EDIT

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.io.specimen.abcd206.in;

import static org.junit.Assert.assertEquals;

import static org.junit.Assert.assertNotNull;

import static org.junit.Assert.assertTrue;

import java.io.FileNotFoundException;

import java.net.URI;

import java.net.URISyntaxException;

import java.net.URL;

import java.text.ParseException;

import java.util.List;

import java.util.Set;

import java.util.UUID;

import org.joda.time.DateTime;

import org.junit.Assert;

import org.junit.Test;

import org.unitils.dbunit.annotation.DataSet;

import org.unitils.spring.annotation.SpringBeanByName;

import org.unitils.spring.annotation.SpringBeanByType;

import eu.etaxonomy.cdm.api.service.IOccurrenceService;

import eu.etaxonomy.cdm.api.service.IReferenceService;

import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;

import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport;

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

import eu.etaxonomy.cdm.model.media.MediaUtils;

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;

import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;

import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;

import eu.etaxonomy.cdm.model.occurrence.FieldUnit;

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;

import eu.etaxonomy.cdm.model.reference.Reference;

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

import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;

/**

 * @author a.mueller

 * @created 29.01.2009

 */

public class AbcdGgbnImportTest extends CdmTransactionalIntegrationTest {

	@SpringBeanByName

	private CdmApplicationAwareDefaultImport<?> defaultImport;

	@SpringBeanByType

	private IOccurrenceService occurrenceService;

	@SpringBeanByType

	private IReferenceService referenceService;

	/**

	 * Tests import import of DNA unit and all its parameters

	 * and sub derivatives (sequence, amplification, etc.)

	 * @throws ParseException

	 */

	@Test

    @DataSet( value="../../../BlankDataSet.xml", loadStrategy=CleanSweepInsertLoadStrategy.class)

    public void testImportGgbn() throws ParseException {

        String inputFile = "/eu/etaxonomy/cdm/io/specimen/abcd206/in/db6.xml";

        URL url = this.getClass().getResource(inputFile);

        assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);

        Abcd206ImportConfigurator importConfigurator = null;

        try {

            importConfigurator = Abcd206ImportConfigurator.NewInstance(url.toURI(), null,false);

        } catch (URISyntaxException e) {

            e.printStackTrace();

            Assert.fail();

        }

        assertNotNull("Configurator could not be created", importConfigurator);

        boolean result = defaultImport.invoke(importConfigurator);

        assertTrue("Return value for import.invoke should be true", result);

        assertEquals("Number of derived units is incorrect", 1, occurrenceService.count(DerivedUnit.class));

        assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));

        assertEquals("Number of field units is incorrect", 1, occurrenceService.count(FieldUnit.class));

        //associated specimen

        FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();

        config.setSignificantIdentifier("B 10 0066577");

        List<SpecimenOrObservationBase> records = occurrenceService.findByTitle(config).getRecords();

        assertEquals(1, records.size());

        SpecimenOrObservationBase derivedUnitSpecimen = records.iterator().next();

        assertEquals(DerivedUnit.class, derivedUnitSpecimen.getClass());

        DerivedUnit specimen = (DerivedUnit) derivedUnitSpecimen;

        assertEquals("Herbarium Berolinense", specimen.getCollection().getName());

        assertTrue(SpecimenOrObservationType.DnaSample!=specimen.getRecordBasis());

        //dna sample

        FindOccurrencesConfigurator dnaConfig = new FindOccurrencesConfigurator();

        dnaConfig.setSignificantIdentifier("DB 6");

        List<SpecimenOrObservationBase> dnaRecords = occurrenceService.findByTitle(dnaConfig).getRecords();

        assertEquals(1, dnaRecords.size());

        SpecimenOrObservationBase dnaSpecimen = dnaRecords.iterator().next();

        assertEquals(DnaSample.class, dnaSpecimen.getClass());

        DnaSample dnaSample = (DnaSample) dnaSpecimen;

        DerivationEvent derivedFrom = dnaSample.getDerivedFrom();

        assertNotNull(derivedFrom);

        assertEquals("Wrong derivation type!", DerivationEventType.DNA_EXTRACTION(), derivedFrom.getType());

        assertEquals("Wrong number of originals", 1, derivedFrom.getOriginals().size());

        assertEquals("DNA Bank", dnaSample.getCollection().getCode());

        assertEquals(SpecimenOrObservationType.DnaSample, dnaSample.getRecordBasis());

        //preservation/preparation

        assertNotNull(derivedFrom.getActor());

        assertEquals("Bansemer, Jana", derivedFrom.getActor().getTitleCache());

        assertNotNull(derivedFrom.getTimeperiod());

        assertEquals((Integer)2002,derivedFrom.getTimeperiod().getStartYear());

        assertEquals((Integer)8,derivedFrom.getTimeperiod().getStartMonth());

        assertEquals((Integer)13,derivedFrom.getTimeperiod().getStartDay());

        assertNotNull(dnaSample.getPreservation());

        //dna quality

        DnaQuality dnaQuality = dnaSample.getDnaQuality();

        assertNotNull("Dna quality is null", dnaQuality!=null);

        assertEquals(new Double("0.77"),dnaQuality.getRatioOfAbsorbance260_230());

        assertEquals(new Double("1.38"),dnaQuality.getRatioOfAbsorbance260_280());

        assertEquals(new DateTime(2008, 4, 15, 0, 0),dnaQuality.getQualityCheckDate());

//        assertEquals(MeasurementUnit.NewInstance(, label, labelAbbrev)DateTime(2008, 4, 15, 0, 0),dnaQuality.getQualityCheckDate());

        //amplifications

        Set<AmplificationResult> amplificationResults = dnaSample.getAmplificationResults();

        assertNotNull(amplificationResults);

        assertEquals(1,  amplificationResults.size());

        AmplificationResult amplificationResult = amplificationResults.iterator().next();

        Amplification amplification = amplificationResult.getAmplification();

        assertNotNull("Amplification is null", amplification);

        DefinedTerm dnaMarker = amplification.getDnaMarker();

        assertNotNull(dnaMarker);

        assertEquals("ITS (ITS1, 5.8S rRNA, ITS2)", dnaMarker.getLabel());

        //amplification primers

        Primer forwardPrimer = amplification.getForwardPrimer();

        assertNotNull(forwardPrimer);

        assertEquals("PIpetB1411F", forwardPrimer.getLabel());

        assertEquals("5´-GCCGTMTTTATGTTAATGC-3´", forwardPrimer.getSequence().getString());

        assertNotNull(forwardPrimer.getPublishedIn());

        assertEquals("Löhne & Borsch 2005", forwardPrimer.getPublishedIn().getTitle());

        Primer reversePrimer = amplification.getReversePrimer();

        assertNotNull(reversePrimer);

        assertEquals("PIpetD738R", reversePrimer.getLabel());

        assertEquals("5´-AATTTAGCYCTTAATACAGG-3´", reversePrimer.getSequence().getString());

        //sequencing

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

        assertNotNull(sequences);

        assertEquals(1, sequences.size());

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

        SequenceString consensusSequence = sequence.getConsensusSequence();

        assertNotNull(consensusSequence);

        assertEquals(

                "TTTCGGGTCC TTTATAGTGA AGATATAGCA TAGATAGTTG TAATCCATTA" +

        		" TGTATCATTG GGGAAGGAAG GAGAATATTT TTTTGATAGA ATACAAGTAT" +

        		" GGATTATTGA AACTAATACG CCATGTATTT GGATATTTCC CTTGAACTGC" +

        		" ATAATATTCT TTATTTTCCA TGAATAGTGT AAGGGAATTT TTCGAAGAGA" +

        		" AAATGGATTA TGGGAGTGTG TGACTTGAGC TATTGATTGG TCTGTGCAGA" +

        		" TACGGGCTTT TATCTATCTG CCACATTGTA ATTCACAAAC CAATGTGTCT" +

        		" TTGTTCCAAC CATCGCGTAA GCCCCATACA GAAGATAGGC TGGTTCGCTT" +

        		" GAAGAGAATC TTTTCTATGA TCAGATCCGA ATTATGTCGT ACATGAGCAG" +

        		" GCTCCGTAAG ATCTAGTTGA CTTAAGTCAA ACTTCAATAG TATAAAAATG" +

        		" CACTCATTTC CTCTGCATTG ACACGAGCTA TGAGACTATC GGAGTGAAAG" +

        		" AAAGGGTCTA AAGAAGAAGA AAGCTTGGGC TAGATTAGTA ACAAGTAAAT" +

        		" CCTTTGTGTG TGTGTTTGTA ATTAGTAAAT GGGCTCTCAA TATTTTGGGG" +

        		" CTAATTACTG ATCCTAAGGT TTGAGACGAC CCAGAAAGCA CTTGATCATA" +

        		" TCACGATTGA CTTTGTAAGC CTACTTGGGT ATTGAGTATT TACTTGTAAG" +

        		" AACCGAATTC TTTGGGGGAT AGTTGCAAAA AGAATCCAGT CAATTGTTCT" +

        		" TACGTAAAAC CATTCATATC TCGTATATGG ATATGTCTAG ATAGGCTATC" +

        		" GATTTTCGAT GGATTCGTTT GGTTCTTTTG ATTATTGCTC GAGCTGGATG" +

        		" ATGAAAAATT ATCATGTCCG GTTCCTTCG",consensusSequence.getString());

//        assertEquals((Integer)912, consensusSequence.getLength());

        assertNotNull(sequence.getContigFile());

        assertEquals(URI.create("http://ww2.biocase.org/websvn/filedetails.php?repname=campanula&path=%2FCAM385_Campa_drabifolia.pde"), MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile()).getUri());

        assertEquals(1, sequence.getCitations().size());

        Reference<?> reference = sequence.getCitations().iterator().next();

        assertEquals("Gemeinholzer,B., Bachmann,K. (2005): Examining morphological "

                + "and molecular diagnostic character states in "

                + "Cichorium intybus L. (Asteraceae) and Cichorium spinosum L."

                + " Plant Systematics and Evolution 253 (1-3): 105-123.", reference.getTitle());

        //single reads

        Set<SingleRead> singleReads = sequence.getSingleReads();

        assertNotNull(singleReads);

        assertEquals(2, singleReads.size());

        for (SingleRead singleRead : singleReads) {

            if(singleRead.getDirection().equals(SequenceDirection.Forward)){

                assertNotNull(singleRead.getPherogram());

                assertEquals(URI.create("http://ww2.biocase.org/websvn/filedetails.php?repname=campanula&path=%2FCAM385_GM312-petD_F.ab1"), MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram()).getUri());

            }

            else{

                assertNotNull(singleRead.getPherogram());

                assertEquals(URI.create("http://ww2.biocase.org/websvn/filedetails.php?repname=campanula&path=%2FCAM385_GM312-petD_R.ab1"), MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram()).getUri());

            }

        }

        assertNotNull(amplificationResult.getSingleReads());

        assertEquals(amplificationResult.getSingleReads(), singleReads);

	}

	/**

	 * Tests import of DNA unit and attaching it to an existing specimen to which

	 * it has a UnitAssociation.

	 */

	@Test

	@DataSet( value="AbcdGgbnImportTest.testAttachDnaSampleToDerivedUnit.xml", loadStrategy=CleanSweepInsertLoadStrategy.class)

	public void testAttachDnaSampleToDerivedUnit(){

	    UUID derivedUnit1Uuid = UUID.fromString("eb40cb0f-efb2-4985-819e-a9168f6d61fe");

//        DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);

//        derivedUnit.setAccessionNumber("B 10 0066577");

//        derivedUnit.setTitleCache("testUnit1", true);

//

//        derivedUnit.setUuid(derivedUnit1Uuid );

//

//        occurrenceService.save(derivedUnit);

//

//        commitAndStartNewTransaction(null);

//

//        setComplete();

//        endTransaction();

//

//

//        try {

//            writeDbUnitDataSetFile(new String[] {

//                    "SpecimenOrObservationBase",

//            }, "testAttachDnaSampleToDerivedUnit");

//        } catch (FileNotFoundException e) {

//            e.printStackTrace();

//        }

	    String inputFile = "/eu/etaxonomy/cdm/io/specimen/abcd206/in/db6.xml";

	    URL url = this.getClass().getResource(inputFile);

	    assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);

	    Abcd206ImportConfigurator importConfigurator = null;

	    try {

	        importConfigurator = Abcd206ImportConfigurator.NewInstance(url.toURI(), null,false);

	    } catch (URISyntaxException e) {

	        e.printStackTrace();

	        Assert.fail();

	    }

	    assertNotNull("Configurator could not be created", importConfigurator);

	    boolean result = defaultImport.invoke(importConfigurator);

	    assertTrue("Return value for import.invoke should be true", result);

	    assertEquals("Number of derived units is incorrect", 2, occurrenceService.count(DerivedUnit.class));

	    List<DerivedUnit> derivedUnits = occurrenceService.list(DerivedUnit.class, null, null, null, null);

	    assertEquals("Number of derived units is incorrect", 2, derivedUnits.size());

	    assertEquals("Number of field units is incorrect", 1, occurrenceService.count(FieldUnit.class));

	    assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));

	    DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnit1Uuid);

	    assertTrue(derivedUnits.contains(derivedUnit));

	    assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));

	    DnaSample dnaSample = occurrenceService.list(DnaSample.class, null, null, null, null).get(0);

	    assertEquals("Wrong derivation type!", DerivationEventType.DNA_EXTRACTION(), dnaSample.getDerivedFrom().getType());

	    assertEquals("Wrong number of originals", 1, dnaSample.getDerivedFrom().getOriginals().size());

	}

	/**

	 * Tests importing of DNA unit without attaching it to an existing specimen.

	 * Creates a FieldUnit with an attached DnaSample.

	 */

	@Test

	@DataSet( value="AbcdGgbnImportTest.testNoAttachDnaSampleToDerivedUnit.xml", loadStrategy=CleanSweepInsertLoadStrategy.class)

	public void testNoAttachDnaSampleToDerivedUnit(){

	    UUID derivedUnit1Uuid = UUID.fromString("eb40cb0f-efb2-4985-819e-a9168f6d61fe");

//        DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);

//        derivedUnit.setAccessionNumber("B 10 0066577");

//        derivedUnit.setTitleCache("testUnit1", true);

//

//        derivedUnit.setUuid(derivedUnit1Uuid );

//

//        occurrenceService.save(derivedUnit);

//

//        commitAndStartNewTransaction(null);

//

//        setComplete();

//        endTransaction();

//

//

//        try {

//            writeDbUnitDataSetFile(new String[] {

//                    "SpecimenOrObservationBase",

//            }, "testAttachDnaSampleToDerivedUnit");

//        } catch (FileNotFoundException e) {

//            e.printStackTrace();

//        }

	    String inputFile = "/eu/etaxonomy/cdm/io/specimen/abcd206/in/db6.xml";

	    URL url = this.getClass().getResource(inputFile);

	    assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);

	    Abcd206ImportConfigurator importConfigurator = null;

	    try {

	        importConfigurator = Abcd206ImportConfigurator.NewInstance(url.toURI(), null,false);

	    } catch (URISyntaxException e) {

	        e.printStackTrace();

	        Assert.fail();

	    }

	    assertNotNull("Configurator could not be created", importConfigurator);

	    assertEquals("Number of derived units is incorrect", 1, occurrenceService.count(DerivedUnit.class));

	    boolean result = defaultImport.invoke(importConfigurator);

	    assertTrue("Return value for import.invoke should be true", result);

	    assertEquals("Number of derived units is incorrect", 3, occurrenceService.count(DerivedUnit.class));

	    List<DerivedUnit> derivedUnits = occurrenceService.list(DerivedUnit.class, null, null, null, null);

	    assertEquals("Number of derived units is incorrect", 3, derivedUnits.size());

	    assertEquals("Number of field units is incorrect", 1, occurrenceService.count(FieldUnit.class));

	    assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));

	    DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnit1Uuid);

	    assertTrue(derivedUnits.contains(derivedUnit));

	    assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));

	    DnaSample dnaSample = occurrenceService.list(DnaSample.class, null, null, null, null).get(0);

	    assertEquals("Wrong derivation type!", DerivationEventType.DNA_EXTRACTION(), dnaSample.getDerivedFrom().getType());

	    assertEquals("Wrong number of originals", 1, dnaSample.getDerivedFrom().getOriginals().size());

	}

    @Override

    public void createTestDataSet() throws FileNotFoundException {

        UUID derivedUnit1Uuid = UUID.fromString("eb40cb0f-efb2-4985-819e-a9168f6d61fe");

        DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);

        derivedUnit.setAccessionNumber("B 10 0066577");

        derivedUnit.setTitleCache("testUnit1", true);

        derivedUnit.setUuid(derivedUnit1Uuid );

        occurrenceService.save(derivedUnit);

        commitAndStartNewTransaction(null);

        setComplete();

        endTransaction();

        try {

            writeDbUnitDataSetFile(new String[] {

                    "SpecimenOrObservationBase",

            }, "testAttachDnaSampleToDerivedUnit");

        } catch (FileNotFoundException e) {

            e.printStackTrace();

        }

    }

}