tests/testthat/test_ensembl_ssl_settings.R

In grimbough/biomaRt: Interface to BioMart databases (i.e. Ensembl)

cache <- file.path(tempdir(), "biomart_cache_test")
Sys.setenv(BIOMART_CACHE = cache)
bfc <- BiocFileCache::BiocFileCache(biomartCacheInfo(), ask = FALSE)

test_that("Both SSL settings are applied if needed", { 
    
    skip_if_not_installed('mockery')
    
    m <- mockery::mock(stop("sslv3 alert handshake failure"),
              stop("unable to get local issuer certificate"), 
              "")
    mockery::stub(.checkEnsemblSSL, ".test_ensembl", m)
    
    expect_silent(http_config <- .checkEnsemblSSL())
    expect_is(http_config, "list")
    expect_length(http_config, 2L)
    expect_identical(http_config$ssl_cipher_list, "DEFAULT@SECLEVEL=1")
    expect_false(http_config$ssl_verifypeer)
    
})

test_that("Only one SSL setting is applied", { 

    skip_if_not_installed('mockery')

    m <- mockery::mock(stop("sslv3 alert handshake failure"),
              "",
              stop("unable to get local issuer certificate"),
              "")
    mockery::stub(.checkEnsemblSSL, ".test_ensembl", m)
    
    expect_silent(http_config <- .checkEnsemblSSL())
    expect_length(http_config, 1L)
    expect_identical(http_config[[1]], "DEFAULT@SECLEVEL=1")
    
    expect_silent(http_config <- .checkEnsemblSSL())
    expect_length(http_config, 1L)
    expect_false(http_config[[1]])
    
})

test_that("If we hit an unknown error", { 
    
    skip_if_not_installed('mockery')
    
    m <- mockery::mock(stop("This is an unexpected SSL error"), 
              "")
    mockery::stub(.checkEnsemblSSL, ".test_ensembl", m)
    
    expect_message(.checkEnsemblSSL(), "Possible SSL connectivity problems detected")

})


test_that("SSL settings are stored in the cache", {
    
    skip_if_not_installed('mockery')
    
    m <- mockery::mock(stop("sslv3 alert handshake failure"),
                       stop("unable to get local issuer certificate"), 
                       "")
    mockery::stub(.checkEnsemblSSL, ".test_ensembl", m)
    
    expect_silent(http_config <- .getEnsemblSSL())
    expect_is(http_config, "list")
    expect_true(.checkInCache(bfc, "ensembl-ssl-settings-httr2"))
})

test_that("We can manually set SSL settings", {
  
  ## empty list 
  settings <- list()
  expect_true(setEnsemblSSL(settings = settings))
  expect_identical(settings, .getEnsemblSSL())
  
  ## one element 
  settings <- list("foo" = "A")
  expect_true(setEnsemblSSL(settings = settings))
  expect_identical(settings, .getEnsemblSSL())
  
  ## add element 
  settings <- list("baa" = "B")
  expect_true(setEnsemblSSL(settings = settings))
  expect_identical(list("foo" = "A", "baa" = "B"), 
                   .getEnsemblSSL())
  
  ## update existing element 
  settings <- list("baa" = "C")
  expect_true(setEnsemblSSL(settings = settings))
  expect_identical(list("foo" = "A", "baa" = "C"), 
                   .getEnsemblSSL())
  
  ## remove these entries from the cache so they aren't used in later tests
  biomartCacheClear()

})