Added test for normalization.

phyloref · Apr 24, 2024 · 0f9af87 · 0f9af87
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diff --git a/test/examples/correct/normalization/brochu_2003_normalization.json b/test/examples/correct/normalization/brochu_2003_normalization.json
@@ -0,0 +1,221 @@
+{
+  "@context": "https://www.phyloref.org/phyx.js/context/v1.0.0/phyx.json",
+  "doi": "10.5281/zenodo.4562685",
+  "source": {
+    "authors": [
+      {
+        "firstname": "Gaurav",
+        "lastname": "Vaidya"
+      }
+    ],
+    "year": 2021,
+    "title": "Digital representation of some of the clade definitions in Brochu 2003 in the Phyloreference Exchange (Phyx) format",
+    "journal": {
+      "name": "Zenodo"
+    },
+    "identifier": [
+      {
+        "type": "doi",
+        "id": "10.5281/zenodo.4562685"
+      }
+    ]
+  },
+  "phylogenies": [
+    {
+      "newick": "(Parasuchia,(rauisuchians,Aetosauria,(sphenosuchians,(protosuchians,(mesosuchians,(Hylaeochampsa,Aegyptosuchus,Stomatosuchus,(Allodaposuchus,('Gavialis gangeticus',(('Diplocynodon ratelii',('Alligator mississippiensis','Caiman crocodilus')Alligatoridae)Alligatoroidea,('Tomistoma schlegelii',('Osteolaemus tetraspis','Crocodylus niloticus')Crocodylinae)Crocodylidae)Brevirostres)Crocodylia))Eusuchia)Mesoeucrocodylia)Crocodyliformes)Crocodylomorpha))root;",
+      "label": "Fig 1 from Brochu 2003",
+      "@id": "#phylogeny0",
+      "source": {
+        "type": "article",
+        "title": "Phylogenetic approaches toward crocodylian history",
+        "authors": [
+          {
+            "name": "Christopher A. Brochu",
+            "alternate": [
+              "Brochu, Christopher A."
+            ],
+            "firstname": "Christopher",
+            "middlename": "A.",
+            "lastname": "Brochu"
+          }
+        ],
+        "year": 2003,
+        "figure": "1",
+        "identifier": [
+          {
+            "type": "doi",
+            "id": "10.1146/annurev.earth.31.100901.141308"
+          }
+        ],
+        "link": [
+          {
+            "url": "https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308"
+          }
+        ],
+        "journal": {
+          "name": "Annual Review of Earth and Planetary Sciences",
+          "volume": "31",
+          "pages": "357--397",
+          "identifier": [
+            {
+              "type": "eISSN",
+              "id": "1545-4495"
+            }
+          ]
+        }
+      }
+    }
+  ],
+  "phylorefs": [
+    {
+      "@id": "#Alligatoridae1_same",
+      "label": "Alligatoridae",
+      "scientificNameAuthorship": {
+        "bibliographicCitation": "(Cuvier 1807)"
+      },
+      "phylorefType": "phyloref:PhyloreferenceUsingMinimumClade",
+      "definition": "Alligatoridae (Cuvier 1807).\n\nLast common ancestor of Alligator mississippiensis and Caiman crocodilus and all of its descendents.",
+      "definitionSource": {
+        "type": "article",
+        "title": "Phylogenetic approaches toward crocodylian history",
+        "authors": [
+          {
+            "name": "Christopher A. Brochu",
+            "alternate": [
+              "Brochu, Christopher A."
+            ],
+            "firstname": "Christopher",
+            "middlename": "A.",
+            "lastname": "Brochu"
+          }
+        ],
+        "year": 2003,
+        "figure": "1",
+        "identifier": [
+          {
+            "type": "doi",
+            "id": "10.1146/annurev.earth.31.100901.141308"
+          }
+        ],
+        "link": [
+          {
+            "url": "https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308"
+          }
+        ],
+        "journal": {
+          "name": "Annual Review of Earth and Planetary Sciences",
+          "volume": "31",
+          "pages": "357--397",
+          "identifier": [
+            {
+              "type": "eISSN",
+              "id": "1545-4495"
+            }
+          ]
+        }
+      },
+      "internalSpecifiers": [
+        {
+          "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+          "hasName": {
+            "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+            "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN",
+            "label": "Caiman crocodilus",
+            "nameComplete": "Caiman crocodilus",
+            "genusPart": "Caiman",
+            "specificEpithet": "crocodilus"
+          }
+        },
+        {
+          "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+          "hasName": {
+            "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+            "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN",
+            "label": "Alligator mississippiensis",
+            "nameComplete": "Alligator mississippiensis",
+            "genusPart": "Alligator",
+            "specificEpithet": "mississippiensis"
+          },
+          "label": "Alligator mississippiensis"
+        }
+      ],
+      "externalSpecifiers": []
+    },
+    {
+      "@id": "#Alligatoridae2_same",
+      "label": "Alligatoridae",
+      "scientificNameAuthorship": {
+        "bibliographicCitation": "(Cuvier 1807)"
+      },
+      "phylorefType": "phyloref:PhyloreferenceUsingMinimumClade",
+      "definition": "Alligatoridae (Cuvier 1807).\n\nLast common ancestor of Alligator mississippiensis and Caiman crocodilus and all of its descendents.",
+      "definitionSource": {
+        "type": "article",
+        "title": "Phylogenetic approaches toward crocodylian history",
+        "authors": [
+          {
+            "name": "Christopher A. Brochu",
+            "alternate": [
+              "Brochu, Christopher A."
+            ],
+            "firstname": "Christopher",
+            "middlename": "A.",
+            "lastname": "Brochu"
+          }
+        ],
+        "year": 2003,
+        "figure": "1",
+        "identifier": [
+          {
+            "type": "doi",
+            "id": "10.1146/annurev.earth.31.100901.141308"
+          }
+        ],
+        "link": [
+          {
+            "url": "https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308"
+          }
+        ],
+        "journal": {
+          "name": "Annual Review of Earth and Planetary Sciences",
+          "volume": "31",
+          "pages": "357--397",
+          "identifier": [
+            {
+              "type": "eISSN",
+              "id": "1545-4495"
+            }
+          ]
+        }
+      },
+      "internalSpecifiers": [
+        {
+          "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+          "hasName": {
+            "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+            "label": "Caiman crocodilus",
+            "nameComplete": "Caiman crocodilus",
+            "genusPart": "Caiman",
+            "specificEpithet": "crocodilus",
+            "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN"
+          },
+          "label": "Caiman crocodilus"
+        },
+        {
+          "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
+          "hasName": {
+            "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
+            "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN",
+            "label": "Alligator mississippiensis",
+            "nameComplete": "Alligator mississippiensis",
+            "genusPart": "Alligator",
+            "specificEpithet": "mississippiensis"
+          },
+          "label": "Alligator mississippiensis"
+        }
+      ],
+      "externalSpecifiers": []
+    }
+  ],
+  "defaultNomenclaturalCodeIRI": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN"
+}
diff --git a/test/normalization.js b/test/normalization.js
@@ -0,0 +1,124 @@
+/*
+ * Test normalization on examples/correct/normalization files.
+ */
+
+const fs = require('fs');
+const path = require('path');
+
+const chai = require('chai');
+
+const phyx = require('../src');
+
+const expect = chai.expect;
+
+/**
+ * When making the comparisons, we need to remove the `@id`s which would otherwise be different
+ * between the phylorefs being compared.
+ *
+ * @param phyloref The phyloref whose '@id' needs to be removed.
+ */
+function removeId(phyloref) {
+  // Shallow copy the phyloref.
+  const copiedPhyloref = Object.assign({}, phyloref);
+  // Delete the '@id'.
+  delete copiedPhyloref['@id'];
+  return copiedPhyloref;
+}
+
+
+/**
+ * Test whether normalization of phyloreferences and phylogenies work as expected.
+ * This test does not cover Phyx normalization.
+ */
+
+describe('Phyloref and phylogeny normalization', function () {
+  describe('Test all normalization Phyx files', function () {
+    /*
+     * Normalization Phyx files consist of a number of phyloreferences and phylogenies. We can
+     * test them by confirming:
+     * - every phyloref or phylogeny should be DIFFERENT from every other.
+     * - every phyloref or phylogeny whose `@id` ends with `_same` should be IDENTICAL to
+     *   every other phyloref or phylogeny whose `@id` ends with `_same` after NORMALIZATION (to
+     *   test non-same phyloref or phylogeny files, they should be placed in different files).
+     * - every phyloref or phylogeny whose `@id` ends with `_different` should be DIFFERENT to
+     *   every phyloref or phylogeny whose `@id` ends with `_same` even after NORMALIZATION.
+     */
+    const normalizationExamples = fs
+      .readdirSync(path.resolve(__dirname, './examples/correct/normalization'))
+      .filter(filename => filename.endsWith('.json'));
+
+    normalizationExamples.forEach((example) => {
+      const basename = path.resolve(__dirname, './examples/correct/normalization', path.parse(example).name);
+      const jsonFilename = `${basename}.json`;
+
+      describe(`Normalization test file '${example}'`, function () {
+        const phyxDoc = JSON.parse(fs.readFileSync(jsonFilename));
+        const phylorefs = phyxDoc.phylorefs || [];
+        const samePhylorefs = phylorefs.filter(p => (p['@id'] || '').endsWith('_same'));
+        const differentPhylorefs = phylorefs.filter(p => (p['@id'] || '').endsWith('_different'));
+
+        // We don't need phylogeny normalization yet, so there's no point in testing them.
+        describe('Test phylogenies', function () {
+          it("These tests have not yet been implemented since we don't have an urgent need for them.");
+        });
+
+        // So we only focus on phyloreference normalization.
+        describe('Test phyloreferences', function () {
+          it('should have multiple same phyloreferences for testing', function () {
+            expect(samePhylorefs).to.not.be.empty;
+          });
+
+          // No two phyloreferences in a normalization file should be deeply identical to each
+          // other, otherwise the test will be pointless.
+          phylorefs.forEach((phyloref1) => {
+            phylorefs.forEach((phyloref2) => {
+              if (phyloref1 === phyloref2) return;
+              expect(removeId(phyloref1))
+                .to
+                .not
+                .deep
+                .equal(removeId(phyloref2),
+                  'No two phyloreferences in a single normalization file should be identical.');
+            });
+          });
+
+          // Every pair of `_same` phyloreferences should be different.
+          samePhylorefs.forEach((phyloref1) => {
+            samePhylorefs.forEach((phyloref2) => {
+              if (phyloref1 === phyloref2) return;
+              expect(
+                removeId(phyx.PhylorefWrapper.normalize(phyloref1))
+              )
+                .to
+                .deep
+                .equal(
+                  removeId(phyx.PhylorefWrapper.normalize(phyloref2)),
+                  `Expected phyloref ${phyloref1['@id']} to deeply equal ${phyloref2['@id']} `
+                  + 'after normalization'
+                );
+            });
+          });
+
+          // Every pair of `_different` phyloreferences should be different from every `_same`
+          // phyloreference, even after normalization.
+          differentPhylorefs.forEach((phyloref1) => {
+            samePhylorefs.forEach((phyloref2) => {
+              if (phyloref1 === phyloref2) return;
+              expect(
+                removeId(phyx.PhylorefWrapper.normalize(phyloref1))
+              )
+                .to
+                .not
+                .deep
+                .equal(
+                  removeId(phyx.PhylorefWrapper.normalize(phyloref2)),
+                  `Expected phyloref ${phyloref1['@id']} to not deeply equal ${phyloref2['@id']} `
+                  + 'after normalization'
+                );
+            });
+          });
+        });
+      });
+    });
+  });
+});