  expect_true(this_data[, 5][1] == "setosa")
  expect_that(length(grep("\r|\n",as.matrix(this_data))), equals(0)) # no \r and \n
  
})

test_that("chunkR can read data w/o column names and row names and generate a valid data frame", {
  
  # test object creation
  my_chunker_object <- chunker(tmp_txt_nrnc, chunksize = 120, 
                               has_colnames = FALSE, has_rownames = FALSE)
  
  # test object creation
  expect_that(my_chunker_object, is_a("chunker"))
  
  # test next_chunk
  expect_true(next_chunk(my_chunker_object))
  
  # test get_table
  this_data <- get_table(my_chunker_object)
  expect_that(this_data, is_a("data.frame"))
  
  expect_true(rownames(this_data)[1] == "R_1")
  expect_true(colnames(this_data)[1] == "C_1")
  expect_that(length(grep("\r|\n",as.matrix(this_data))), equals(0)) # no \r and \n
  
})

test_that("chunkR can read data w/o column names and row names and generate a valid matrix", {
  
  # test object creation
  my_chunker_object <- chunker(tmp_txt_nrnc, chunksize = 120, 
                               has_colnames = FALSE, has_rownames = FALSE,
                               data_format = "matrix")
  
  # test object creation
  expect_that(my_chunker_object, is_a("chunker"))
  
  # test next_chunk
  expect_true(next_chunk(my_chunker_object))
  
  # test get_table
  this_data <- get_table(my_chunker_object)
  expect_that(this_data, is_a("matrix"))
  
  expect_true(rownames(this_data)[1] == "R_1")
  expect_true(colnames(this_data)[1] == "C_1")
  expect_that(length(grep("\r|\n",as.matrix(this_data))), equals(0)) # no \r and \n
  
})


test_that("chunkR matrix works", {
  
  # test object creation
  my_chunker_object <- chunker(tmp_txt, chunksize = 120, data_format = "matrix")
  expect_that(my_chunker_object, is_a("chunker"))
  
  # test read_chunk
  expect_true(next_chunk(my_chunker_object))
  expect_true(next_chunk(my_chunker_object))
  
  # test get_table
  this_data <- get_table(my_chunker_object)
  expect_that(this_data, is_a("matrix"))
  
  # Matrix data can be converted to data frame with the C++ method get_table. 
  # , which is much faster than the native function "as.data.frame"
  this_data_as_df <- get_table(my_chunker_object)
  expect_that(length(grep("\r|\n",as.matrix(this_data))), equals(0)) # no \r and \n
  # The package also provides a fast generic C++ function for conversion from
  # matrix (any R type) to dataframe
  this_data_as_df2 <- matrix2df(this_data)
  expect_that(length(grep("\r|\n",as.matrix(this_data))), equals(0)) # no \r and \n
})


test_that("chunkR is able to read csv files", {
 
  # test object creation
  my_chunker_object <- chunker(tmp_csv, chunksize = 30, sep = ",")
  
  #test next_chunk
  expect_that(my_chunker_object, is_a("chunker"))
  expect_true(next_chunk(my_chunker_object))
  
  this_data <- get_table(my_chunker_object)
  expect_that(length(grep("\r|\n",as.matrix(this_data))), equals(0)) # no \r and \n
  # test get_table
  expect_that(this_data, is_a("data.frame"))
  
})


# remove temporal files
file.remove(tmp_txt)
file.remove(tmp_csv)
file.remove(tmp_txt_q)
file.remove(tmp_txt_nrnc)