source: trunk/test/integration/gscf/OntologyTests.groovy @ 398

package gscf

import grails.test.*
import dbnp.data.*

/**
 * OntologyTests Test
 *
 * Test ontology/term functionality on domain model level
 *
 * @author keesvb
 * @since 20100510
 * @package dbnp.studycapturing
 *
 * Revision information:
 * $Rev$
 * $Author$
 * $Date$
 */
class OntologyTests extends GrailsUnitTestCase {

        final String testOntologyName = "Test ontology"
        final String testOntologyDescription = "Test description"
        final String testOntologyUrl = "http://www.test.com"
        final String testOntologyVersionNumber = "1.0"
        final int testOntologyNcboId = 0
        final int testOntologyNcboVersionedId = 0
        final String testTermName = "Test term"
        final String testAccession = 'TEST01234$'

        protected void setUp() {
                super.setUp()
        }

        protected void tearDown() {
                super.tearDown()
        }

        /**
         * Test creation and saving of ontologies and terms
         * and giveTerms and giveTermByName methods
         */
        void testAll () {

                // === TEST Ontology

                def ontology = new Ontology(
                                name: testOntologyName,
                                description: testOntologyDescription,
                                url: testOntologyUrl,
                                versionNumber: testOntologyVersionNumber,
                                ncboId: testOntologyNcboId,
                                ncboVersionedId: testOntologyNcboVersionedId
                );

                // Validate and save ontology
                assert ontology.validate()
                assert ontology.save(flush:true)

                // Try to retrieve the ontology and make sure it's the same
                def ontologyDB = Ontology.findByName(testOntologyName)
                assert ontologyDB
                assert ontologyDB.name.equals(testOntologyName)
                assert ontologyDB.description.equals(testOntologyDescription)
                assert ontologyDB.url.equals(testOntologyUrl)
                assert ontologyDB.versionNumber.equals(testOntologyVersionNumber)
                assert ontologyDB.ncboId.equals(testOntologyNcboId)
                assert ontologyDB.ncboVersionedId.equals(testOntologyNcboVersionedId)

                // Apparently, the saved ontology is not persisted between test methods :-(
                // Otherwise, we could separate these parts into different tests

                // === TEST Term and giveTermByName

                // Find created ontology
                def testOntology = Ontology.findByName(testOntologyName)
                assert testOntology

                // Create a new term
                def term = new Term(
                        name: testTermName,
                        accession: testAccession,
                        ontology: testOntology
                )

                assert term.validate()
                assert term.save(flush:true)

                // Try to retrieve the term from the ontology and make sure it's the same
                def termDB = testOntology.giveTermByName(testTermName)
                assert termDB.name.equals(testTermName)
                assert termDB.accession.equals(testAccession)
                assert termDB.ontology == testOntology

                // === TEST giveTerms
                
                def terms = testOntology.giveTerms()
                assert terms
                assert terms.size() == 1
                assert terms.asList().first().name.equals(testTermName)

        }
}