tests/testthat/test-as_emld.R

In cboettig/emljson: Ecological Metadata as Linked Data

library(magrittr)
library(xml2)
library(jsonlite)
library(testthat)
testthat::context("as_* methods")

hf205 <- system.file("extdata/hf205.xml", package="emld")
ex <- system.file("extdata/example.xml", package="emld")


test_that("we can convert example.xml into complete JSON-LD", {
  X <- as_emld(ex)
  expect_true("dataset" %in% names(X))
  expect_length(unlist(X), 18)
})

test_that("we can round-trip and validate a simple example", {
  emld <- as_emld(ex)

  tmp <- tempfile("test", fileext=".xml")
  as_xml(emld, tmp)
  expect_true(eml_validate(tmp))


  elements_at_end <- sort(names(unlist(as_emld(tmp), recursive = TRUE)))
  elements_at_start <- sort(names(unlist(emld, recursive = TRUE)))
  testthat::expect_equal(elements_at_start, elements_at_end)

})



test_that("explict 'from' types", {
  f <- system.file("extdata/example.xml", package="emld")
  tmp <- tempfile("ex", fileext=".json")

  x <- as_emld(f, from="xml")
  as_json(x, tmp)
  json <- jsonlite::read_json(tmp)
  my_eml <- as_emld(json, "guess")
  my_eml2 <- as_emld(json, "json")
  my_eml3 <- as_emld(my_eml2, "list")
  expect_true(file.exists(tmp))

  class(x) <- "list"
  json2 <- as_json(x)


  f2 <- xml2::read_xml(f)
  my_eml4 <- as_emld(f, from="xml")
  expect_identical(my_eml, my_eml2)

  })

test_that("we can convert SON-LD into xml", {
  f <- system.file("extdata/hf205.xml", package="emld")
  tmp <- tempfile("ex", fileext=".json")

  as_json(as_emld(f), tmp)
  expect_true(file.exists(tmp))
  unlink("ex.json")
})


test_that(
  "We can parse an EML <url> element with an attribute into JSON",
  {
    xml <- xml2::read_xml(
'<url name="Ecophysiology">http://harvardforest.fas.harvard.edu:8080/exist/xquery/data.xq?id=hf168</url>')
    emld <- as_emld(xml)
    expect_is(emld, "emld")
    json <- as_json(emld)
    expect_is(json, "json")
  })


test_that("we can parse repeated name elements", {
  xml <-
    xml2::read_xml(
  '<additionalLinks>
    <url name="Ecophysiology">http://harvardforest.fas.harvard.edu:8080/exist/xquery/data.xq?id=hf168</url>
    <url name="Effects of Prey">http://harvardforest.fas.harvard.edu:8080/exist/xquery/data.xq?id=hf109</url>
  </additionalLinks>')

  emld <- as_emld(xml)
  expect_is(emld, "emld")
  json <- as_json(emld)
  expect_is(json, "json")
  })


test_that("raw files can be parsed", {
  emld <- as_emld(ex)

  ex_char <- paste(readLines(ex), collapse = "\n")
  # potentially test for char formats here. currently doesn't work (converts to list of 1 instead of 6)
  # emld_char <- as_emld(ex_char)
  # expect_equal(emld, emld_char)

  ex_raw <- charToRaw(ex_char)
  emld_raw <- as_emld(ex_raw, "xml")
  expect_equal(emld, emld_raw)
  expect_warning(emld_raw <- as_emld(ex_raw), "assuming raw vector is xml")
})

test_that("a schemaLocation can be guessed", {
  emld <- as_emld(ex)
  emld$schemaLocation <- NULL
  doc <- as_xml(emld)
  expect_true("xsi:schemaLocation" %in% names(xml_attrs(xml_root(doc))))
})

test_that("schemaLocation=FALSE produces a message when already set on the document", {
  emld <- as_emld(ex)
  emld$schemaLocation <- "FOO BAR"

  expect_true("schemaLocation" %in% names(emld))
  expect_message(doc <- as_xml(emld, schemaLocation = FALSE))
})

test_that("schemaLocation=FALSE doesn't nuke the already set value on the document", {
  emld <- as_emld(ex)
  emld$schemaLocation <- "FOO BAR"

  doc <- suppressMessages({as_xml(emld, schemaLocation = FALSE)})
  doc_attrs <- xml_attrs(xml_root(doc))
  expect_equal(doc_attrs["xsi:schemaLocation"][[1]], "FOO BAR")
})

test_that("a custom schemaLocation can be given at serialization-time", {
  emld <- as_emld(ex)
  emld$schemaLocation <- NULL
  doc <- as_xml(emld, schemaLocation = "FOO BAR")
  doc_attrs <- xml_attrs(xml_root(doc))

  expect_true("xsi:schemaLocation" %in% names(doc_attrs))
  expect_equal(doc_attrs["xsi:schemaLocation"][[1]], "FOO BAR")
})