tests/testthat/test-cr_works.R

In rcrossref: Client for Various 'CrossRef' 'APIs'

context("testing cr_works")

test_that("cr_works returns", {
  vcr::use_cassette("cr_works", {

    a <- cr_works(query="NSF")
    b <- cr_works(query="renear+-ontologies")
    c <- cr_works(query="global state", filter=c(has_orcid=TRUE), limit=3)
    d <- cr_works(filter=c(has_full_text = TRUE))
    e <- cr_works(dois=c('10.1007/12080.1874-1746','10.1007/10452.1573-5125', '10.1111/(issn)1442-9993'))
    f <- cr_works(query="lagotto", facet=TRUE, limit=0)
    g <- cr_works(sample=1)
   # h <- cr_works(query="lagotto", facet=TRUE)
    i <- suppressWarnings(cr_works(dois=c('blblbl', '10.1038/nnano.2014.279')))

    # correct class
    expect_is(a, "list")
    expect_is(b, "list")
    expect_is(c, "list")
    expect_is(d, "list")
    expect_is(e, "list")
    expect_is(f, "list")
    expect_is(g, "list")
   # expect_is(h, "list")
    expect_is(i, "list")

    expect_is(a$meta, "data.frame")
    expect_is(a$data, "data.frame")
    expect_is(a$data, "tbl_df")
    expect_is(a$data$url, "character")
    expect_equal(a$facets, NULL)

    expect_is(f, "list")
    expect_is(f$meta, "data.frame")
    expect_is(f$facets, "list")
    expect_is(f$facets$license, "data.frame")
    expect_is(f$facets$license$.id, "character")

    expect_equal(i$meta, NULL)
    expect_equal(i$facets, NULL)
    expect_is(i$data, "tbl_df")

    # dimensions are correct
    expect_equal(length(a), 3)
    expect_equal(length(b), 3)
    expect_equal(length(c), 3)
    expect_equal(length(d), 3)
    expect_equal(length(e), 3)
    expect_equal(length(f), 3)
    expect_equal(length(g), 3)
   # expect_equal(length(h), 3)
    expect_equal(length(i), 3)

  })
})

test_that("cr_works fails correctly", {
  vcr::use_cassette("cr_works_fails_well", {

    expect_error(cr_works(timeout_ms = 1))
    expect_equal(NROW(cr_works(query = "adfaaf")$data), 0)
    expect_warning(cr_works(sample = 200), "less than or equal to 100")
  })
})


test_that("cr_works warns correctly", {
  vcr::use_cassette("cr_works_warns_well", {

    expect_warning(cr_works(dois = c('blblbl', '10.1038/nnano.2014.279')), "Resource not found")
    expect_equal(NROW(suppressWarnings(cr_works(dois = c('blblbl', '10.1038/nnano.2014.279'))$data)), 1)
  })
})


test_that("cr_works - parses links data correctly", {
  vcr::use_cassette("cr_works_parses_links", {

    aa <- cr_works(filter = c(has_full_text = FALSE), limit = 10)
    bb <- cr_works(filter = c(has_full_text = TRUE), limit = 10)

    expect_is(aa, "list")
    expect_is(bb, "list")

    expect_equal(length(Filter(Negate(is.null), suppressWarnings(aa$data$link))), 0)
    expect_gt(length(Filter(Negate(is.null), bb$data$link)), 0)

    expect_is(bb$data$link[[1]], "data.frame")
    expect_match(bb$data$link[[1]]$URL, "http")
  })
})

test_that("cr_works - parses funders correctly", {
  vcr::use_cassette("cr_works_parses_funders", {

    doi <- "10.1515/crelle-2013-0024"
    aa <- cr_works(doi)

    expect_is(aa, "list")
    expect_is(aa$data, "data.frame")
    expect_is(aa$data$container.title, "character")
    expect_equal(aa$facets, NULL)
    expect_is(aa$data$funder, "list")
    expect_is(aa$data$funder[[1]], "data.frame")
    expect_true(any(grepl("funder", names(aa$data))))

    doi <- "10.1186/isrctn11093872"
    bb <- cr_works(doi)
    expect_true(any(grepl("funder", names(bb$data))))
    expect_named(bb$data$funder[[1]], c("DOI", "name", "doi.asserted.by"))

    doi <- "10.1145/2831244.2831252"
    cc <- cr_works(doi)
    expect_true(any(grepl("funder", names(cc$data))))
    expect_named(cc$data$funder[[1]], c("name", "award"))

    doi <- "10.1145/2834800.2834802"
    dd <- cr_works(doi)
    expect_true(any(grepl("funder", names(dd$data))))
    expect_named(dd$data$funder[[1]],
                 c("DOI", "name", "doi.asserted.by", "award"),
                 ignore.order = TRUE)

    doi <- "10.1145/2834800.2834802"
    dd <- cr_works(doi)
    expect_true(any(grepl("funder", names(dd$data))))
    expect_named(dd$data$funder[[1]],
                 c("DOI", "name", "doi.asserted.by", "award"),
                 ignore.order = TRUE)

    doi <- "10.1145/2832099.2832103"
    ee <- cr_works(doi)
    expect_true(any(grepl("funder", names(ee$data))))
    expect_named(ee$data$funder[[1]],
                 c("DOI", "name", "doi.asserted.by", "award"))

    doi <- "10.1016/j.pediatrneurol.2015.06.002"
    ff <- cr_works(doi)
    expect_true(any(grepl("funder", names(ff$data))))
    expect_named(ff$data$funder[[1]], c("DOI", "name", "doi.asserted.by"))

    doi <- "10.1016/j.tcs.2015.06.001"
    gg <- cr_works(doi)
    expect_true(any(grepl("funder", names(gg$data))))
    expect_named(gg$data$funder[[1]],
                 c("DOI", "name", "doi.asserted.by", "award"))

    doi <- "10.1016/j.ffa.2015.10.008"
    hh <- cr_works(doi)
    expect_true(any(grepl("funder", names(hh$data))))
    expect_named(
      hh$data$funder[[1]],
      c("DOI", "name", "doi.asserted.by", "award", "award1", "award2"),
      ignore.order = TRUE)
  })
})

test_that("cr_works - parses affiliation inside authors correctly", {
  vcr::use_cassette("cr_works_parses_affilitation", {

    doi <- "10.4018/978-1-4666-9588-7.les2"
    aa <- cr_works(doi)
    expect_true(any(grepl("author", names(aa$data))))
    expect_named(aa$data$author[[1]], c("given", "family", "sequence", "affiliation.name"))
  })
})

test_that("cr_works - select works", {
  vcr::use_cassette("cr_works_param_select", {

    aa <- cr_works(query = "science", select = c('DOI', 'title'))
    expect_named(aa$data, c("doi", "title"))
  })
})

test_that("cr_works - email works", {
  vcr::use_cassette("cr_works_email_works", {
     withr::with_envvar(
      new = c("crossref_email" = "name@example.com"),
      expect_is(cr_works(query = "NSF"), "list")
      )
  })
})

test_that("cr_works - email is validated", {
    withr::with_envvar(
      new = c("crossref_email" = "name@example"),
      expect_error(cr_works(query = "NSF"))
    )
})

test_that("cr_works - email NULL works", {
  vcr::use_cassette("cr_works_email_null_works", {
     withr::with_envvar(
      new = c("crossref_email" = ""),
      expect_is(cr_works(query = "NSF"), "list")
     )
  })
})

test_that("cr_works - handles empty funder item", {
  # a 2nd empty array comes through in the funder array: { award: [ ] }
  # it should be dropped in the parse_todf() internal function
  vcr::use_cassette("cr_works_empty_funder", {
    a <- cr_works(dois = "10.3389/fgene.2017.00147")
    expect_is(a, "list")
    expect_is(a$data, "data.frame")
    expect_is(a$data$funder, "list")
    expect_is(a$data$funder[[1]], "data.frame")
  })
})

# test_that("cr_works - async", {
#   skip_on_cran() # async mocking/webmockr/vcr not supported yet

#   queries <- c("ecology", "science", "cellular", "birds", "European",
#     "bears", "beets", "laughter", "hapiness", "funding")
#   x <- cr_works(query = queries, async = TRUE, limit = 3)
#   expect_true(all(vapply(x, is.data.frame, logical(1))))
#   expect_equal(length(queries), length(x))
#   expect_is(x[[1]], "data.frame")
# })

test_that("cr_works fails well: arguments that dont require http requests", {
  skip_on_cran()

  expect_error(cr_works(limit = 'foo'), "limit value illegal")
  expect_error(cr_works(limit = 1050), "limit parameter must be 1000 or less")

  expect_error(cr_works(offset = 'foo'), "offset value illegal")

  expect_error(cr_works(sample = 'foo'), "sample value illegal")
  
  expect_error(cr_works(async = 5), "is not TRUE")
})

# see https://github.com/ropensci/rcrossref/issues/211
test_that("content domain parsing fix", {
  # this DOI caused a failure in parsing content domain
  vcr::use_cassette("cr_works_no_content_domain_fail", {
    expect_is(cr_works(dois = "10.7287/peerj.3819v0.1/reviews/2"), "list")
  })
})