added many expects to test_inheritance for conversions and for some v…

…alue checking

inst/tests/test_inheritance.R

@@ -6,46 +6,81 @@ context("inheritance")
 ## Add tests to check values on some nodes/attributes...
 
 test_that("we can perform simple conversions between NeXML XML and S4", {
-require(XML)
-require(RNeXML)
-# basic example
-node <- newXMLNode("meta", 
-                   attrs = c(id="dict1",
-                             property="cdao:has_tag",
-			                       content="true", 
-                             'xsi:type'="nex:LiteralMeta",
-			                       datatype="xsd:boolean"),
-                   suppressNamespaceWarning=TRUE)
-n2 <- newXMLNode("node", 
-                 attrs = c(id = "n4", 
-                           label="n4", 
-                           about="#n4"), 
-                 .children = node)
-
-# check conversions to/from NeXML
- s4 <- as(n2, "node")
- as(s4, "XMLInternalNode")
+  require(XML)
+  require(RNeXML)
+  # basic example
+  node <- newXMLNode("meta", 
+                     attrs = c(id="dict1",
+                               property="cdao:has_tag",
+                               content="true", 
+                               'xsi:type'="nex:LiteralMeta",
+                               datatype="xsd:boolean"),
+                     suppressNamespaceWarning=TRUE)
+  n2 <- newXMLNode("node", 
+                   attrs = c(id = "n4", 
+                             label="n4", 
+                             about="#n4"), 
+                   .children = node)
+
+  # check conversions to/from NeXML
+  s4 <- as(n2, "node")
+  xmlfroms4 <- as(s4, "XMLInternalNode")
+  expect_that(identical(n2, xmlfroms4), is_true())
 })
 
-
-
-## Should be separate unit tests here to facilitate debugging...
-
-test_that("We can parse a complete NeXML file and toggle back and forth between XML and S4", {
+# test_that("We can parse a complete NeXML file and toggle back and forth between XML and S4", {
+test_that("Parse a complete NeXML file to a single otu", {
   doc <- xmlParse(system.file("examples", "trees.xml", package="RNeXML"))
   root <- xmlRoot(doc)
 
-# check conversions
   otu <- as(root[["otus"]][[1]], "otu")
+  expect_that(otu, is_a("otu"))
   as(otu, "XMLInternalNode")
+})
 
+test_that("Parse a complete NeXML file to trees", {
   trees <- as(root[["trees"]], "trees")
+  expect_that(trees, is_a("trees"))
   as(trees, "XMLInternalNode")
+})
 
+test_that("Parse a complete NeXML file to many otus", {
   otus <- as(root[["otus"]], "otus")
-  as(otus, "XMLInternalNode")
-
+  expect_that(otus, is_a("otus"))
+  tt <- as(otus, "XMLInternalNode")
+  expect_that(tt, is_a("XMLInternalNode"))
+})
 
+test_that("Parse a complete NeXML file to xmlinternalnode", {
   parsed <- as(root, "nexml")
+  expect_that(parsed, is_a("nexml"))
   serialized <- as(parsed, "XMLInternalNode")
+  expect_that(serialized, is_a("XMLInternalNode"))
 })
+
+test_that("Check that values are correct in the otu class element", {
+  otu <- as(root[["otus"]][[1]], "otu")
+  expect_that(otu@id[[1]], equals("t1"))
+  expect_that(otu@label[[1]], equals("species 1"))
+  expect_that(otu@meta, is_a("list"))
+  expect_that(otu@about, is_identical_to(character(0)))
+})
+
+test_that("Check that values are correct in the trees class element", {
+  trees <- as(root[["trees"]], "trees")
+  expect_that(trees@tree, is_a("ListOftree"))
+  expect_that(trees@otus[[1]], equals("tax1"))
+  expect_that(trees@id[[1]], equals("Trees"))
+  expect_that(trees@label[[1]], equals("TreesBlockFromXML"))
+  expect_that(trees@meta, is_a("list"))
+  expect_that(trees@about, is_identical_to(character(0)))
+})
+
+test_that("Check that values are correct in the otus class element", {
+  otus <- as(root[["otus"]], "otus")
+  expect_that(otus@otu, is_a("ListOfotu"))
+  expect_that(otus@id[[1]], equals("tax1"))
+  expect_that(otus@label[[1]], equals("RootTaxaBlock"))
+  expect_that(otus@meta, is_a(class=c("list","ListOfmeta")))
+  expect_that(otus@about, is_identical_to(character(0)))
+})