tests/testthat/test-fct_external_tools.R

In CCICB/CRUX: Easily explore patterns of somatic variation in cancer using 'CRUX'

test_that("external_tools_convert_maf_to_bbglab", {
  maf = maftools::read.maf(system.file(package = "CRUX","/test_data/external_data_conversion_input.maf.gz"), verbose = FALSE)
  maf_dataset_wrapper = new_maf_dataset_wrapper(maf_data_pool = new_maf_data_pool(), display_name = "Hi", is_dataset_downloadable = FALSE,function_to_load_data = function(file){},  short_name = "Hello", unique_name = "bob", start_status = "not_loaded", data_description = "adasda", loaded_data = maf)
  cgi_output.path = tempfile()
  external_tools_convert_maf_to_bbglab(maf_dataset_wrapper =  maf_dataset_wrapper, filepath = cgi_output.path)
  cgi_output_df <- read.table(cgi_output.path, header = TRUE, sep = "\t")
  
  expected_output_path <- system.file(package = "CRUX","/test_data/test_cgi_export.tsv")
  expected_output_df <- read.table(expected_output_path, header = TRUE, sep = "\t")

  expect_identical(
    cgi_output_df,
    expected_output_df
    )    
  # expect_equivalent(
  #   tools::md5sum(cgi_output.path),
  #   expected = "c05ce92686cf7d5d81dad613bb489d75"
  #   )
  
  unlink(cgi_output.path)
  
})

test_that("external_tool_metadata dataset is up to date", {
  #if this fails try running external_tools_update_builtin_dataset()
  
  # We remove maf_conversion_function since function environment will be different (CRUX vs GLOBAL)
  live_external_tool_metadata <- subset(external_tools_load_all_tools(), select = -c(maf_conversion_function))
  stored_external_tool_metadata <- subset(external_tool_metadata, select = -c(maf_conversion_function))
  
  expect_equal(live_external_tool_metadata, stored_external_tool_metadata)
  
  # Check bodies and names of functions
  live_function_strings <- unlist(external_tools_load_all_tools()[["maf_conversion_function"]]) %>%
    lapply(deparse1)
  
  stored_function_strings <- unlist(external_tool_metadata[["maf_conversion_function"]]) %>%
    lapply(deparse1)
  
  expect_equal(live_function_strings, stored_function_strings)
})