tests/testthat/test-read_files.R

In r-spark/variantspark: A 'Sparklyr' Extension for 'VariantSpark'

context("Read files")

test_that("Read VCF", {
  skip_on_cran()
  skip_if(installed_versions() == 0)
  
  sc <- sparklyr::spark_connect(master = "local")
  vsc <- vs_connect(sc)
  
  hipster_vcf <- vs_read_vcf(vsc, 
                             system.file("extdata/hipster.vcf.bz2",
                                         package = "variantspark"))

  vcf_class <- invoke(hipster_vcf, "toString")

  expect_true(grepl("VCFFeatureSource",vcf_class))
})

test_that("Read CSV", {
  skip_on_cran()
  skip_if(installed_versions() == 0)
  
  sc <- sparklyr::spark_connect(master = "local")
  vsc <- vs_connect(sc)

  hipster_labels <- vs_read_csv(vsc, 
                                system.file("extdata/hipster_labels.txt",
                                            package = "variantspark"))
  
  csv_class <- invoke(hipster_labels, "toString")
  
  expect_true(grepl("CsvFeatureSource",csv_class))
})

test_that("Read labels", {
  skip_on_cran()
  skip_if(installed_versions() == 0)
  
  sc <- sparklyr::spark_connect(master = "local")
  vsc <- vs_connect(sc)

  labels <- vs_read_labels(vsc, 
                           system.file("extdata/hipster_labels.txt",
                                            package = "variantspark")) 
  label_class <- invoke(labels, "toString")
  
  expect_true(grepl("CsvLabelSource",label_class))
})