tests/testthat/test_ensemblFunctions.R

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

library(biomaRt)
cache <- file.path(tempdir(), "biomart_cache_test")
Sys.setenv(BIOMART_CACHE = cache)

context('Ensembl specific functions')

test_that("useEnsembl() works", { 

  ensembl <- useEnsembl(biomart = "snp")
  expect_is(ensembl, class = "Mart")

})

test_that("useEnsembl() options are respected", { 
  
  expect_silent(ensembl_mirror <- useEnsembl(biomart = "snp", mirror = "uswest"))
  expect_equal(ensembl_mirror@host, 
               "https://uswest.ensembl.org:443/biomart/martservice?redirect=no")
  
  expect_silent(ensembl_archive <- useEnsembl(biomart = "ensembl", version = 87))
  expect_equal(ensembl_archive@host,
               "http://dec2016.archive.ensembl.org:80/biomart/martservice")
})


test_that("useEnsembl() error handling is OK", { 
  
  expect_error(useEnsembl(), regexp = "You must provide the argument")
  
  expect_warning(ensembl <- useEnsembl(biomart = "snp", mirror = "INVALID_MIRROR"), 
                 regexp = "Invalid mirror\\. Select a mirror")
  expect_equal(ensembl@host, 
               "https://www.ensembl.org:443/biomart/martservice")
  
  expect_error(useEnsembl(biomart = "snp", version = "00"), 
               regexp = "Specified Ensembl version is not available")
})