source: trunk/test/integration/gscf/OntologyTests.groovy @ 440

package gscf

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

import uk.ac.ebi.ontocat.*

/**
 * 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()

                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)
        }

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

        /**
         * Test if ontology was properly saved
         */
        void testSave() {

                // 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)

        }

        /**
         * Test saving and retrieving a term within the ontology and test giveTermByName(name) and giveTerms()
         */
        void testTermSave() {

                // 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() and make sure the term is in there
                def terms = testOntology.giveTerms()
                assert terms
                assert terms.size() == 1
                assert terms.asList().first().name.equals(testTermName)
        }

        /**
         * Ontocat test for debug purposes: show all properties of a certain ontology
         */
        private void testOntocatBioPortalDebug() {
                // Instantiate OLS service
                uk.ac.ebi.ontocat.OntologyService os = new uk.ac.ebi.ontocat.bioportal.BioportalOntologyService()

                // Find ontology by ncboId
                uk.ac.ebi.ontocat.Ontology o = os.getOntology("1005")
                StringBuilder sb = new StringBuilder();
                def bean = os.getOntologyBean()
                String codingScheme = bean.codingScheme
                sb.append("OntologyBean:\n")
                sb.append("property codingScheme=" + codingScheme + "\n")
                sb.append("Bean.properties:\n")
                bean.properties.each {
                        sb.append(it.key + "=" + it.value + "\n")
                }
                sb.append "Bean:\t" + bean.dump()
                sb.append(bean.properties['codingScheme'])
                sb.append("\t");
                sb.append(o.getAbbreviation());
                sb.append("\t");
                sb.append(o.getLabel());
                sb.append("\t");
                sb.append(o.getOntologyAccession());
                sb.append("\t");
                sb.append("Ontology meta properties:\n")
                o.getVersionNumber() + o.getMetaPropertyValues().each {
                        sb.append(it.name + "=" + it.value + "\n")
                }
                sb.append("Ontology properties:\n");
                o.getProperties().each {
                        sb.append(it.key + "=" + it.value + "\n")
                }
                sb.append("Ontology root terms:\n");
                os.getRootTerms(o).each {
                        sb.append("Term ${os.makeLookupHyperlink(it.properties.get('accession'))} properties:\n")
                        it.properties.each {
                                sb.append it.key + "=" + it.value + "\n"
                        }
                }
                System.out.println(sb.toString());
        }

        /**
         * Add all OLS ontologies to the database via the Ontocat framework
         */
        void testOntocatOLSOntologies() {
                // Instantiate EBI OLS service
                uk.ac.ebi.ontocat.OntologyService os = new uk.ac.ebi.ontocat.ols.OlsOntologyService()
                addOntologies(os)
        }

        /**
         * Add all BioPortal ontologies to the database via the Ontocat framework
         */
        void testOntocatBioPortalOntologies() {
                // Instantiate BioPortal service
                uk.ac.ebi.ontocat.OntologyService os = new uk.ac.ebi.ontocat.bioportal.BioportalOntologyService()
                addOntologies(os)
        }

        private void addOntologies(uk.ac.ebi.ontocat.OntologyService os) {

                // Iterate over all ontologies in OLS
                os.getOntologies().each {

                        // Get bean and extract versionedId
                        def bean = os.ontologyBean
                        def matcher = bean.codingScheme =~ "/(\\d{5})/"
                        assert matcher
                        assert matcher.size() == 1
                        assert matcher[0].size() == 2
                        def versionedId = matcher[0][1]

                        // Instantiate ontology
                        def ontology = new Ontology(
                            name: o.label,
                            description: o.description,
                            url: bean.properties['homepage'],
                            //url: 'http://bioportal.bioontology.org/ontologies/' + versionedId,
                            versionNumber: o.versionNumber,
                            ncboId: o.ontologyAccession,
                            ncboVersionedId: versionedId
                        );

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

                        //println ontology.dump()
                }
        }
}