EDIT

// $Id$

/**

* 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.assertEquals;

import static org.junit.Assert.assertTrue;

import java.io.FileNotFoundException;

import java.util.Arrays;

import java.util.List;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.junit.Before;

import org.junit.Test;

import org.unitils.dbunit.annotation.DataSet;

import org.unitils.dbunit.annotation.DataSets;

import org.unitils.spring.annotation.SpringBeanByType;

import eu.etaxonomy.cdm.api.service.description.TransmissionEngineDistribution;

import eu.etaxonomy.cdm.api.service.description.TransmissionEngineDistribution.AggregationMode;

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

import eu.etaxonomy.cdm.model.description.DescriptionElementBase;

import eu.etaxonomy.cdm.model.description.Distribution;

import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;

import eu.etaxonomy.cdm.model.description.TaxonDescription;

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

import eu.etaxonomy.cdm.model.name.BotanicalName;

import eu.etaxonomy.cdm.model.name.Rank;

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

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;

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

/**

 * @author a.kohlbecker

 * @date Feb 26, 2013

 *

 */

public class TransmissionEngineDistributionTest extends CdmTransactionalIntegrationTest {

    @SuppressWarnings("unused")

    private static Logger logger = Logger.getLogger(TransmissionEngineDistributionTest.class);

    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_COMMUNIS_UUID = UUID.fromString("441a3c40-0c84-11de-8c30-0800200c9a66");

    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");

    @SpringBeanByType

    private ITermService termService;

    @SpringBeanByType

    private ITaxonService taxonService;

    @SpringBeanByType

    private IClassificationService classificationService;

    @SpringBeanByType

    private IReferenceService referenceService;

    @SpringBeanByType

    private TransmissionEngineDistribution engine;

    // --- 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

    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;

    @Before

    public void setUp() {

        superAreas = Arrays.asList(new NamedArea[]{

        		termService.getAreaByTdwgAbbreviation("YUG")

        });

        lowerRank = Rank.SUBSPECIES();

        upperRank = Rank.GENUS();

        classification = classificationService.load(CLASSIFICATION_UUID);

        yug = termService.getAreaByTdwgAbbreviation("YUG");

        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");

        engine.updatePriorities();

    }

    @Test

    @DataSet

    public void testPriorities(){

        Set<Extension> extensions = termService.load(PresenceAbsenceTerm.CULTIVATED().getUuid()).getExtensions();

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

    }

    @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"),

    })

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

    public void test_ignore() {

        addDistributions(

                T_LAPSANA_COMMUNIS_ALPINA_UUID,

                new Distribution[] {

                        // should succeed during area aggregation be ignored by rank aggregation

                        // => yug will get status ENDEMIC_FOR_THE_RELEVANT_AREA

                        //    but only for LAPSANA_COMMUNIS_ALPINA

                        Distribution.NewInstance(yug_mn, PresenceAbsenceTerm.ENDEMIC_FOR_THE_RELEVANT_AREA()),

                        // should be ignored by area aggregation

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

                        Distribution.NewInstance(yug_ko, PresenceAbsenceTerm.INTRODUCED_FORMERLY_INTRODUCED()),

               }

            );

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

        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("aggregated status of area YUG-KO wrong", PresenceAbsenceTerm.INTRODUCED_FORMERLY_INTRODUCED().getLabel(), distribution.getStatus().getLabel());

            }

        }

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

    }

    @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"),

    })

    public void testArea_area() {

        addDistributions(

                T_LAPSANA_COMMUNIS_ALPINA_UUID,

                new Distribution[] {

                        Distribution.NewInstance(yug_mn, PresenceAbsenceTerm.CULTIVATED()),

                        Distribution.NewInstance(yug_ko, PresenceAbsenceTerm.NATIVE()), // should succeed

                        Distribution.NewInstance(yug_bh, PresenceAbsenceTerm.INTRODUCED())

               }

            );

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

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

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

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

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

        boolean expectedAreaFound = false;

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

            Distribution distribution = (Distribution) description.getElements().iterator().next(); // only one aggregated area expected

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

                expectedAreaFound = true;

                assertEquals("aggregated status of area YUG is wrong", PresenceAbsenceTerm.NATIVE().getLabel(), distribution.getStatus().getLabel());

            }

        }

        assertTrue("The areae YUG should have been found", expectedAreaFound);

    }

    @Test

    @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)

    public void testArea_rank_and_area() {

        addDistributions(

                T_LAPSANA_COMMUNIS_ALPINA_UUID,

                new Distribution[] {

                        Distribution.NewInstance(yug_mn, PresenceAbsenceTerm.CULTIVATED()),

                        Distribution.NewInstance(yug_ko, PresenceAbsenceTerm.NATIVE()), // should succeed

               }

            );

        addDistributions(

                T_LAPSANA_COMMUNIS_UUID,

                new Distribution[] {

                        Distribution.NewInstance(yug_mn, PresenceAbsenceTerm.INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION()),

                        Distribution.NewInstance(yug_ko, PresenceAbsenceTerm.CULTIVATED()),

               }

            );

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

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

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

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

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

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

        assertEquals(3, description.getElements().size());

        int numExpectedFound = 0;

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

            Distribution distribution = (Distribution)element;

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

                numExpectedFound++;

                assertEquals("aggregated status of area YUG is wrong", PresenceAbsenceTerm.NATIVE().getLabel(), distribution.getStatus().getLabel());

            }

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

                numExpectedFound++;

                assertEquals("aggregated status of area YUG-MN is wrong", PresenceAbsenceTerm.CULTIVATED().getLabel(), distribution.getStatus().getLabel());

            }

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

                numExpectedFound++;

                assertEquals("aggregated status of area YUG-KO wrong", PresenceAbsenceTerm.NATIVE().getLabel(), distribution.getStatus().getLabel());

            }

        }

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

    }

    /**

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

     * @param taxonUuid

     * @param distributions

     */

    private void addDistributions(UUID taxonUuid, Distribution[] distributions) {

        Taxon taxon = (Taxon) taxonService.load(taxonUuid);

        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);

        // need to write to database for transmission engine

        commitAndStartNewTransaction(null);

    }

    //@Test //  uncomment to create test data file//

    @Override

    public void createTestDataSet() throws FileNotFoundException {

        // --- References --- //

        Reference sec = ReferenceFactory.newDatabase();

        sec.setTitleCache("Test", true);

        Reference nomRef = ReferenceFactory.newBook();

        sec.setTitleCache("Sp.Pl.", true);

        referenceService.save(sec);

        referenceService.save(nomRef);

        // --- Taxa --- //

        //  Lapsana

        //        L. communis

        //            L. communis subsp. communis

        //            L. communis subsp. adenophora

        //            L. communis subsp. alpina

        //  Sonchella

        //        S. dentata

        //        S. stenoma

        BotanicalName n_lapsana = BotanicalName.NewInstance(Rank.GENUS());

        n_lapsana.setTitleCache("Lapsana", true);

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

        t_lapsana.setUuid(T_LAPSANA_UUID);

        taxonService.saveOrUpdate(t_lapsana);

        BotanicalName n_lapsana_communis = BotanicalName.NewInstance(Rank.SPECIES());

        n_lapsana_communis.setTitleCache("L. communis", true);

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

        t_lapsana_communis.setUuid(T_LAPSANA_COMMUNIS_UUID);

        taxonService.saveOrUpdate(t_lapsana_communis);

        BotanicalName n_lapsana_communis_communis = BotanicalName.NewInstance(Rank.SUBSPECIES());

        n_lapsana_communis_communis.setTitleCache("L. communis subsp. communis", true);

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

        t_lapsana_communis_communis.setUuid(T_LAPSANA_COMMUNIS_COMMUNIS_UUID);

        taxonService.saveOrUpdate(t_lapsana_communis_communis);

        BotanicalName n_lapsana_communis_adenophora = BotanicalName.NewInstance(Rank.SUBSPECIES());

        n_lapsana_communis_adenophora.setTitleCache("L. communis subsp. adenophora", true);

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

        t_lapsana_communis_adenophora.setUuid(T_LAPSANA_COMMUNIS_ADENOPHORA_UUID);

        taxonService.saveOrUpdate(t_lapsana_communis_adenophora);

        BotanicalName n_lapsana_communis_alpina = BotanicalName.NewInstance(Rank.SUBSPECIES());

        n_lapsana_communis_alpina.setTitleCache("L. communis subsp. alpina", true);

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

        t_lapsana_communis_alpina.setUuid(T_LAPSANA_COMMUNIS_ALPINA_UUID);

        taxonService.saveOrUpdate(t_lapsana_communis_alpina);

        // --- Classification --- //

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

        classification.setUuid(CLASSIFICATION_UUID);

        classificationService.save(classification);

        TaxonNode node_lapsana = classification.addChildTaxon(t_lapsana, sec, null);

        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);

        classificationService.saveOrUpdate(classification);

        // --- 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

//                    );

        commitAndStartNewTransaction(null);

        writeDbUnitDataSetFile(new String[] {

                "TAXONBASE", "TAXONNAMEBASE",

                "REFERENCE", "DESCRIPTIONELEMENTBASE", "DESCRIPTIONBASE",

                "AGENTBASE", "CLASSIFICATION",  "TAXONNODE",

                "HOMOTYPICALGROUP", "LANGUAGESTRING",

         });

    }

}