tests/testthat/test-get_traits.R

In gwasrapidd: 'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog

context("test-get_traits")

# with_mock_api({
#   test_that("get_traits: get all traits", {
#     my_traits <- get_traits()
#     expect_is(my_traits, 'traits')
#   })
# })

#
## get_traits, exceptions
#
test_that("get_traits: exceptions", {
  expect_error(get_traits(set_operation = 'invalid_option'),
               "set_operation must be either 'union' or 'intersection'")
  expect_error(get_traits(verbose = 1L),
               "verbose must be either TRUE or FALSE")
  expect_error(get_traits(verbose = NA),
               "verbose must be either TRUE or FALSE")
  expect_error(get_traits(warnings = NA),
               "warnings must be either TRUE or FALSE")
})


## get_traits, by study id
#

with_mock_api({
  test_that("get_traits: GCST002420", {
    my_trait <- get_traits(study_id = 'GCST002420')
    expect_is(my_trait, 'traits')
  })
})


#
## get_traits, by association id
#
with_mock_api({
  test_that("get_traits: by association id", {
    my_traits <- get_traits(association_id = '15608')
    expect_is(my_traits, 'traits')
  })
})

#
## get_traits, by efo id
#
with_mock_api({
  test_that("get_traits: by efo id", {
    my_traits <- get_traits(efo_id = c('EFO_0000537', 'EFO_0004291'))
    expect_is(my_traits, 'traits')
  })
})

#
## get_traits, by pubmed id
#
with_mock_api({
  test_that("get_traits: by pubmed id", {
    my_traits <- get_traits(pubmed_id = '25890600')
    expect_is(my_traits, 'traits')
  })
})

#
## get_traits, by efo_uri
#
with_mock_api({
  test_that("get_traits: by efo_uri", {
    my_traits <- get_traits(efo_uri = 'http://www.ebi.ac.uk/efo/EFO_0004761')
    expect_is(my_traits, 'traits')
  })
})

#
## get_traits, by efo_trait
#
with_mock_api({
  test_that("get_traits: by efo_trait", {
    my_traits <- get_traits(efo_trait = "lung adenocarcinoma")
    expect_is(my_traits, 'traits')
  })
})