EDIT

/**

* Copyright (C) 2013 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.api.service;

import static org.junit.Assert.assertNull;

import java.util.Arrays;

import java.util.HashSet;

import java.util.Iterator;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.junit.Before;

import org.unitils.dbunit.annotation.DataSet;

import eu.etaxonomy.cdm.model.location.NamedArea;

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

import eu.etaxonomy.cdm.model.taxon.Classification;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonNode;

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

/**

 * @author a.kohlbecker

 */

    private static final UUID T_LAPSANA_UUID = UUID.fromString("f65d47bd-4f49-4ab1-bc4a-bc4551eaa1a8");

    private static final UUID T_LAPSANA_COMMUNIS_UUID = UUID.fromString("2a5ceebb-4830-4524-b330-78461bf8cb6b");

    private static final UUID T_LAPSANA_COMMUNIS_ADENOPHORA_UUID = UUID.fromString("e4acf200-63b6-11dd-ad8b-0800200c9a66");

    private static final UUID T_LAPSANA_COMMUNIS_ALPINA_UUID = UUID.fromString("596b1325-be50-4b0a-9aa2-3ecd610215f2");

    private static final UUID CLASSIFICATION_UUID = UUID.fromString("4b266053-a841-4980-b548-3f21d8d7d712");

    private ITermService termService;

    @SpringBeanByType

    private ITaxonService taxonService;

    @SpringBeanByType

    private IClassificationService classificationService;

    @SpringBeanByType

    private IReferenceService referenceService;

    @SpringBeanByType

    // tdwg3 level YUG :  Yugoslavia

    // contains tdwg4 level areas :

    //   YUG-BH	Bosnia-Herzegovina

    //   YUG-CR	Croatia

    //   YUG-KO	Kosovo

    //   YUG-MA	Macedonia

    //   YUG-MN	Montenegro

    private NamedArea yug = null;

    private NamedArea yug_bh = null;

    private NamedArea yug_cr = null;

    private NamedArea yug_ko = null;

    private NamedArea yug_ma = null;

    private NamedArea yug_mn = null;

    List<NamedArea> superAreas = null;

    Rank upperRank = null;

    Rank lowerRank = null;

    private Classification classification;

    private Reference book_b = null;

    @Before

    public void setUp() {

        superAreas = Arrays.asList(new NamedArea[]{

        classification = classificationService.load(CLASSIFICATION_UUID);

        yug_bh = termService.getAreaByTdwgAbbreviation("YUG-BH");

        yug_cr = termService.getAreaByTdwgAbbreviation("YUG-CR");

        yug_ko = termService.getAreaByTdwgAbbreviation("YUG-KO");

        yug_ma = termService.getAreaByTdwgAbbreviation("YUG-MA");

        yug_mn = termService.getAreaByTdwgAbbreviation("YUG-MN");

        book_a.setTitle("book_a");

        book_b = ReferenceFactory.newBook();

        book_b.setTitle("book_a");

    }

        assertEquals(TransmissionEngineDistribution.EXTENSION_VALUE_PREFIX + "45", extensions.iterator().next().getValue());

    @Test

        @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),

        @DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml"),

        @DataSet(value="TransmissionEngineDistributionTest.xml"),

    })

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

        addDistributions(

                T_LAPSANA_COMMUNIS_ALPINA_UUID,

                        // => yug will get status ENDEMIC_FOR_THE_RELEVANT_AREA

                        //    but only for LAPSANA_COMMUNIS_ALPINA

                        // => LAPSANA_COMMUNIS will wave distribution with yug_ko and INTRODUCED_FORMERLY_INTRODUCED

        Taxon lapsana_communis_alpina  = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_ALPINA_UUID);

        assertEquals(2, lapsana_communis_alpina.getDescriptions().size());

        // TODO test for yug => ENDEMIC_FOR_THE_RELEVANT_AREA in computed description

        Taxon lapsana_communis  = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_UUID);

        assertEquals(1, lapsana_communis.getDescriptions().size());

        TaxonDescription description = lapsana_communis.getDescriptions().iterator().next();

        assertEquals(1, description.getElements().size());

        int numExpectedFound = 0;

        for (DescriptionElementBase element : description.getElements()){

            Distribution distribution = (Distribution)element;

            if(distribution.getArea().equals(yug_ko)){

                numExpectedFound++;

        }

        assertEquals("All three expected areas should have been found before", numExpectedFound, 1);

    }

    @Test

        @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),

        @DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml"),

        @DataSet(value="TransmissionEngineDistributionTest.xml"),

    })

        distributions_LCA.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "2")); // NATIVE should succeed

        distributions_LCA.add(newDistribution(book_a, yug_bh, PresenceAbsenceTerm.INTRODUCED(), "3"));

        distributions_LCA.add(newDistribution(book_a, yug_ma, PresenceAbsenceTerm.NATIVE(), "4")); // NATIVE should succeed

                T_LAPSANA_COMMUNIS_ALPINA_UUID,

        Taxon lapsana_communis_alpina  = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_ALPINA_UUID);

        assertEquals(1, lapsana_communis_alpina.getDescriptions().size());

        lapsana_communis_alpina  = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_ALPINA_UUID);

        assertEquals(2, lapsana_communis_alpina.getDescriptions().size());

                assertNull("only one computed Distribution should exists", accumulatedDistribution);

                assertEquals("Expecting area to be YUG", yug, accumulatedDistribution.getArea());

                assertEquals("Expecting status to be NATIVE", PresenceAbsenceTerm.NATIVE().getLabel(), accumulatedDistribution.getStatus().getLabel());

        }

        Iterator<DescriptionElementSource> sourceIt = accumulatedDistribution.getSources().iterator();

        // should contain source_LCA_yug_ma and source_LCA_yug_ko, testing the microreference which is unique in the tests

        assertTrue(" 2  4 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));

        assertTrue(" 2  4 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));

    @Test

        @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),

        @DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml"),

        @DataSet(value="TransmissionEngineDistributionTest.xml"),

    })

        Set<Distribution> distributions_LCA = new HashSet<>();

        distributions_LCA.add(newDistribution(book_a, yug_mn, PresenceAbsenceTerm.CULTIVATED(), "1"));

        distributions_LCA.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "2")); // NATIVE should succeed

        addDistributions(

                T_LAPSANA_COMMUNIS_ALPINA_UUID,

        Set<Distribution> distributions_LC = new HashSet<>();

        distributions_LC.add(newDistribution(book_a, yug_mn, PresenceAbsenceTerm.CULTIVATED(), "3"));

        distributions_LC.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "4")); // NATIVE should succeed

        commitAndStartNewTransaction(null);

                T_LAPSANA_COMMUNIS_UUID,

        Taxon lapsana_communis  = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_UUID);

        Taxon lapsana = (Taxon) taxonService.load(T_LAPSANA_UUID);

        int numExpectedFound = 0;

        for (DescriptionElementBase element : description.getElements()){

            Distribution distribution = (Distribution)element;

            if(distribution.getArea().equals(yug)){

                numExpectedFound++;

                Iterator<DescriptionElementSource> sourceIt = distribution.getSources().iterator();

                // should contain source_LCA_yug_ma and source_LCA_yug_ko, testing the microreference which is unique in the tests

                assertTrue(" 2  4 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));

                assertTrue(" 2  4 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));

            if(distribution.getArea().equals(yug_mn)){

                numExpectedFound++;

                Iterator<DescriptionElementSource> sourceIt = distribution.getSources().iterator();

                // should contain source_LCA_yug_ma and source_LCA_yug_ko, testing the microreference which is unique in the tests

                assertTrue(" 1  3 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));

                assertTrue(" 1  3 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));

            if(distribution.getArea().equals(yug_ko)){

                numExpectedFound++;

                Iterator<DescriptionElementSource> sourceIt = distribution.getSources().iterator();

                // should contain source_LCA_yug_ma and source_LCA_yug_ko, testing the microreference which is unique in the tests

                assertTrue(" 2  4 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));

                assertTrue(" 2  4 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));

        }

        assertEquals("All three expected areas should have been found before", numExpectedFound, 3);

    }

     * Variant of {@link #testArea_rank_and_area_1()} with alternate source references to check the

     * suppression of duplicates.

     *

     * This test relies on {@link #testArea_rank_and_area_1()}

     * an makes assertions only on the alternative source references

    @Test

        @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),

        @DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml"),

        @DataSet(value="TransmissionEngineDistributionTest.xml"),

    })

        Set<Distribution> distributions_LCA = new HashSet<Distribution>();

        distributions_LCA.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "1"));

        distributions_LCA.add(newDistribution(book_b, yug_ko, PresenceAbsenceTerm.NATIVE(), "2"));

        addDistributions(

                T_LAPSANA_COMMUNIS_ALPINA_UUID,

                distributions_LCA

            );

        engine.accumulate(AggregationMode.byAreasAndRanks, superAreas, lowerRank, upperRank, null, null);

        Taxon lapsana_communis = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_UUID);

        int computedDescriptionsCnt = 0;

        for(TaxonDescription description : lapsana_communis.getDescriptions()) {

            if(description.hasMarker(MarkerType.COMPUTED(), true)) {

                computedDescriptionsCnt++;

                assertEquals(2, description.getElements().size()); // yug, yug_ko

                for(DescriptionElementBase distribution : description.getElements()) {

                    logger.debug(((Distribution)distribution).getArea() + " " + sourcesToString(distribution));

                    if(((Distribution)distribution).getArea().equals(yug_ko)){

                        assertEquals(2, distribution.getSources().size());

                    }

                    if(((Distribution)distribution).getArea().equals(yug)){

                        assertEquals(2, distribution.getSources().size());

                    }

                }

            }

        }

        assertEquals(1, computedDescriptionsCnt);

    }

    /**

     * Variant of {@link #testArea_rank_and_area_1()} with alternate source references to check the

     * suppression of duplicates.

     *

     * This test relies on {@link #testArea_rank_and_area_1()}

     * an makes assertions only on the alternative source references

    @Test

    @DataSets({

        @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),

        @DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml"),

        @DataSet(value="TransmissionEngineDistributionTest.xml"),

    })

        Set<Distribution> distributions_LCA = new HashSet<Distribution>();

        distributions_LCA.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "1"));

        distributions_LCA.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "3"));

        addDistributions(

                T_LAPSANA_COMMUNIS_ALPINA_UUID,

                distributions_LCA

            );

        Set<Distribution> distributions_LC = new HashSet<>();

        distributions_LC.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "1"));

        distributions_LC.add(newDistribution(book_b, yug_ko, PresenceAbsenceTerm.NATIVE(), "2"));

        addDistributions(

                T_LAPSANA_COMMUNIS_UUID,

                distributions_LC

            );

        engine.accumulate(AggregationMode.byAreasAndRanks, superAreas, lowerRank, upperRank, null, null);

        Taxon lapsana_communis = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_UUID);

        int computedDescriptionsCnt = 0;

        for(TaxonDescription description : lapsana_communis.getDescriptions()) {

            if(description.hasMarker(MarkerType.COMPUTED(), true)) {

                computedDescriptionsCnt++;

                assertEquals(2, description.getElements().size());

                for(DescriptionElementBase distribution : description.getElements()) {

                    logger.debug(((Distribution)distribution).getArea() + " " + sourcesToString(distribution));

                    if(((Distribution)distribution).getArea().equals(yug_ko)){

                        assertEquals(2, distribution.getSources().size());

                    }

                    if(((Distribution)distribution).getArea().equals(yug)){

                        assertEquals(3, distribution.getSources().size());

                    }

                }

            }

        }

        assertEquals(1, computedDescriptionsCnt);

    }

    /**

     * Variant of {@link #testArea_rank_and_area_1()} with alternate source references to

     * check the handling of the case where the target taxon already has the distribution which is the

     * result of the aggregation (see http://dev.e-taxonomy.eu/trac/ticket/4366#comment:12)

     *

     * This test relies on {@link #testArea_rank_and_area_1()}

     * an makes assertions only on the alternative source references

    @Test

        @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),

        @DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml"),

        @DataSet(value="TransmissionEngineDistributionTest.xml"),

    })

        Set<Distribution> distributions_LCA = new HashSet<>();

        distributions_LCA.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "1"));

        addDistributions(

                T_LAPSANA_COMMUNIS_ALPINA_UUID,

                distributions_LCA

            );

        Set<Distribution> distributions_LC = new HashSet<>();

        distributions_LC.add(newDistribution(book_a, yug, PresenceAbsenceTerm.NATIVE(), "2")); //  should succeed

        addDistributions(

                T_LAPSANA_COMMUNIS_UUID,

                distributions_LC

            );

        engine.accumulate(AggregationMode.byAreasAndRanks, superAreas, lowerRank, upperRank, null, null);

        Taxon lapsana_communis = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_UUID);

        int computedDescriptionsCnt = 0;

        for(TaxonDescription description : lapsana_communis.getDescriptions()) {

            if(description.hasMarker(MarkerType.COMPUTED(), true)) {

                computedDescriptionsCnt++;

                assertEquals(2, description.getElements().size());

                Distribution distribution = (Distribution)description.getElements().iterator().next();

                if(distribution.getArea().equals(yug_ko)){

                    assertEquals(2, distribution.getSources().size());

                    DescriptionElementSource source = distribution.getSources().iterator().next();

                    assertEquals("2", source.getCitationMicroReference());

                }

            }

        }

        assertEquals(1, computedDescriptionsCnt);

    }

    /**

     * @param referenceTitle

     * @param area

     * @param status

     * @param microCitation

     * @return

     */

    private Distribution newDistribution(Reference reference, NamedArea area, PresenceAbsenceTerm status,

            String microCitation) {

        DescriptionElementSource source = DescriptionElementSource.NewPrimarySourceInstance(reference, microCitation);

        Distribution distribution = Distribution.NewInstance(area, status);

        distribution.getSources().add(source);

        return distribution;

    }

     * creates a new description for the taxon identified by the UUIDs

     * @param taxonUuid

     * @param distributions

     */

        if(taxon == null) {

            throw new NullPointerException("No taxon found for " + taxonUuid);

        }

        TaxonDescription description = TaxonDescription.NewInstance(taxon);

         for (Distribution distribution : distributions) {

             description.addElement(distribution);

        }

        taxonService.saveOrUpdate(taxon);

        commitAndStartNewTransaction(null);

        StringBuffer out = new StringBuffer();

        for ( DescriptionElementSource source : deb.getSources()) {

            out.append(source.getCitation().getTitle() + " : " + source.getCitationMicroReference() + ", ");

        }

        return out.toString();

    }

    public void createTestDataSet() throws FileNotFoundException {

        // --- References --- //

        referenceService.save(sec);

        referenceService.save(nomRef);

        //  Lapsana

        //        L. communis

        //            L. communis subsp. communis

        //            L. communis subsp. adenophora

        //            L. communis subsp. alpina

        //  Sonchella

        //        S. dentata

        //        S. stenoma

        Taxon t_lapsana = Taxon.NewInstance(n_lapsana, sec);

        t_lapsana.setUuid(T_LAPSANA_UUID);

        taxonService.saveOrUpdate(t_lapsana);

        Taxon t_lapsana_communis = Taxon.NewInstance(n_lapsana_communis, sec);

        t_lapsana_communis.setUuid(T_LAPSANA_COMMUNIS_UUID);

        Taxon t_lapsana_communis_communis = Taxon.NewInstance(n_lapsana_communis_communis, sec);

        t_lapsana_communis_communis.setUuid(T_LAPSANA_COMMUNIS_COMMUNIS_UUID);

        Taxon t_lapsana_communis_adenophora = Taxon.NewInstance(n_lapsana_communis_adenophora, sec);

        t_lapsana_communis_adenophora.setUuid(T_LAPSANA_COMMUNIS_ADENOPHORA_UUID);

        Taxon t_lapsana_communis_alpina = Taxon.NewInstance(n_lapsana_communis_alpina, sec);

        t_lapsana_communis_alpina.setUuid(T_LAPSANA_COMMUNIS_ALPINA_UUID);

        // --- Classification --- //

        Classification classification = Classification.NewInstance("TestClassification");

        TaxonNode node_lapsana_communis = node_lapsana.addChildTaxon(t_lapsana_communis, sec, null);

        node_lapsana_communis.addChildTaxon(t_lapsana_communis_communis, sec, null);

        node_lapsana_communis.addChildTaxon(t_lapsana_communis_adenophora, sec, null);

        node_lapsana_communis.addChildTaxon(t_lapsana_communis_alpina, sec, null);

        // --- Distributions --- //

        // tdwg3 level YUG :  Yugoslavia

        // contains tdwg4 level areas :

        //   YUG-BH	Bosnia-Herzegovina

        //   YUG-CR	Croatia

        //   YUG-KO	Kosovo

        //   YUG-MA	Macedonia

        //   YUG-MN	Montenegro

        // assigning distribution information to taxa

        // expectations regarding the aggregation can be found in the comments below

//        TaxonDescription d_lapsana_communis_communis = TaxonDescription.NewInstance(t_lapsana_communis_communis);

//        d_lapsana_communis_communis.addElement(Distribution.NewInstance(

//                    TdwgArea.getAreaByTdwgAbbreviation("YUG-MN"),

//                    PresenceTerm.ENDEMIC_FOR_THE_RELEVANT_AREA() // should be ignored

//                    );

    }

}