tests/testthat/test-02-eutil-methods.R

In reutils: Talk to the NCBI EUtils

context("Test eutil methods")

test_that("The methods we want to test are all present in an eutil class", {
  expect_true(all(c("database", "eutil", "get_content", "get_error", "get_url", "perform_query", "no_errors", 
                    "retmode", "rettype",  "xmlAttr", "xmlName", "xmlSet", "xmlValue") %in% eutil$methods()))
})

## generate a test esearch instance.
## if not on CRAN go to NCBI, if on CRAN use locally stored instance.
if (getOption('reutils.test.remote')) {
  a <- .esearch('GET', db = 'pubmed', term = 'Chlamydia psittaci', retstart = 6, 
                retmax = 2, rettype = "uilist", retmode = 'xml')
  
  test_that("#database works", {
    expect_equal(a$database(), "pubmed")
  })
  
  test_that("#eutil works", {
    expect_equivalent(a$eutil(), "esearch")
  })
  
  test_that("#get_content works", {
    expect_is(a$get_content("text"), "character")
    expect_is(a$get_content("xml"), "XMLInternalDocument")
    expect_that(a$get_content("json"), throws_error("Cannot return data of retmode.+"))
    expect_that(a$get_content("textConnection"), throws_error("Cannot return data of retmode.+"))
    expect_is(a$get_content("parsed"), "entrez_uid")
    expect_is(a$get_content("parsed"), "character")
    expect_error(a$get_content("bla"))
  })
  
  test_that("#get_error returns an 'eutil_error' object", {
    expect_that(a$get_error(), is_a("eutil_error"))
  })
  
  test_that("#get_url returns the query URL", {
    expect_match(a$get_url(), "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi\\?db=pubmed&term=Chlamydia%20psittaci&retstart=6&retmax=2.+")
  })
  
  test_that("#no_errors works as expected", {
    expect_true(a$no_errors())
  })
  
  test_that("'#xmlName() works", {
    tagnames <- a$xmlName('/eSearchResult/*')
    expect_is(tagnames, 'character')
    expect_equal(tagnames[1], 'Count')
  })
  
  test_that("'#xmlSet() works", {
    nodeset <- a$xmlSet('/eSearchResult/IdList')
    expect_is(nodeset, 'XMLNodeSet')
  })
  
  test_that("'#xmlValue works", {
    character.uids <- a$xmlValue('/eSearchResult/IdList/*')
    expect_is(character.uids, 'character')
    expect_equal(length(character.uids), 2)
    integer.uids <- a$xmlValue('/eSearchResult/IdList/*', as = 'integer')
    expect_is(integer.uids, 'integer')
    expect_equal(length(integer.uids), 2)
    expect_equal(a$xmlValue('/eSearchResult/Bla'), NA_character_)
    expect_equal(a$xmlValue('/eSearchResult/Bla', as = 'integer'), NA_integer_)
    expect_equal(a$xmlValue('/eSearchResult/Bla', default = NULL), NULL)
    expect_equal(a$xmlValue('/eSearchResult/Bla', default = NULL), NULL)
    expect_equal(a$xmlValue('/eSearchResult/Bla', default = ''), '')
  })
  
  test_that("#perform_query updates an existing query", {
    a$perform_query(retmax = 10, usehistory = "y")
    expect_match(webenv(a), "^NCID_\\d_\\d+_.+")
    expect_equal(querykey(a), 1)
  })
  
  test_that("#rettype and #retmode work", {
    b <- efetch(uid = "8655742", db = "protein", rettype = "fasta", retmode = "xml")
    expect_equal(b$rettype(), "fasta")
    expect_equal(b$retmode(), "xml")
  })
}