From e75866f838e6dbf18601c60669908cfd9b3dac52 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Thu, 4 Mar 2021 15:23:54 -0500
Subject: [PATCH 1/7] Improved testing of unresolvable phylorefs.

We allow "correct" Phyx files to be "empty" (i.e. to complete with no
successes or failures, such as for a Phyx file containing only an
apomorphy). This change now displays a notice indicating that no
successes were found in the file.
---
 test/jphyloref.js | 30 ++++++++++++++++++++----------
 1 file changed, 20 insertions(+), 10 deletions(-)

diff --git a/test/jphyloref.js b/test/jphyloref.js
index 8c005d3e..ed3a78dd 100644
--- a/test/jphyloref.js
+++ b/test/jphyloref.js
@@ -55,7 +55,7 @@ describe('JPhyloRef', function () {
     fs.readdirSync(path.resolve(__dirname, 'examples', 'correct'))
       .filter(filename => filename.endsWith('.nq'))
       .forEach((filename) => {
-        it(`testing ${filename}`, function () {
+        describe(`testing ${filename}`, function () {
           this.timeout(20000);
 
           // Start JPhyloRef to test filename.
@@ -71,24 +71,34 @@ describe('JPhyloRef', function () {
               shell: true,
             }
           );
+
           const matches = /Testing complete:(\d+) successes, (\d+) failures, (\d+) failures marked TODO, (\d+) skipped./.exec(child.stderr);
 
-          expect(matches, `Test result line not found in STDERR <${child.stderr}>`).to.have.lengthOf(5);
+          it('should return the expected result line', () => {
+            expect(matches, `Test result line not found in STDERR <${child.stderr}>`).to.have.lengthOf(5);
+          });
 
-          // const countSuccess = Number(matches[1]);
+          const countSuccess = Number(matches[1]);
           const countFailure = Number(matches[2]);
           const countTODOs = Number(matches[3]);
           // const countSkipped = Number(matches[4]);
 
+          it('should run without any failures or TODOs', () => {
+            expect(countFailure, 'Expected zero failures').to.equal(0);
+            expect(countTODOs, 'Expected zero TODOs').to.equal(0);
+          });
+
           // We can't test for one or more successes since some example Phyx file
           // such as apomorphy-based phyloreferences don't have any successes at all.
-          // expect(countSuccess, 'Expected one or more successes').to.be.greaterThan(0);
-          expect(countFailure, 'Expected zero failures').to.equal(0);
-          expect(countTODOs, 'Expected zero TODOs').to.equal(0);
-
-          // An exit code of 0 means success. An exit code of 255 means that while
-          // there were no successes, there were also no failures. Either is acceptable here.
-          expect(child.status).to.be.oneOf([0, 255]);
+          // But we'll report both.
+          if (countSuccess === 0 && child.status === 255) {
+            it('No phyloreferences resolved successfully');
+          } else {
+            it('should resolve one or more phyloreferences', () => {
+              expect(countSuccess, 'Expected one or more successes').to.be.greaterThan(0);
+              expect(child.status).to.be.oneOf([0, 255]);
+            });
+          }
         });
       });
   });

From 3d6faa0b1d03a415cbe53e069f5e99b0b586b00f Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Thu, 4 Mar 2021 15:28:32 -0500
Subject: [PATCH 2/7] Added a test file with a phyloref without an expected
 resolution.

---
 .../correct/example_no_successes.json         |  28 +
 .../correct/example_no_successes.jsonld       | 597 ++++++++++++++++++
 test/examples/correct/example_no_successes.nq | 328 ++++++++++
 3 files changed, 953 insertions(+)
 create mode 100644 test/examples/correct/example_no_successes.json
 create mode 100644 test/examples/correct/example_no_successes.jsonld
 create mode 100644 test/examples/correct/example_no_successes.nq

diff --git a/test/examples/correct/example_no_successes.json b/test/examples/correct/example_no_successes.json
new file mode 100644
index 00000000..bb8b3ddc
--- /dev/null
+++ b/test/examples/correct/example_no_successes.json
@@ -0,0 +1,28 @@
+{
+  "@context": "../../../docs/context/development/phyx.json",
+  "phylogenies": [{
+    "newick": "((((Aa_a, Bb_b)Expected, Cc_c), (Dd_d, (Ee_e, Ff_f, (Gg_g, Hh_h)))), Ii_i)"
+  }],
+  "phylorefs": [{
+    "label": "Unexpected",
+    "definition": "Includes A_a, excludes C_c.",
+    "internalSpecifiers": [
+      {
+          "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+          "hasName": {
+              "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+              "nameComplete": "Aa a"
+          }
+      }
+    ],
+    "externalSpecifiers": [
+      {
+          "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+          "hasName": {
+              "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+              "nameComplete": "Cc c"
+          }
+      }
+    ]
+  }]
+}
diff --git a/test/examples/correct/example_no_successes.jsonld b/test/examples/correct/example_no_successes.jsonld
new file mode 100644
index 00000000..457ebc25
--- /dev/null
+++ b/test/examples/correct/example_no_successes.jsonld
@@ -0,0 +1,597 @@
+{
+  "@context": "../../../docs/context/development/phyx.json",
+  "phylogenies": [
+    {
+      "newick": "((((Aa_a, Bb_b)Expected, Cc_c), (Dd_d, (Ee_e, Ff_f, (Gg_g, Hh_h)))), Ii_i)",
+      "@id": "http://example.org/phyx.js/example#phylogeny0",
+      "@type": "testcase:PhyloreferenceTestPhylogeny",
+      "nodes": [
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node0",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            }
+          ],
+          "children": [
+            "http://example.org/phyx.js/example#phylogeny0_node1",
+            "http://example.org/phyx.js/example#phylogeny0_node2"
+          ]
+        },
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node1",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            },
+            {
+              "@type": "owl:Restriction",
+              "onProperty": "obo:CDAO_0000187",
+              "someValuesFrom": {
+                "@type": "owl:Restriction",
+                "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName",
+                "someValuesFrom": {
+                  "@type": "owl:Restriction",
+                  "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete",
+                  "hasValue": "Ii i"
+                }
+              }
+            }
+          ],
+          "labels": [
+            "Ii_i"
+          ],
+          "representsTaxonomicUnits": [
+            {
+              "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+              "hasName": {
+                "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+                "label": "Ii_i",
+                "nameComplete": "Ii i",
+                "genusPart": "Ii",
+                "specificEpithet": "i"
+              },
+              "label": "Ii_i"
+            }
+          ],
+          "parent": "http://example.org/phyx.js/example#phylogeny0_node0",
+          "siblings": [
+            "http://example.org/phyx.js/example#phylogeny0_node2"
+          ]
+        },
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node2",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            }
+          ],
+          "parent": "http://example.org/phyx.js/example#phylogeny0_node0",
+          "siblings": [
+            "http://example.org/phyx.js/example#phylogeny0_node1"
+          ],
+          "children": [
+            "http://example.org/phyx.js/example#phylogeny0_node3",
+            "http://example.org/phyx.js/example#phylogeny0_node11"
+          ]
+        },
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node3",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            }
+          ],
+          "parent": "http://example.org/phyx.js/example#phylogeny0_node2",
+          "siblings": [
+            "http://example.org/phyx.js/example#phylogeny0_node11"
+          ],
+          "children": [
+            "http://example.org/phyx.js/example#phylogeny0_node4",
+            "http://example.org/phyx.js/example#phylogeny0_node10"
+          ]
+        },
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node4",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            }
+          ],
+          "parent": "http://example.org/phyx.js/example#phylogeny0_node3",
+          "siblings": [
+            "http://example.org/phyx.js/example#phylogeny0_node10"
+          ],
+          "children": [
+            "http://example.org/phyx.js/example#phylogeny0_node5",
+            "http://example.org/phyx.js/example#phylogeny0_node8",
+            "http://example.org/phyx.js/example#phylogeny0_node9"
+          ]
+        },
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node5",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            }
+          ],
+          "parent": "http://example.org/phyx.js/example#phylogeny0_node4",
+          "siblings": [
+            "http://example.org/phyx.js/example#phylogeny0_node8",
+            "http://example.org/phyx.js/example#phylogeny0_node9"
+          ],
+          "children": [
+            "http://example.org/phyx.js/example#phylogeny0_node6",
+            "http://example.org/phyx.js/example#phylogeny0_node7"
+          ]
+        },
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node6",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            },
+            {
+              "@type": "owl:Restriction",
+              "onProperty": "obo:CDAO_0000187",
+              "someValuesFrom": {
+                "@type": "owl:Restriction",
+                "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName",
+                "someValuesFrom": {
+                  "@type": "owl:Restriction",
+                  "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete",
+                  "hasValue": "Hh h"
+                }
+              }
+            }
+          ],
+          "labels": [
+            "Hh_h"
+          ],
+          "representsTaxonomicUnits": [
+            {
+              "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+              "hasName": {
+                "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+                "label": "Hh_h",
+                "nameComplete": "Hh h",
+                "genusPart": "Hh",
+                "specificEpithet": "h"
+              },
+              "label": "Hh_h"
+            }
+          ],
+          "parent": "http://example.org/phyx.js/example#phylogeny0_node5",
+          "siblings": [
+            "http://example.org/phyx.js/example#phylogeny0_node7"
+          ]
+        },
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node7",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            },
+            {
+              "@type": "owl:Restriction",
+              "onProperty": "obo:CDAO_0000187",
+              "someValuesFrom": {
+                "@type": "owl:Restriction",
+                "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName",
+                "someValuesFrom": {
+                  "@type": "owl:Restriction",
+                  "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete",
+                  "hasValue": "Gg g"
+                }
+              }
+            }
+          ],
+          "labels": [
+            "Gg_g"
+          ],
+          "representsTaxonomicUnits": [
+            {
+              "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+              "hasName": {
+                "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+                "label": "Gg_g",
+                "nameComplete": "Gg g",
+                "genusPart": "Gg",
+                "specificEpithet": "g"
+              },
+              "label": "Gg_g"
+            }
+          ],
+          "parent": "http://example.org/phyx.js/example#phylogeny0_node5",
+          "siblings": [
+            "http://example.org/phyx.js/example#phylogeny0_node6"
+          ]
+        },
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node8",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            },
+            {
+              "@type": "owl:Restriction",
+              "onProperty": "obo:CDAO_0000187",
+              "someValuesFrom": {
+                "@type": "owl:Restriction",
+                "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName",
+                "someValuesFrom": {
+                  "@type": "owl:Restriction",
+                  "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete",
+                  "hasValue": "Ff f"
+                }
+              }
+            }
+          ],
+          "labels": [
+            "Ff_f"
+          ],
+          "representsTaxonomicUnits": [
+            {
+              "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+              "hasName": {
+                "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+                "label": "Ff_f",
+                "nameComplete": "Ff f",
+                "genusPart": "Ff",
+                "specificEpithet": "f"
+              },
+              "label": "Ff_f"
+            }
+          ],
+          "parent": "http://example.org/phyx.js/example#phylogeny0_node4",
+          "siblings": [
+            "http://example.org/phyx.js/example#phylogeny0_node5",
+            "http://example.org/phyx.js/example#phylogeny0_node9"
+          ]
+        },
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node9",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            },
+            {
+              "@type": "owl:Restriction",
+              "onProperty": "obo:CDAO_0000187",
+              "someValuesFrom": {
+                "@type": "owl:Restriction",
+                "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName",
+                "someValuesFrom": {
+                  "@type": "owl:Restriction",
+                  "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete",
+                  "hasValue": "Ee e"
+                }
+              }
+            }
+          ],
+          "labels": [
+            "Ee_e"
+          ],
+          "representsTaxonomicUnits": [
+            {
+              "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+              "hasName": {
+                "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+                "label": "Ee_e",
+                "nameComplete": "Ee e",
+                "genusPart": "Ee",
+                "specificEpithet": "e"
+              },
+              "label": "Ee_e"
+            }
+          ],
+          "parent": "http://example.org/phyx.js/example#phylogeny0_node4",
+          "siblings": [
+            "http://example.org/phyx.js/example#phylogeny0_node5",
+            "http://example.org/phyx.js/example#phylogeny0_node8"
+          ]
+        },
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node10",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            },
+            {
+              "@type": "owl:Restriction",
+              "onProperty": "obo:CDAO_0000187",
+              "someValuesFrom": {
+                "@type": "owl:Restriction",
+                "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName",
+                "someValuesFrom": {
+                  "@type": "owl:Restriction",
+                  "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete",
+                  "hasValue": "Dd d"
+                }
+              }
+            }
+          ],
+          "labels": [
+            "Dd_d"
+          ],
+          "representsTaxonomicUnits": [
+            {
+              "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+              "hasName": {
+                "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+                "label": "Dd_d",
+                "nameComplete": "Dd d",
+                "genusPart": "Dd",
+                "specificEpithet": "d"
+              },
+              "label": "Dd_d"
+            }
+          ],
+          "parent": "http://example.org/phyx.js/example#phylogeny0_node3",
+          "siblings": [
+            "http://example.org/phyx.js/example#phylogeny0_node4"
+          ]
+        },
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node11",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            }
+          ],
+          "parent": "http://example.org/phyx.js/example#phylogeny0_node2",
+          "siblings": [
+            "http://example.org/phyx.js/example#phylogeny0_node3"
+          ],
+          "children": [
+            "http://example.org/phyx.js/example#phylogeny0_node12",
+            "http://example.org/phyx.js/example#phylogeny0_node13"
+          ]
+        },
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node12",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            },
+            {
+              "@type": "owl:Restriction",
+              "onProperty": "obo:CDAO_0000187",
+              "someValuesFrom": {
+                "@type": "owl:Restriction",
+                "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName",
+                "someValuesFrom": {
+                  "@type": "owl:Restriction",
+                  "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete",
+                  "hasValue": "Cc c"
+                }
+              }
+            }
+          ],
+          "labels": [
+            "Cc_c"
+          ],
+          "representsTaxonomicUnits": [
+            {
+              "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+              "hasName": {
+                "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+                "label": "Cc_c",
+                "nameComplete": "Cc c",
+                "genusPart": "Cc",
+                "specificEpithet": "c"
+              },
+              "label": "Cc_c"
+            }
+          ],
+          "parent": "http://example.org/phyx.js/example#phylogeny0_node11",
+          "siblings": [
+            "http://example.org/phyx.js/example#phylogeny0_node13"
+          ]
+        },
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node13",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            },
+            {
+              "@type": "owl:Restriction",
+              "onProperty": "obo:CDAO_0000187",
+              "someValuesFrom": {
+                "@type": "owl:Restriction",
+                "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName",
+                "someValuesFrom": {
+                  "@type": "owl:Restriction",
+                  "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete",
+                  "hasValue": "Expected"
+                }
+              }
+            }
+          ],
+          "labels": [
+            "Expected"
+          ],
+          "representsTaxonomicUnits": [
+            {
+              "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+              "hasName": {
+                "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+                "label": "Expected",
+                "nameComplete": "Expected",
+                "uninomial": "Expected"
+              },
+              "label": "Expected"
+            }
+          ],
+          "parent": "http://example.org/phyx.js/example#phylogeny0_node11",
+          "siblings": [
+            "http://example.org/phyx.js/example#phylogeny0_node12"
+          ],
+          "children": [
+            "http://example.org/phyx.js/example#phylogeny0_node14",
+            "http://example.org/phyx.js/example#phylogeny0_node15"
+          ]
+        },
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node14",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            },
+            {
+              "@type": "owl:Restriction",
+              "onProperty": "obo:CDAO_0000187",
+              "someValuesFrom": {
+                "@type": "owl:Restriction",
+                "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName",
+                "someValuesFrom": {
+                  "@type": "owl:Restriction",
+                  "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete",
+                  "hasValue": "Bb b"
+                }
+              }
+            }
+          ],
+          "labels": [
+            "Bb_b"
+          ],
+          "representsTaxonomicUnits": [
+            {
+              "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+              "hasName": {
+                "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+                "label": "Bb_b",
+                "nameComplete": "Bb b",
+                "genusPart": "Bb",
+                "specificEpithet": "b"
+              },
+              "label": "Bb_b"
+            }
+          ],
+          "parent": "http://example.org/phyx.js/example#phylogeny0_node13",
+          "siblings": [
+            "http://example.org/phyx.js/example#phylogeny0_node15"
+          ]
+        },
+        {
+          "@id": "http://example.org/phyx.js/example#phylogeny0_node15",
+          "rdf:type": [
+            {
+              "@id": "obo:CDAO_0000140"
+            },
+            {
+              "@type": "owl:Restriction",
+              "onProperty": "obo:CDAO_0000187",
+              "someValuesFrom": {
+                "@type": "owl:Restriction",
+                "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName",
+                "someValuesFrom": {
+                  "@type": "owl:Restriction",
+                  "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete",
+                  "hasValue": "Aa a"
+                }
+              }
+            }
+          ],
+          "labels": [
+            "Aa_a"
+          ],
+          "representsTaxonomicUnits": [
+            {
+              "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+              "hasName": {
+                "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+                "label": "Aa_a",
+                "nameComplete": "Aa a",
+                "genusPart": "Aa",
+                "specificEpithet": "a"
+              },
+              "label": "Aa_a"
+            }
+          ],
+          "parent": "http://example.org/phyx.js/example#phylogeny0_node13",
+          "siblings": [
+            "http://example.org/phyx.js/example#phylogeny0_node14"
+          ]
+        }
+      ],
+      "hasRootNode": {
+        "@id": "http://example.org/phyx.js/example#phylogeny0_node0"
+      }
+    }
+  ],
+  "phylorefs": [
+    {
+      "label": "Unexpected",
+      "definition": "Includes A_a, excludes C_c.",
+      "internalSpecifiers": [
+        {
+          "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+          "hasName": {
+            "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+            "nameComplete": "Aa a"
+          }
+        }
+      ],
+      "externalSpecifiers": [
+        {
+          "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+          "hasName": {
+            "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+            "nameComplete": "Cc c"
+          }
+        }
+      ],
+      "@id": "http://example.org/phyx.js/example#phyloref0",
+      "@type": "owl:Class",
+      "hasComponentClass": [],
+      "equivalentClass": {
+        "@type": "owl:Class",
+        "intersectionOf": [
+          {
+            "@type": "owl:Restriction",
+            "onProperty": "phyloref:includes_TU",
+            "someValuesFrom": {
+              "@type": "owl:Restriction",
+              "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName",
+              "someValuesFrom": {
+                "@type": "owl:Restriction",
+                "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete",
+                "hasValue": "Aa a"
+              }
+            }
+          },
+          {
+            "@type": "owl:Restriction",
+            "onProperty": "phyloref:excludes_TU",
+            "someValuesFrom": {
+              "@type": "owl:Restriction",
+              "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName",
+              "someValuesFrom": {
+                "@type": "owl:Restriction",
+                "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete",
+                "hasValue": "Cc c"
+              }
+            }
+          }
+        ]
+      },
+      "subClassOf": [
+        "phyloref:Phyloreference",
+        "phyloref:PhyloreferenceUsingMaximumClade"
+      ]
+    }
+  ],
+  "hasTaxonomicUnitMatches": [],
+  "@id": "http://example.org/phyx.js/example#",
+  "@type": [
+    "testcase:PhyloreferenceTestCase",
+    "owl:Ontology"
+  ],
+  "owl:imports": [
+    "http://raw.githubusercontent.com/phyloref/curation-workflow/develop/ontologies/phyloref_testcase.owl",
+    "http://ontology.phyloref.org/2018-12-14/phyloref.owl",
+    "http://ontology.phyloref.org/2018-12-14/tcan.owl"
+  ]
+}
\ No newline at end of file
diff --git a/test/examples/correct/example_no_successes.nq b/test/examples/correct/example_no_successes.nq
new file mode 100644
index 00000000..ae42204c
--- /dev/null
+++ b/test/examples/correct/example_no_successes.nq
@@ -0,0 +1,328 @@
+<http://example.org/phyx.js/example#> <http://vocab.phyloref.org/phyloref/testcase.owl#has_phylogeny> <http://example.org/phyx.js/example#phylogeny0> .
+<http://example.org/phyx.js/example#> <http://vocab.phyloref.org/phyloref/testcase.owl#has_phyloreference> <http://example.org/phyx.js/example#phyloref0> .
+<http://example.org/phyx.js/example#> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vocab.phyloref.org/phyloref/testcase.owl#PhyloreferenceTestCase> .
+<http://example.org/phyx.js/example#> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Ontology> .
+<http://example.org/phyx.js/example#> <http://www.w3.org/2002/07/owl#imports> <http://ontology.phyloref.org/2018-12-14/phyloref.owl> .
+<http://example.org/phyx.js/example#> <http://www.w3.org/2002/07/owl#imports> <http://ontology.phyloref.org/2018-12-14/tcan.owl> .
+<http://example.org/phyx.js/example#> <http://www.w3.org/2002/07/owl#imports> <http://raw.githubusercontent.com/phyloref/curation-workflow/develop/ontologies/phyloref_testcase.owl> .
+<http://example.org/phyx.js/example#phylogeny0> <http://ontology.phyloref.org/phyloref.owl#newick_expression> "((((Aa_a, Bb_b)Expected, Cc_c), (Dd_d, (Ee_e, Ff_f, (Gg_g, Hh_h)))), Ii_i)" .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node0> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node10> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node11> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node12> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node13> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node14> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node15> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node1> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node2> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node3> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node4> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node5> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node6> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node7> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node8> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_node> <http://example.org/phyx.js/example#phylogeny0_node9> .
+<http://example.org/phyx.js/example#phylogeny0> <http://vocab.phyloref.org/phyloref/testcase.owl#has_root_node> <http://example.org/phyx.js/example#phylogeny0_node0> .
+<http://example.org/phyx.js/example#phylogeny0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vocab.phyloref.org/phyloref/testcase.owl#PhyloreferenceTestPhylogeny> .
+<http://example.org/phyx.js/example#phylogeny0_node0> <http://purl.obolibrary.org/obo/CDAO_0000149> <http://example.org/phyx.js/example#phylogeny0_node1> .
+<http://example.org/phyx.js/example#phylogeny0_node0> <http://purl.obolibrary.org/obo/CDAO_0000149> <http://example.org/phyx.js/example#phylogeny0_node2> .
+<http://example.org/phyx.js/example#phylogeny0_node0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node10> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node4> .
+<http://example.org/phyx.js/example#phylogeny0_node10> <http://purl.obolibrary.org/obo/CDAO_0000179> <http://example.org/phyx.js/example#phylogeny0_node3> .
+<http://example.org/phyx.js/example#phylogeny0_node10> <http://purl.obolibrary.org/obo/CDAO_0000187> _:b25 .
+<http://example.org/phyx.js/example#phylogeny0_node10> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node10> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:b27 .
+<http://example.org/phyx.js/example#phylogeny0_node10> <http://www.w3.org/2000/01/rdf-schema#label> "Dd_d" .
+<http://example.org/phyx.js/example#phylogeny0_node11> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node3> .
+<http://example.org/phyx.js/example#phylogeny0_node11> <http://purl.obolibrary.org/obo/CDAO_0000149> <http://example.org/phyx.js/example#phylogeny0_node12> .
+<http://example.org/phyx.js/example#phylogeny0_node11> <http://purl.obolibrary.org/obo/CDAO_0000149> <http://example.org/phyx.js/example#phylogeny0_node13> .
+<http://example.org/phyx.js/example#phylogeny0_node11> <http://purl.obolibrary.org/obo/CDAO_0000179> <http://example.org/phyx.js/example#phylogeny0_node2> .
+<http://example.org/phyx.js/example#phylogeny0_node11> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node12> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node13> .
+<http://example.org/phyx.js/example#phylogeny0_node12> <http://purl.obolibrary.org/obo/CDAO_0000179> <http://example.org/phyx.js/example#phylogeny0_node11> .
+<http://example.org/phyx.js/example#phylogeny0_node12> <http://purl.obolibrary.org/obo/CDAO_0000187> _:b30 .
+<http://example.org/phyx.js/example#phylogeny0_node12> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node12> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:b32 .
+<http://example.org/phyx.js/example#phylogeny0_node12> <http://www.w3.org/2000/01/rdf-schema#label> "Cc_c" .
+<http://example.org/phyx.js/example#phylogeny0_node13> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node12> .
+<http://example.org/phyx.js/example#phylogeny0_node13> <http://purl.obolibrary.org/obo/CDAO_0000149> <http://example.org/phyx.js/example#phylogeny0_node14> .
+<http://example.org/phyx.js/example#phylogeny0_node13> <http://purl.obolibrary.org/obo/CDAO_0000149> <http://example.org/phyx.js/example#phylogeny0_node15> .
+<http://example.org/phyx.js/example#phylogeny0_node13> <http://purl.obolibrary.org/obo/CDAO_0000179> <http://example.org/phyx.js/example#phylogeny0_node11> .
+<http://example.org/phyx.js/example#phylogeny0_node13> <http://purl.obolibrary.org/obo/CDAO_0000187> _:b35 .
+<http://example.org/phyx.js/example#phylogeny0_node13> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node13> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:b37 .
+<http://example.org/phyx.js/example#phylogeny0_node13> <http://www.w3.org/2000/01/rdf-schema#label> "Expected" .
+<http://example.org/phyx.js/example#phylogeny0_node14> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node15> .
+<http://example.org/phyx.js/example#phylogeny0_node14> <http://purl.obolibrary.org/obo/CDAO_0000179> <http://example.org/phyx.js/example#phylogeny0_node13> .
+<http://example.org/phyx.js/example#phylogeny0_node14> <http://purl.obolibrary.org/obo/CDAO_0000187> _:b40 .
+<http://example.org/phyx.js/example#phylogeny0_node14> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node14> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:b42 .
+<http://example.org/phyx.js/example#phylogeny0_node14> <http://www.w3.org/2000/01/rdf-schema#label> "Bb_b" .
+<http://example.org/phyx.js/example#phylogeny0_node15> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node14> .
+<http://example.org/phyx.js/example#phylogeny0_node15> <http://purl.obolibrary.org/obo/CDAO_0000179> <http://example.org/phyx.js/example#phylogeny0_node13> .
+<http://example.org/phyx.js/example#phylogeny0_node15> <http://purl.obolibrary.org/obo/CDAO_0000187> _:b45 .
+<http://example.org/phyx.js/example#phylogeny0_node15> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node15> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:b47 .
+<http://example.org/phyx.js/example#phylogeny0_node15> <http://www.w3.org/2000/01/rdf-schema#label> "Aa_a" .
+<http://example.org/phyx.js/example#phylogeny0_node1> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node2> .
+<http://example.org/phyx.js/example#phylogeny0_node1> <http://purl.obolibrary.org/obo/CDAO_0000179> <http://example.org/phyx.js/example#phylogeny0_node0> .
+<http://example.org/phyx.js/example#phylogeny0_node1> <http://purl.obolibrary.org/obo/CDAO_0000187> _:b0 .
+<http://example.org/phyx.js/example#phylogeny0_node1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:b2 .
+<http://example.org/phyx.js/example#phylogeny0_node1> <http://www.w3.org/2000/01/rdf-schema#label> "Ii_i" .
+<http://example.org/phyx.js/example#phylogeny0_node2> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node1> .
+<http://example.org/phyx.js/example#phylogeny0_node2> <http://purl.obolibrary.org/obo/CDAO_0000149> <http://example.org/phyx.js/example#phylogeny0_node11> .
+<http://example.org/phyx.js/example#phylogeny0_node2> <http://purl.obolibrary.org/obo/CDAO_0000149> <http://example.org/phyx.js/example#phylogeny0_node3> .
+<http://example.org/phyx.js/example#phylogeny0_node2> <http://purl.obolibrary.org/obo/CDAO_0000179> <http://example.org/phyx.js/example#phylogeny0_node0> .
+<http://example.org/phyx.js/example#phylogeny0_node2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node3> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node11> .
+<http://example.org/phyx.js/example#phylogeny0_node3> <http://purl.obolibrary.org/obo/CDAO_0000149> <http://example.org/phyx.js/example#phylogeny0_node10> .
+<http://example.org/phyx.js/example#phylogeny0_node3> <http://purl.obolibrary.org/obo/CDAO_0000149> <http://example.org/phyx.js/example#phylogeny0_node4> .
+<http://example.org/phyx.js/example#phylogeny0_node3> <http://purl.obolibrary.org/obo/CDAO_0000179> <http://example.org/phyx.js/example#phylogeny0_node2> .
+<http://example.org/phyx.js/example#phylogeny0_node3> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node4> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node10> .
+<http://example.org/phyx.js/example#phylogeny0_node4> <http://purl.obolibrary.org/obo/CDAO_0000149> <http://example.org/phyx.js/example#phylogeny0_node5> .
+<http://example.org/phyx.js/example#phylogeny0_node4> <http://purl.obolibrary.org/obo/CDAO_0000149> <http://example.org/phyx.js/example#phylogeny0_node8> .
+<http://example.org/phyx.js/example#phylogeny0_node4> <http://purl.obolibrary.org/obo/CDAO_0000149> <http://example.org/phyx.js/example#phylogeny0_node9> .
+<http://example.org/phyx.js/example#phylogeny0_node4> <http://purl.obolibrary.org/obo/CDAO_0000179> <http://example.org/phyx.js/example#phylogeny0_node3> .
+<http://example.org/phyx.js/example#phylogeny0_node4> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node5> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node8> .
+<http://example.org/phyx.js/example#phylogeny0_node5> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node9> .
+<http://example.org/phyx.js/example#phylogeny0_node5> <http://purl.obolibrary.org/obo/CDAO_0000149> <http://example.org/phyx.js/example#phylogeny0_node6> .
+<http://example.org/phyx.js/example#phylogeny0_node5> <http://purl.obolibrary.org/obo/CDAO_0000149> <http://example.org/phyx.js/example#phylogeny0_node7> .
+<http://example.org/phyx.js/example#phylogeny0_node5> <http://purl.obolibrary.org/obo/CDAO_0000179> <http://example.org/phyx.js/example#phylogeny0_node4> .
+<http://example.org/phyx.js/example#phylogeny0_node5> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node6> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node7> .
+<http://example.org/phyx.js/example#phylogeny0_node6> <http://purl.obolibrary.org/obo/CDAO_0000179> <http://example.org/phyx.js/example#phylogeny0_node5> .
+<http://example.org/phyx.js/example#phylogeny0_node6> <http://purl.obolibrary.org/obo/CDAO_0000187> _:b5 .
+<http://example.org/phyx.js/example#phylogeny0_node6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:b7 .
+<http://example.org/phyx.js/example#phylogeny0_node6> <http://www.w3.org/2000/01/rdf-schema#label> "Hh_h" .
+<http://example.org/phyx.js/example#phylogeny0_node7> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node6> .
+<http://example.org/phyx.js/example#phylogeny0_node7> <http://purl.obolibrary.org/obo/CDAO_0000179> <http://example.org/phyx.js/example#phylogeny0_node5> .
+<http://example.org/phyx.js/example#phylogeny0_node7> <http://purl.obolibrary.org/obo/CDAO_0000187> _:b10 .
+<http://example.org/phyx.js/example#phylogeny0_node7> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node7> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:b12 .
+<http://example.org/phyx.js/example#phylogeny0_node7> <http://www.w3.org/2000/01/rdf-schema#label> "Gg_g" .
+<http://example.org/phyx.js/example#phylogeny0_node8> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node5> .
+<http://example.org/phyx.js/example#phylogeny0_node8> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node9> .
+<http://example.org/phyx.js/example#phylogeny0_node8> <http://purl.obolibrary.org/obo/CDAO_0000179> <http://example.org/phyx.js/example#phylogeny0_node4> .
+<http://example.org/phyx.js/example#phylogeny0_node8> <http://purl.obolibrary.org/obo/CDAO_0000187> _:b15 .
+<http://example.org/phyx.js/example#phylogeny0_node8> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node8> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:b17 .
+<http://example.org/phyx.js/example#phylogeny0_node8> <http://www.w3.org/2000/01/rdf-schema#label> "Ff_f" .
+<http://example.org/phyx.js/example#phylogeny0_node9> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node5> .
+<http://example.org/phyx.js/example#phylogeny0_node9> <http://ontology.phyloref.org/phyloref.owl#has_Sibling> <http://example.org/phyx.js/example#phylogeny0_node8> .
+<http://example.org/phyx.js/example#phylogeny0_node9> <http://purl.obolibrary.org/obo/CDAO_0000179> <http://example.org/phyx.js/example#phylogeny0_node4> .
+<http://example.org/phyx.js/example#phylogeny0_node9> <http://purl.obolibrary.org/obo/CDAO_0000187> _:b20 .
+<http://example.org/phyx.js/example#phylogeny0_node9> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/CDAO_0000140> .
+<http://example.org/phyx.js/example#phylogeny0_node9> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:b22 .
+<http://example.org/phyx.js/example#phylogeny0_node9> <http://www.w3.org/2000/01/rdf-schema#label> "Ee_e" .
+<http://example.org/phyx.js/example#phyloref0> <http://purl.obolibrary.org/obo/IAO_0000115> "Includes A_a, excludes C_c." .
+<http://example.org/phyx.js/example#phyloref0> <http://vocab.phyloref.org/phyloref/testcase.owl#external_specifier> _:b50 .
+<http://example.org/phyx.js/example#phyloref0> <http://vocab.phyloref.org/phyloref/testcase.owl#internal_specifier> _:b52 .
+<http://example.org/phyx.js/example#phyloref0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .
+<http://example.org/phyx.js/example#phyloref0> <http://www.w3.org/2000/01/rdf-schema#label> "Unexpected" .
+<http://example.org/phyx.js/example#phyloref0> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://ontology.phyloref.org/phyloref.owl#Phyloreference> .
+<http://example.org/phyx.js/example#phyloref0> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://ontology.phyloref.org/phyloref.owl#PhyloreferenceUsingMaximumClade> .
+<http://example.org/phyx.js/example#phyloref0> <http://www.w3.org/2002/07/owl#equivalentClass> _:b54 .
+_:b0 <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> _:b1 .
+_:b0 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept> .
+_:b0 <http://www.w3.org/2000/01/rdf-schema#label> "Ii_i" .
+_:b1 <http://rs.tdwg.org/ontology/voc/TaxonName#genusPart> "Ii" .
+_:b1 <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> "Ii i" .
+_:b1 <http://rs.tdwg.org/ontology/voc/TaxonName#specificEpithet> "i" .
+_:b1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName> .
+_:b1 <http://www.w3.org/2000/01/rdf-schema#label> "Ii_i" .
+_:b10 <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> _:b11 .
+_:b10 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept> .
+_:b10 <http://www.w3.org/2000/01/rdf-schema#label> "Gg_g" .
+_:b11 <http://rs.tdwg.org/ontology/voc/TaxonName#genusPart> "Gg" .
+_:b11 <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> "Gg g" .
+_:b11 <http://rs.tdwg.org/ontology/voc/TaxonName#specificEpithet> "g" .
+_:b11 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName> .
+_:b11 <http://www.w3.org/2000/01/rdf-schema#label> "Gg_g" .
+_:b12 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b12 <http://www.w3.org/2002/07/owl#onProperty> <http://purl.obolibrary.org/obo/CDAO_0000187> .
+_:b12 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b13 .
+_:b13 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b13 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> .
+_:b13 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b14 .
+_:b14 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b14 <http://www.w3.org/2002/07/owl#hasValue> "Gg g" .
+_:b14 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> .
+_:b15 <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> _:b16 .
+_:b15 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept> .
+_:b15 <http://www.w3.org/2000/01/rdf-schema#label> "Ff_f" .
+_:b16 <http://rs.tdwg.org/ontology/voc/TaxonName#genusPart> "Ff" .
+_:b16 <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> "Ff f" .
+_:b16 <http://rs.tdwg.org/ontology/voc/TaxonName#specificEpithet> "f" .
+_:b16 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName> .
+_:b16 <http://www.w3.org/2000/01/rdf-schema#label> "Ff_f" .
+_:b17 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b17 <http://www.w3.org/2002/07/owl#onProperty> <http://purl.obolibrary.org/obo/CDAO_0000187> .
+_:b17 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b18 .
+_:b18 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b18 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> .
+_:b18 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b19 .
+_:b19 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b19 <http://www.w3.org/2002/07/owl#hasValue> "Ff f" .
+_:b19 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> .
+_:b2 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b2 <http://www.w3.org/2002/07/owl#onProperty> <http://purl.obolibrary.org/obo/CDAO_0000187> .
+_:b2 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b3 .
+_:b20 <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> _:b21 .
+_:b20 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept> .
+_:b20 <http://www.w3.org/2000/01/rdf-schema#label> "Ee_e" .
+_:b21 <http://rs.tdwg.org/ontology/voc/TaxonName#genusPart> "Ee" .
+_:b21 <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> "Ee e" .
+_:b21 <http://rs.tdwg.org/ontology/voc/TaxonName#specificEpithet> "e" .
+_:b21 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName> .
+_:b21 <http://www.w3.org/2000/01/rdf-schema#label> "Ee_e" .
+_:b22 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b22 <http://www.w3.org/2002/07/owl#onProperty> <http://purl.obolibrary.org/obo/CDAO_0000187> .
+_:b22 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b23 .
+_:b23 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b23 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> .
+_:b23 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b24 .
+_:b24 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b24 <http://www.w3.org/2002/07/owl#hasValue> "Ee e" .
+_:b24 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> .
+_:b25 <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> _:b26 .
+_:b25 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept> .
+_:b25 <http://www.w3.org/2000/01/rdf-schema#label> "Dd_d" .
+_:b26 <http://rs.tdwg.org/ontology/voc/TaxonName#genusPart> "Dd" .
+_:b26 <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> "Dd d" .
+_:b26 <http://rs.tdwg.org/ontology/voc/TaxonName#specificEpithet> "d" .
+_:b26 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName> .
+_:b26 <http://www.w3.org/2000/01/rdf-schema#label> "Dd_d" .
+_:b27 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b27 <http://www.w3.org/2002/07/owl#onProperty> <http://purl.obolibrary.org/obo/CDAO_0000187> .
+_:b27 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b28 .
+_:b28 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b28 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> .
+_:b28 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b29 .
+_:b29 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b29 <http://www.w3.org/2002/07/owl#hasValue> "Dd d" .
+_:b29 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> .
+_:b3 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b3 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> .
+_:b3 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b4 .
+_:b30 <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> _:b31 .
+_:b30 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept> .
+_:b30 <http://www.w3.org/2000/01/rdf-schema#label> "Cc_c" .
+_:b31 <http://rs.tdwg.org/ontology/voc/TaxonName#genusPart> "Cc" .
+_:b31 <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> "Cc c" .
+_:b31 <http://rs.tdwg.org/ontology/voc/TaxonName#specificEpithet> "c" .
+_:b31 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName> .
+_:b31 <http://www.w3.org/2000/01/rdf-schema#label> "Cc_c" .
+_:b32 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b32 <http://www.w3.org/2002/07/owl#onProperty> <http://purl.obolibrary.org/obo/CDAO_0000187> .
+_:b32 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b33 .
+_:b33 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b33 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> .
+_:b33 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b34 .
+_:b34 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b34 <http://www.w3.org/2002/07/owl#hasValue> "Cc c" .
+_:b34 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> .
+_:b35 <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> _:b36 .
+_:b35 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept> .
+_:b35 <http://www.w3.org/2000/01/rdf-schema#label> "Expected" .
+_:b36 <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> "Expected" .
+_:b36 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName> .
+_:b36 <http://www.w3.org/2000/01/rdf-schema#label> "Expected" .
+_:b37 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b37 <http://www.w3.org/2002/07/owl#onProperty> <http://purl.obolibrary.org/obo/CDAO_0000187> .
+_:b37 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b38 .
+_:b38 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b38 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> .
+_:b38 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b39 .
+_:b39 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b39 <http://www.w3.org/2002/07/owl#hasValue> "Expected" .
+_:b39 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> .
+_:b4 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b4 <http://www.w3.org/2002/07/owl#hasValue> "Ii i" .
+_:b4 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> .
+_:b40 <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> _:b41 .
+_:b40 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept> .
+_:b40 <http://www.w3.org/2000/01/rdf-schema#label> "Bb_b" .
+_:b41 <http://rs.tdwg.org/ontology/voc/TaxonName#genusPart> "Bb" .
+_:b41 <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> "Bb b" .
+_:b41 <http://rs.tdwg.org/ontology/voc/TaxonName#specificEpithet> "b" .
+_:b41 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName> .
+_:b41 <http://www.w3.org/2000/01/rdf-schema#label> "Bb_b" .
+_:b42 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b42 <http://www.w3.org/2002/07/owl#onProperty> <http://purl.obolibrary.org/obo/CDAO_0000187> .
+_:b42 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b43 .
+_:b43 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b43 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> .
+_:b43 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b44 .
+_:b44 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b44 <http://www.w3.org/2002/07/owl#hasValue> "Bb b" .
+_:b44 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> .
+_:b45 <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> _:b46 .
+_:b45 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept> .
+_:b45 <http://www.w3.org/2000/01/rdf-schema#label> "Aa_a" .
+_:b46 <http://rs.tdwg.org/ontology/voc/TaxonName#genusPart> "Aa" .
+_:b46 <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> "Aa a" .
+_:b46 <http://rs.tdwg.org/ontology/voc/TaxonName#specificEpithet> "a" .
+_:b46 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName> .
+_:b46 <http://www.w3.org/2000/01/rdf-schema#label> "Aa_a" .
+_:b47 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b47 <http://www.w3.org/2002/07/owl#onProperty> <http://purl.obolibrary.org/obo/CDAO_0000187> .
+_:b47 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b48 .
+_:b48 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b48 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> .
+_:b48 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b49 .
+_:b49 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b49 <http://www.w3.org/2002/07/owl#hasValue> "Aa a" .
+_:b49 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> .
+_:b5 <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> _:b6 .
+_:b5 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept> .
+_:b5 <http://www.w3.org/2000/01/rdf-schema#label> "Hh_h" .
+_:b50 <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> _:b51 .
+_:b50 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept> .
+_:b51 <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> "Cc c" .
+_:b51 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName> .
+_:b52 <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> _:b53 .
+_:b52 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept> .
+_:b53 <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> "Aa a" .
+_:b53 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName> .
+_:b54 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .
+_:b54 <http://www.w3.org/2002/07/owl#intersectionOf> _:b61 .
+_:b55 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b55 <http://www.w3.org/2002/07/owl#onProperty> <http://ontology.phyloref.org/phyloref.owl#includes_TU> .
+_:b55 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b56 .
+_:b56 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b56 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> .
+_:b56 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b57 .
+_:b57 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b57 <http://www.w3.org/2002/07/owl#hasValue> "Aa a" .
+_:b57 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> .
+_:b58 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b58 <http://www.w3.org/2002/07/owl#onProperty> <http://ontology.phyloref.org/phyloref.owl#excludes_TU> .
+_:b58 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b59 .
+_:b59 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b59 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> .
+_:b59 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b60 .
+_:b6 <http://rs.tdwg.org/ontology/voc/TaxonName#genusPart> "Hh" .
+_:b6 <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> "Hh h" .
+_:b6 <http://rs.tdwg.org/ontology/voc/TaxonName#specificEpithet> "h" .
+_:b6 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName> .
+_:b6 <http://www.w3.org/2000/01/rdf-schema#label> "Hh_h" .
+_:b60 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b60 <http://www.w3.org/2002/07/owl#hasValue> "Cc c" .
+_:b60 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> .
+_:b61 <http://www.w3.org/1999/02/22-rdf-syntax-ns#first> _:b55 .
+_:b61 <http://www.w3.org/1999/02/22-rdf-syntax-ns#rest> _:b62 .
+_:b62 <http://www.w3.org/1999/02/22-rdf-syntax-ns#first> _:b58 .
+_:b62 <http://www.w3.org/1999/02/22-rdf-syntax-ns#rest> <http://www.w3.org/1999/02/22-rdf-syntax-ns#nil> .
+_:b7 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b7 <http://www.w3.org/2002/07/owl#onProperty> <http://purl.obolibrary.org/obo/CDAO_0000187> .
+_:b7 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b8 .
+_:b8 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b8 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName> .
+_:b8 <http://www.w3.org/2002/07/owl#someValuesFrom> _:b9 .
+_:b9 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+_:b9 <http://www.w3.org/2002/07/owl#hasValue> "Hh h" .
+_:b9 <http://www.w3.org/2002/07/owl#onProperty> <http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete> .

From 0529858220241e8ec2e41090230a7b3bd2ab17b3 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Thu, 4 Mar 2021 23:43:58 -0500
Subject: [PATCH 3/7] Improved tests for cases with incorrect JPhyloRef output.

---
 test/jphyloref.js | 41 +++++++++++++++++++++++------------------
 1 file changed, 23 insertions(+), 18 deletions(-)

diff --git a/test/jphyloref.js b/test/jphyloref.js
index ed3a78dd..6d54b142 100644
--- a/test/jphyloref.js
+++ b/test/jphyloref.js
@@ -78,26 +78,31 @@ describe('JPhyloRef', function () {
             expect(matches, `Test result line not found in STDERR <${child.stderr}>`).to.have.lengthOf(5);
           });
 
-          const countSuccess = Number(matches[1]);
-          const countFailure = Number(matches[2]);
-          const countTODOs = Number(matches[3]);
-          // const countSkipped = Number(matches[4]);
+          // If this is not true, the previous expect with fail. Unfortunately,
+          // code execution continues even if that one `it()` fails, so we need
+          // to test it here as well.
+          if (matches.length === 5) {
+            const countSuccess = Number(matches[1]);
+            const countFailure = Number(matches[2]);
+            const countTODOs = Number(matches[3]);
+            // const countSkipped = Number(matches[4]);
 
-          it('should run without any failures or TODOs', () => {
-            expect(countFailure, 'Expected zero failures').to.equal(0);
-            expect(countTODOs, 'Expected zero TODOs').to.equal(0);
-          });
-
-          // We can't test for one or more successes since some example Phyx file
-          // such as apomorphy-based phyloreferences don't have any successes at all.
-          // But we'll report both.
-          if (countSuccess === 0 && child.status === 255) {
-            it('No phyloreferences resolved successfully');
-          } else {
-            it('should resolve one or more phyloreferences', () => {
-              expect(countSuccess, 'Expected one or more successes').to.be.greaterThan(0);
-              expect(child.status).to.be.oneOf([0, 255]);
+            it('should run without any failures or TODOs', () => {
+              expect(countFailure, 'Expected zero failures').to.equal(0);
+              expect(countTODOs, 'Expected zero TODOs').to.equal(0);
             });
+
+            // We can't test for one or more successes since some example Phyx file
+            // such as apomorphy-based phyloreferences don't have any successes at all.
+            // But we'll report both.
+            if (countSuccess === 0 && child.status === 255) {
+              it('No phyloreferences resolved successfully');
+            } else {
+              it('should resolve one or more phyloreferences', () => {
+                expect(countSuccess, 'Expected one or more successes').to.be.greaterThan(0);
+                expect(child.status).to.be.oneOf([0, 255]);
+              });
+            }
           }
         });
       });

From b10c7ddc4e28beac37afc1cfdfe2b37ebdaa0731 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Thu, 4 Mar 2021 23:47:31 -0500
Subject: [PATCH 4/7] Further attempts to improve status line detection.

---
 test/jphyloref.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/jphyloref.js b/test/jphyloref.js
index 6d54b142..f25ca420 100644
--- a/test/jphyloref.js
+++ b/test/jphyloref.js
@@ -81,7 +81,7 @@ describe('JPhyloRef', function () {
           // If this is not true, the previous expect with fail. Unfortunately,
           // code execution continues even if that one `it()` fails, so we need
           // to test it here as well.
-          if (matches.length === 5) {
+          if (matches && matches.length === 5) {
             const countSuccess = Number(matches[1]);
             const countFailure = Number(matches[2]);
             const countTODOs = Number(matches[3]);

From 4accbada2d523ebd2c162eb1e160cad6400bfb0b Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Thu, 4 Mar 2021 23:55:56 -0500
Subject: [PATCH 5/7] Possible fix to incomplete download bug.

---
 test/jphyloref.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/jphyloref.js b/test/jphyloref.js
index f25ca420..fd13b76f 100644
--- a/test/jphyloref.js
+++ b/test/jphyloref.js
@@ -42,7 +42,7 @@ describe('JPhyloRef', function () {
       it('should be downloadable', function () {
         this.timeout(10000);
         // Download JPhyloRef from Maven and save it to JPHYLOREF_PATH.
-        return new Downloader({
+        new Downloader({
           url: JPHYLOREF_URL,
           directory: path.dirname(JPHYLOREF_PATH),
           fileName: path.basename(JPHYLOREF_PATH),

From 8eadfa1a6832cf7ed2b8f3377967affd8fc809c8 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Fri, 5 Mar 2021 01:14:30 -0500
Subject: [PATCH 6/7] Reorganized JPhyloRef tests to ensure JAR is downloaded
 before testing.

---
 test/jphyloref.js | 47 ++++++++++++++++++++++++++++-------------------
 1 file changed, 28 insertions(+), 19 deletions(-)

diff --git a/test/jphyloref.js b/test/jphyloref.js
index fd13b76f..436f9e15 100644
--- a/test/jphyloref.js
+++ b/test/jphyloref.js
@@ -24,31 +24,40 @@ const JPHYLOREF_URL = `https://repo.maven.apache.org/maven2/org/phyloref/jphylor
 // Where should the JPhyloRef be stored?
 const JPHYLOREF_PATH = path.resolve(__dirname, `jphyloref-${JPHYLOREF_VERSION}.jar`);
 
+// TODO: we should eventually use SHA to ensure that we have the expected file.
+if (fs.existsSync(JPHYLOREF_PATH) && fs.statSync(JPHYLOREF_PATH).size > 0) {
+  // We've already downloaded it! Nothing to do.
+} else {
+  // Download JPhyloRef from Maven and save it to JPHYLOREF_PATH.
+  // Since Downloader() works asynchronously, we need to wrap it in
+  // an async() here to ensure that it finishes the download *before*
+  // we start the `describe()` below.
+  (async () => {
+    const downloader = new Downloader({
+      url: JPHYLOREF_URL,
+      directory: path.dirname(JPHYLOREF_PATH),
+      fileName: path.basename(JPHYLOREF_PATH),
+    });
+
+    try {
+      await downloader.download();
+    } catch (error) {
+      throw new Error(`Could not download JPhyloRef from Maven: ${error}`);
+    }
+  })();
+}
+
 /**
  * Test whether the expected JSON-LD files pass testing using JPhyloRef.
  */
 
 describe('JPhyloRef', function () {
-  describe('download JPhyloRef', function () {
+  describe('make sure JPhyloRef has been downloaded', function () {
     // TODO: we should eventually use SHA to ensure that we have the expected file.
-    if (
-      fs.existsSync(JPHYLOREF_PATH)
-      && fs.statSync(JPHYLOREF_PATH).size > 0
-    ) {
-      it('has already been downloaded', function () {
-        expect(true);
-      });
-    } else {
-      it('should be downloadable', function () {
-        this.timeout(10000);
-        // Download JPhyloRef from Maven and save it to JPHYLOREF_PATH.
-        new Downloader({
-          url: JPHYLOREF_URL,
-          directory: path.dirname(JPHYLOREF_PATH),
-          fileName: path.basename(JPHYLOREF_PATH),
-        }).download();
-      });
-    }
+    it('has been downloaded', function () {
+      expect(fs.existsSync(JPHYLOREF_PATH)).to.be.true;
+      expect(fs.statSync(JPHYLOREF_PATH).size).to.be.greaterThan(0);
+    });
   });
 
   describe('test example JSON-LD files using JPhyloRef', function () {

From f00292f4fccd90e3dfa02be430b2fdf27ae86ae9 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 7 Mar 2021 16:07:07 -0500
Subject: [PATCH 7/7] Failed attempt to download JPhyloRef before tests.

---
 test/jphyloref.js | 36 +++++++++++++++---------------------
 1 file changed, 15 insertions(+), 21 deletions(-)

diff --git a/test/jphyloref.js b/test/jphyloref.js
index 436f9e15..30e8053c 100644
--- a/test/jphyloref.js
+++ b/test/jphyloref.js
@@ -24,28 +24,22 @@ const JPHYLOREF_URL = `https://repo.maven.apache.org/maven2/org/phyloref/jphylor
 // Where should the JPhyloRef be stored?
 const JPHYLOREF_PATH = path.resolve(__dirname, `jphyloref-${JPHYLOREF_VERSION}.jar`);
 
-// TODO: we should eventually use SHA to ensure that we have the expected file.
-if (fs.existsSync(JPHYLOREF_PATH) && fs.statSync(JPHYLOREF_PATH).size > 0) {
-  // We've already downloaded it! Nothing to do.
-} else {
-  // Download JPhyloRef from Maven and save it to JPHYLOREF_PATH.
-  // Since Downloader() works asynchronously, we need to wrap it in
-  // an async() here to ensure that it finishes the download *before*
-  // we start the `describe()` below.
-  (async () => {
-    const downloader = new Downloader({
-      url: JPHYLOREF_URL,
-      directory: path.dirname(JPHYLOREF_PATH),
-      fileName: path.basename(JPHYLOREF_PATH),
-    });
+// Download JPhyloRef from Maven and save it to JPHYLOREF_PATH.
+// Since Downloader() works asynchronously, we need to wrap it in
+// an async() here to ensure that it finishes the download *before*
+// we start the `describe()` below.
+const downloader = new Downloader({
+  url: JPHYLOREF_URL,
+  directory: path.dirname(JPHYLOREF_PATH),
+  fileName: path.basename(JPHYLOREF_PATH),
+});
 
-    try {
-      await downloader.download();
-    } catch (error) {
-      throw new Error(`Could not download JPhyloRef from Maven: ${error}`);
-    }
-  })();
-}
+before(function (done) {
+  this.timeout(20000);
+  downloader.download()
+    .then(done)
+    .catch(err => done(err));
+});
 
 /**
  * Test whether the expected JSON-LD files pass testing using JPhyloRef.