tests/testthat/test_serializing.R

In RNeXML: Semantically Rich I/O for the 'NeXML' Format

context("serializing")


## More tests at lower-level serializing from S4 to XML in inheritance.R

test_that("We can serialize ape to S4 RNeXML into valid NeXML",{
  
  ## tests are too slow for CRAN
  skip_on_cran()
  
  data(bird.orders)


  nexml <- as(bird.orders, "nexml") 

  saveXML(as(nexml, "XMLInternalNode"), file = "test.xml")
  expect_true_or_null(nexml_validate("test.xml"))

  ###  Higher level API tests
  nexml_write(bird.orders, file="test.xml")
  expect_true_or_null(nexml_validate("test.xml"))

  ## also can write with providing multiple metadata (see README.Rmd)
  expect_silent(nexml_write(bird.orders, file="test.xml",
                            title = "My test title",
                            description = "A description of my test",
                            creator = "Carl Boettiger <cboettig@gmail.com>",
                            publisher = "unpublished data",
                            pubdate = "2012-04-01"))
  nex <- nexml_read("test.xml")
  metavals <- get_metadata_values(nex, props = c("dc:creator", "dcterms:modified"))
  expect_equivalent(metavals["dc:creator"], "Carl Boettiger <cboettig@gmail.com>")
  expect_equivalent(metavals["dcterms:modified"], "2012-04-01")

  ##  Clean up
  unlink("test.xml")

  })


test_that("We can serialize parsed NeXML to S4 RNeXML into valid NeXML",{
  
  ## tests are too slow for CRAN
  skip_on_cran()
  
  root <- xmlRoot(xmlParse(system.file("examples", "trees.xml", package="RNeXML")))
  tree <- as(root, "nexml")
  nexml_write(tree, file="test.xml")

  ## validate
  expect_true_or_null(nexml_validate("test.xml"))

  ##  Clean up
  unlink("test.xml")

  })

test_that("We can correctly serialize XML literals as metadata", {
  
  ## tests are too slow for CRAN
  skip_on_cran()
  
  nex1 <- read.nexml(system.file("examples", "phenex.xml", package="RNeXML"))
  m_xml1 <- get_metadata(nex1, "characters/format/states/state") %>%
    dplyr::filter(property == "ps:describesPhenotype")
  # write it out and then read it back in
  write.nexml(nex1, file="test.xml")
  
  # not sure why XML is considered invalid
  #expect_true_or_null(nexml_validate("test.xml"))
  
  
  nex2 <- read.nexml("test.xml")
  m_xml2 <- get_metadata(nex2, "characters/format/states/state") %>%
    dplyr::filter(property == "ps:describesPhenotype")
  # the XML literals in the form of string values should be the same
  testthat::expect_true(all(dplyr::arrange(m_xml1, state)[,"content"] ==
                              dplyr::arrange(m_xml2, state)[,"content"]))

  ## clean up
  unlink("test.xml")
})

test_that("we can serialize NeXML with rootedge to a valid NeXML file", {
  
  skip("rootedge is not valid by XSD schema?")
  ## tests are too slow for CRAN
  skip_on_cran()
  
  f <- system.file("examples", "coal.xml", package = "RNeXML")
  nex <- read.nexml(f)
  write.nexml(nex, file = "test.xml")
  valid <- nexml_validate("test.xml")
  expect_true_or_null()

  unlink("test.xml")
})