implemented parse test.

ilios · Dec 10, 2016 · dabe801 · dabe801
1 parent 081c6cd
commit dabe801
Showing 1 changed file with 135 additions and 1 deletion.
diff --git a/tests/Ilios/MeSH/ParserTest.php b/tests/Ilios/MeSH/ParserTest.php
@@ -107,6 +107,140 @@ public function testForInvalidStringNodeFailure()
      */
     public function testParse()
     {
-        $this->markTestIncomplete('To be implemented.');
+        $file = __DIR__ . '/desc.xml';
+        $descriptorsSet = $this->parser->parse($file);
+
+        $descriptors = $descriptorsSet->getDescriptors();
+        $this->assertEquals('eng', $descriptorsSet->getLanguageCode());
+        $this->assertEquals(1, count($descriptors));
+
+        $descriptor = $descriptors[0];
+        $this->assertEquals('a descriptor', $descriptor->getName());
+        $this->assertEquals('D000000', $descriptor->getUi());
+        $this->assertEquals('1', $descriptor->getClass());
+        $this->assertEquals('2016/12/08', $descriptor->getDateCreated()->format('Y/m/d'));
+        $this->assertEquals('2016/12/09', $descriptor->getDateRevised()->format('Y/m/d'));
+        $this->assertEquals('2004/04/23', $descriptor->getDateEstablished()->format('Y/m/d'));
+
+        $allowableQualifiers = $descriptor->getAllowableQualifiers();
+        $this->assertEquals(2, count($allowableQualifiers));
+        $this->assertEquals('Q000001', $allowableQualifiers[0]->getQualifierReference()->getUi());
+        $this->assertEquals('a qualifier', $allowableQualifiers[0]->getQualifierReference()->getName());
+        $this->assertEquals('TQ', $allowableQualifiers[0]->getAbbreviation());
+        $this->assertEquals('Q000002', $allowableQualifiers[1]->getQualifierReference()->getUi());
+        $this->assertEquals('another qualifier', $allowableQualifiers[1]->getQualifierReference()->getName());
+        $this->assertEquals('TQ2', $allowableQualifiers[1]->getAbbreviation());
+        $this->assertEquals('an annotation', $descriptor->getAnnotation());
+        $this->assertEquals('a history note', $descriptor->getHistoryNote());
+        $this->assertEquals('a nlm classification number', $descriptor->getNlmClassificationNumber());
+        $this->assertEquals('an online note', $descriptor->getOnlineNote());
+        $this->assertEquals('a public mesh note', $descriptor->getPublicMeshNote());
+
+        $previousIndexing = $descriptor->getPreviousIndexing();
+        $this->assertEquals(2, count($previousIndexing));
+        $this->assertEquals('previously indexed as', $previousIndexing[0]);
+        $this->assertEquals('also previously indexed as', $previousIndexing[1]);
+
+        $entryCombinations = $descriptor->getEntryCombinations();
+        $this->assertEquals(1, count($entryCombinations));
+        $this->assertEquals('D000004', $entryCombinations[0]->getDescriptorIn()->getUi());
+        $this->assertEquals('some descriptor', $entryCombinations[0]->getDescriptorIn()->getName());
+        $this->assertEquals('Q000003', $entryCombinations[0]->getQualifierIn()->getUi());
+        $this->assertEquals('some qualifier', $entryCombinations[0]->getQualifierIn()->getName());
+        $this->assertEquals('D000005', $entryCombinations[0]->getDescriptorOut()->getUi());
+        $this->assertEquals('and another descriptor', $entryCombinations[0]->getDescriptorOut()->getName());
+        $this->assertEquals('Q000006', $entryCombinations[0]->getQualifierOut()->getUi());
+        $this->assertEquals('some other qualifier', $entryCombinations[0]->getQualifierOut()->getName());
+
+        $relatedDescriptors = $descriptor->getRelatedDescriptors();
+        $this->assertEquals(2, count($relatedDescriptors));
+        $this->assertEquals('D000002', $relatedDescriptors[0]->getUi());
+        $this->assertEquals('another descriptor', $relatedDescriptors[0]->getName());
+        $this->assertEquals('D000003', $relatedDescriptors[1]->getUi());
+        $this->assertEquals('yet another descriptor', $relatedDescriptors[1]->getName());
+        $this->assertEquals('other considerations', $descriptor->getConsiderAlso());
+
+        $pharmActions = $descriptor->getPharmacologicalActions();
+        $this->assertEquals(2, count($pharmActions));
+        $this->assertEquals('D000002', $pharmActions[0]->getUi());
+        $this->assertEquals('another descriptor', $pharmActions[0]->getName());
+        $this->assertEquals('D000003', $pharmActions[1]->getUi());
+        $this->assertEquals('yet another descriptor', $pharmActions[1]->getName());
+
+        $treeNumbers = $descriptor->getTreeNumbers();
+        $this->assertEquals(1, count($treeNumbers));
+        $this->assertEquals('D00.000.000.000.001', $treeNumbers[0]);
+
+        $concepts = $descriptor->getConcepts();
+        $this->assertEquals(2, count($concepts));
+
+        $concept = $concepts[0];
+        $this->assertTrue($concept->isPreferred());
+        $this->assertEquals('M0000001', $concept->getUi());
+        $this->assertEquals('a casn1 name', $concept->getCasn1Name());
+        $this->assertEquals('00000AAAAA', $concept->getRegistryNumber());
+        $this->assertEquals('a scope note', $concept->getScopeNote());
+
+        $registryNumbers = $concept->getRelatedRegistryNumbers();
+        $this->assertEquals(1, count($registryNumbers));
+        $this->assertEquals('a related registry number', $registryNumbers[0]);
+
+        $relations = $concept->getConceptRelations();
+        $this->assertEquals(1, count($relations));
+        $this->assertEquals('BRD', $relations[0]->getName());
+        $this->assertEquals('M0000001', $relations[0]->getConcept1Ui());
+        $this->assertEquals('M0000002', $relations[0]->getConcept2Ui());
+
+        $terms = $concept->getTerms();
+        $this->assertEquals(1, count($terms));
+        $this->assertTrue($terms[0]->isConceptPreferred());
+        $this->assertFalse($terms[0]->isPermuted());
+        $this->assertEquals('NON', $terms[0]->getLexicalTag());
+        $this->assertTrue($terms[0]->isRecordPreferred());
+        $this->assertEquals('T000001', $terms[0]->getUi());
+        $this->assertEquals('a term', $terms[0]->getName());
+        $this->assertEquals('1999/01/01', $terms[0]->getDateCreated()->format('Y/m/d'));
+
+        $thesaurusIds = $terms[0]->getThesaurusIds();
+        $this->assertEquals(2, count($thesaurusIds));
+        $this->assertEquals('a thesaurus id', $thesaurusIds[0]);
+        $this->assertEquals('another thesaurus id', $thesaurusIds[1]);
+
+        $concept = $concepts[1];
+        $this->assertFalse($concept->isPreferred());
+        $this->assertEquals('M0000002', $concept->getUi());
+        $this->assertEquals('another concept', $concept->getName());
+        $this->assertEquals('0', $concept->getRegistryNumber());
+
+        $relations = $concept->getConceptRelations();
+        $this->assertEquals(1, count($relations));
+        $this->assertEquals('NRW', $relations[0]->getName());
+        $this->assertEquals('M0000002', $relations[0]->getConcept1Ui());
+        $this->assertEquals('M0000003', $relations[0]->getConcept2Ui());
+
+        $terms = $concept->getTerms();
+        $this->assertEquals(2, count($terms));
+        $this->assertTrue($terms[0]->isConceptPreferred());
+        $this->assertFalse($terms[0]->isPermuted());
+        $this->assertEquals('ABB', $terms[0]->getLexicalTag());
+        $this->assertFalse($terms[0]->isRecordPreferred());
+        $this->assertEquals('T000002', $terms[0]->getUi());
+        $this->assertEquals('another term', $terms[0]->getName());
+        $this->assertEquals('1989/11/09', $terms[0]->getDateCreated()->format('Y/m/d'));
+        $this->assertEquals('a term note', $terms[0]->getNote());
+
+        $thesaurusIds = $terms[0]->getThesaurusIds();
+        $this->assertEquals(1, count($thesaurusIds));
+        $this->assertEquals('yet another thesaurus id', $thesaurusIds[0]);
+
+        $this->assertFalse($terms[1]->isConceptPreferred());
+        $this->assertTrue($terms[1]->isPermuted());
+        $this->assertEquals('TRD', $terms[1]->getLexicalTag());
+        $this->assertTrue($terms[1]->isRecordPreferred());
+        $this->assertEquals('T000003', $terms[1]->getUi());
+        $this->assertEquals('yet another term', $terms[1]->getName());
+        $this->assertEquals('1999/11/10', $terms[1]->getDateCreated()->format('Y/m/d'));
+        $this->assertNull($terms[1]->getNote());
+        $this->assertEquals(0, count($terms[1]->getThesaurusIds()));
     }
 }