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package eu.etaxonomy.cdm.persistence.dao.hibernate.molecular;

import java.util.Set;

import java.util.UUID;

import org.junit.Assert;

import org.junit.Before;

import org.junit.BeforeClass;

import org.junit.Test;

import org.unitils.dbunit.annotation.DataSet;

import org.unitils.spring.annotation.SpringBeanByType;

import eu.etaxonomy.cdm.model.molecular.DnaSample;

import eu.etaxonomy.cdm.model.molecular.PhylogeneticTree;

import eu.etaxonomy.cdm.model.molecular.Sequence;

import eu.etaxonomy.cdm.model.term.DefinedTerm;

import eu.etaxonomy.cdm.persistence.dao.media.IMediaDao;

import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;

import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;

public class MolecularHibernateImplTest  extends CdmTransactionalIntegrationTest {

	private static final String MARKER_LABEL = "ITS1";

	@SpringBeanByType

    private IOccurrenceDao occurrenceDao;

	@SpringBeanByType

    private IMediaDao mediaDao;

	private UUID phyloTreeUuid;

	private UUID sequenceUuid;

	private UUID uuidSample1;// = UUID.fromString("4b451275-655f-40d6-8d4b-0203574bef15");

	@BeforeClass

	public static void setUpBeforeClass() throws Exception {

	}

	@Before

	public void setUp() throws Exception {

	}

//**************** TESTS ************************************************

	//Test if DnaSample can be loaded and if Sequence and Marker data can

	//be lazy loaded from database

	//#3340

	@Test

	@DataSet

	public void testLazyLoadSequenceMarker() {

		createTestDataSet();

		DnaSample sample1 = (DnaSample)occurrenceDao.findByUuid(uuidSample1);

		Set<Sequence> sequences = sample1.getSequences();

		Sequence sequence = sequences.iterator().next();

		DefinedTerm marker = sequence.getDnaMarker();

		Assert.assertNotNull("Marker should not be null", marker);

		Assert.assertEquals("Markers label should be 'Marker'",MARKER_LABEL, marker.getLabel());

		commit();

	}

	@Test

	@DataSet

	public void testLoadUsedSequences() {

		createTestDataSet();

		PhylogeneticTree phyloTree = (PhylogeneticTree)mediaDao.findByUuid(phyloTreeUuid);

		Assert.assertNotNull("Phylogenetic Tree should be found", phyloTree);

		Set<Sequence> sequences = phyloTree.getUsedSequences();

		Assert.assertEquals(1, sequences.size());

		Sequence sequence = sequences.iterator().next();

		Assert.assertEquals(sequenceUuid, sequence.getUuid());

		commit();

	}

	@Override

    public void createTestDataSet(){

		DnaSample sample = DnaSample.NewInstance();

		Sequence sequence = Sequence.NewInstance("Meine Sequence");

		sequenceUuid = sequence.getUuid();

		sample.addSequence(sequence);

		uuidSample1 = sample.getUuid();

		DefinedTerm marker = DefinedTerm.ITS1_MARKER();

		Assert.assertNotNull("ITS1 marker must not be null", marker);

		sequence.setDnaMarker(marker);

		occurrenceDao.save(sample);

		PhylogeneticTree phyloTree = PhylogeneticTree.NewInstance();

		phyloTree.addUsedSequences(sequence);

		mediaDao.saveOrUpdate(phyloTree);

		phyloTreeUuid = phyloTree.getUuid();

		commitAndStartNewTransaction(new String[]{"SpecimenOrObservationBase"});

	}

}