EDIT

	public static final UUID uuidComplete = UUID.fromString("b4b1b2ab-89a8-4ce6-8110-d60b8b1bc433");

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

    /**

     * @param clazz

     * @param markerType

     * @param markerValue

     * @param includeEntity

     * @param pageSize

     * @param pageNumber

     * @param propertyPaths

     * @return

     */

    public <S extends T> long countByMarker(Class<S> clazz, MarkerType markerType, Boolean markerValue);

    /**

     * @param clazz

     * @param markerType

     * @param markerValue

     * @param includeEntity

     * @param pageSize

     * @param pageNumber

     * @param propertyPaths

     * @return

     */

    public <S extends T> List<Object[]> findByMarker(Class<S> clazz, MarkerType markerType, Boolean markerValue, boolean includeEntity,

            Integer pageSize, Integer pageNumber, List<String> propertyPaths);

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

	   @Override

	    public <S extends T> long countByMarker(Class<S> clazz, MarkerType markerType,

	            Boolean markerValue) {

	        checkNotInPriorView("IdentifiableDaoBase.countByMarker(T clazz, MarkerType markerType, Boolean markerValue)");

	        if (markerType == null){

	            return 0;

	        }

	        Class<?> clazzParam = clazz == null ? type : clazz;

	        String queryString = "SELECT count(*) FROM " + clazzParam.getSimpleName() + " as c " +

	                    "INNER JOIN c.markers as mks " +

	                    "WHERE (1=1) ";

	        if (markerValue != null){

	            queryString += " AND mks.flag = :flag";

	        }

            queryString += " AND mks.markerType = :type";

	        Query query = getSession().createQuery(queryString);

            query.setEntity("type", markerType);

	        if (markerValue != null){

	            query.setBoolean("flag", markerValue);

	        }

	        Long c = (Long)query.uniqueResult();

	        return c;

	    }

	@Override

    public <S extends T> List<Object[]> findByMarker(

            Class<S> clazz, MarkerType markerType,

            Boolean markerValue, boolean includeEntity, Integer pageSize, Integer pageNumber,

            List<String> propertyPaths) {

        checkNotInPriorView("IdentifiableDaoBase.findByMarker(T clazz, String identifier, DefinedTerm identifierType, MatchMode matchmode, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths)");

        if (markerType == null){

            return new ArrayList<Object[]>();

        }

        Class<?> clazzParam = clazz == null ? type : clazz;

        String queryString = "SELECT mks.markerType, mks.flag, %s FROM %s as c " +

                " INNER JOIN c.markers as mks " +

                " WHERE (1=1) ";

        queryString = String.format(queryString, (includeEntity ? "c":"c.uuid, c.titleCache") , clazzParam.getSimpleName());

        //Matchmode and identifier

        if (markerValue != null){

            queryString += " AND mks.flag = :flag";

        }

        queryString += " AND mks.markerType = :type";

        //order

        queryString +=" ORDER BY mks.markerType.uuid, mks.flag, c.uuid ";

        Query query = getSession().createQuery(queryString);

        //parameters

        query.setEntity("type", markerType);

        if (markerValue != null){

            query.setBoolean("flag", markerValue);

        }

        //paging

        setPagingParameter(query, pageSize, pageNumber);

        @SuppressWarnings("unchecked")

        List<Object[]> results = query.list();

        //initialize

        if (includeEntity){

            List<S> entities = new ArrayList<S>();

            for (Object[] result : results){

                entities.add((S)result[2]);

            }

            defaultBeanInitializer.initializeAll(entities, propertyPaths);

        }

        return results;

    }

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

		checkNotInPriorView("TaxonDaoHibernateImpl.countByIdentifier(T clazz, String identifier, DefinedTerm identifierType, TaxonNode subMatchMode matchmode)");

		checkNotInPriorView("TaxonDaoHibernateImpl.findByIdentifier(T clazz, String identifier, DefinedTerm identifierType, MatchMode matchmode, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths)");

    /**

     * {@inheritDoc}

     * @see #countByIdentifier(Class, String, DefinedTerm, TaxonNode, MatchMode)

     */

    @Override

    public <S extends TaxonBase> long countByMarker(Class<S> clazz, MarkerType markerType,

            Boolean markerValue, TaxonNode subtreeFilter) {

        if (markerType == null){

            return 0;

        }

        if (subtreeFilter == null){

            return countByMarker(clazz, markerType, markerValue);

        }

        Class<?> clazzParam = clazz == null ? type : clazz;

        checkNotInPriorView("TaxonDaoHibernateImpl.countByMarker(Class<S> clazz, DefinedTerm markerType, boolean markerValue, TaxonNode subtreeFilter)");

        boolean isTaxon = clazzParam == Taxon.class || clazzParam == TaxonBase.class;

        boolean isSynonym = clazzParam == Synonym.class || clazzParam == TaxonBase.class;

        getSession().update(subtreeFilter);  //to avoid LIE when retrieving treeindex

        String filterStr = "'" + subtreeFilter.treeIndex() + "%%'";

        String accTreeJoin = isTaxon? " LEFT JOIN c.taxonNodes tn  " : "";

        String synTreeJoin = isSynonym ? " LEFT JOIN c.synonymRelations sr LEFT  JOIN sr.relatedTo as acc LEFT JOIN acc.taxonNodes synTn  " : "";

        String accWhere = isTaxon ?  "tn.treeIndex like " + filterStr : "(1=0)";

        String synWhere = isSynonym  ?  "synTn.treeIndex like " + filterStr : "(1=0)";

        String queryString = "SELECT count(*)  FROM %s as c " +

                " INNER JOIN c.markers as mks " +

                accTreeJoin +

                synTreeJoin +

                " WHERE (1=1) " +

                    "  AND ( " + accWhere + " OR " + synWhere + ")";

        queryString = String.format(queryString, clazzParam.getSimpleName());

        if (markerValue != null){

            queryString += " AND mks.flag = :flag";

        }

        if (markerType != null){

            queryString += " AND mks.markerType = :type";

        }

        Query query = getSession().createQuery(queryString);

        if (markerType != null){

            query.setEntity("type", markerType);

        }

        if (markerValue != null){

            query.setBoolean("flag", markerValue);

        }

        Long c = (Long)query.uniqueResult();

        return c;

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public <S extends TaxonBase> List<Object[]> findByMarker(Class<S> clazz, MarkerType markerType,

            Boolean markerValue, TaxonNode subtreeFilter, boolean includeEntity, Integer pageSize, Integer pageNumber,

            List<String> propertyPaths) {

        checkNotInPriorView("TaxonDaoHibernateImpl.findByMarker(T clazz, String identifier, DefinedTerm identifierType, MatchMode matchmode, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths)");

        if (markerType == null){

            return new ArrayList<Object[]>();

        }

        Class<?> clazzParam = clazz == null ? type : clazz;

        boolean isTaxon = clazzParam == Taxon.class || clazzParam == TaxonBase.class;

        boolean isSynonym = clazzParam == Synonym.class || clazzParam == TaxonBase.class;

        getSession().update(subtreeFilter);  //to avoid LIE when retrieving treeindex

        String filterStr = "'" + subtreeFilter.treeIndex() + "%%'";

        String accTreeJoin = isTaxon? " LEFT JOIN c.taxonNodes tn  " : "";

        String synTreeJoin = isSynonym ? " LEFT JOIN c.synonymRelations sr LEFT  JOIN sr.relatedTo as acc LEFT JOIN acc.taxonNodes synTn  " : "";

        String accWhere = isTaxon ?  "tn.treeIndex like " + filterStr : "(1=0)";

        String synWhere = isSynonym  ?  "synTn.treeIndex like " + filterStr : "(1=0)";

        String queryString = "SELECT mks.markerType, mks.flag, %s " +

                " FROM %s as c " +

                " INNER JOIN c.markers as mks " +

                accTreeJoin +

                synTreeJoin +

                " WHERE (1=1) " +

                    " AND ( " + accWhere + " OR " + synWhere + ")";

        queryString = String.format(queryString, (includeEntity ? "c":"c.uuid, c.titleCache") , clazzParam.getSimpleName());

        //type and value

        if (markerValue != null){

            queryString += " AND mks.flag = :flag";

        }

        queryString += " AND mks.markerType = :type";

        //order

        queryString +=" ORDER BY mks.markerType.uuid, mks.flag, c.uuid ";

        Query query = getSession().createQuery(queryString);

        //parameters

        query.setEntity("type", markerType);

        if (markerValue != null){

            query.setBoolean("flag", markerValue);

        }

        //paging

        setPagingParameter(query, pageSize, pageNumber);

        List<Object[]> results = query.list();

        //initialize

        if (includeEntity){

            List<S> entities = new ArrayList<S>();

            for (Object[] result : results){

                entities.add((S)result[2]);

            }

            defaultBeanInitializer.initializeAll(entities, propertyPaths);

        }

        return results;

    }

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

	/**

	 * Counts all taxa which match the given identifier (identifier type, identifier string and match mode).

	 * Optionally a subtreefilter can be defined.

	 *

	 * @param clazz optional, the TaxonBase subclass

	 * @param identifier the identifier string

	 * @param identifierType the identifier type

     * @param matchmode the match mode for the identifier string

	 * @param subtreeFilter the subtree filter as taxon node

	 * @return

	 */

	/**

     * Counts all taxa which have the given marker of type markerType and with value markerValue.

     * Additionally an optional subtreefilter can be defined.

     *

     * @param clazz

     * @param markerType

     * @param markerValue

     * @param subtreeFilter

     * @return

     */

    public <S extends TaxonBase> long countByMarker(Class<S> clazz, MarkerType markerType,

            Boolean markerValue, TaxonNode subtreeFilter);

    /**

     * @param clazz

     * @param markerType

     * @param markerValue

     * @param subtreeFilter

     * @param includeEntity

     * @param pageSize

     * @param pageNumber

     * @param propertyPaths

     * @return

     */

    public <S extends TaxonBase> List<Object[]> findByMarker(Class<S> clazz, MarkerType markerType,

            Boolean markerValue, TaxonNode subtreeFilter, boolean includeEntity,

            Integer pageSize, Integer pageNumber, List<String> propertyPaths);

import eu.etaxonomy.cdm.api.service.dto.FindByMarkerDTO;

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

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

	private ITermService termService;

     *

    		definedTerm = CdmBase.deproxy(termService.find(identifierTypeUUID), DefinedTerm.class);

    /**

     * List identifiable entities by markers

     *

     * @param type

     * @param markerType

     * @param value

     * @param pageNumber

     * @param pageSize

     * @param request

     * @param response

     * @return

     * @see IdentifiableListController#doFindByIdentifier(Class, String, String, Integer, Integer, MatchMode, Boolean, HttpServletRequest, HttpServletResponse)

     * @throws IOException

     */

    @RequestMapping(method = RequestMethod.GET, value={"findByMarker"}, params={"subtree"})

    public Pager<FindByMarkerDTO<T>> doFindByMarker(

            @RequestParam(value = "class", required = false) Class<T> type,

            @RequestParam(value = "markerType", required = true) UUID markerTypeUuid,

            @RequestParam(value = "value", required = false) Boolean value,

            @RequestParam(value = "pageNumber", required = false) Integer pageNumber,

            @RequestParam(value = "pageSize", required = false) Integer pageSize,

            @RequestParam(value = "includeEntity", required = false, defaultValue="true") Boolean includeEntity, //TODO true only for debuging

            HttpServletRequest request,

            HttpServletResponse response

            )

            throws IOException {

        MarkerType markerType = null;

        if(markerTypeUuid != null){

            DefinedTermBase<?> term = CdmBase.deproxy(termService.find(markerTypeUuid), MarkerType.class);

            if (term != null && term.isInstanceOf(MarkerType.class)){

                markerType = CdmBase.deproxy(term, MarkerType.class);

            }

        }

        if (logger.isDebugEnabled()){logger.info("doFindByMarker [subtreeUuid]  : " + request.getRequestURI() + "?" + request.getQueryString() );}

        PagerParameters pagerParams = new PagerParameters(pageSize, pageNumber).normalizeAndValidate(response);

        return service.findByMarker(type, markerType, value, includeEntity, pagerParams.getPageSize(), pagerParams.getPageIndex(), initializationStrategy);

    }

import eu.etaxonomy.cdm.api.service.dto.FindByMarkerDTO;

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

import io.swagger.annotations.Api;

    /**

     * List taxa by markers using a subtree filter

     *

     * @param type

     * @param markerType

     * @param value

     * @param pageNumber

     * @param pageSize

     * @param request

     * @param response

     * @return

     * @see IdentifiableListController#doFindByMarker(Class, UUID, Boolean, Integer, Integer, Boolean, HttpServletRequest, HttpServletResponse)

     * @see TaxonListController#doFindByIdentifier(Class, UUID, String, Integer, Integer, MatchMode, Boolean, UUID, HttpServletRequest, HttpServletResponse)

     * @see IdentifiableListController#doFindByIdentifier(Class, String, String, Integer, Integer, MatchMode, Boolean, HttpServletRequest, HttpServletResponse)

     * @throws IOException

     */

    @RequestMapping(method = RequestMethod.GET, value={"findByMarker"}, params={"subtree"})

    public <T extends TaxonBase>  Pager<FindByMarkerDTO<T>> doFindByMarker(

            @RequestParam(value = "class", required = false) Class<T> type,

            @RequestParam(value = "markerType", required = true) UUID markerTypeUuid,

            @RequestParam(value = "value", required = false) Boolean value,

            @RequestParam(value = "pageNumber", required = false) Integer pageNumber,

            @RequestParam(value = "pageSize", required = false) Integer pageSize,

            @RequestParam(value = "includeEntity", required = false, defaultValue="true") Boolean includeEntity, //TODO true only for debuging

            @RequestParam(value = "subtree", required = true) UUID subtreeUuid,

            HttpServletRequest request,

            HttpServletResponse response

            )

            throws IOException {

        MarkerType markerType = null;

        if(markerTypeUuid != null){

            DefinedTermBase<?> term = CdmBase.deproxy(termService.find(markerTypeUuid), MarkerType.class);

            if (term != null && term.isInstanceOf(MarkerType.class)){

                markerType = CdmBase.deproxy(term, MarkerType.class);

            }

        }

        TaxonNode subTree;

        Classification cl = classificationService.load(subtreeUuid);

        if (cl != null){

            subTree = cl.getRootNode();

        }else{

            subTree = taxonNodeService.find(subtreeUuid);

        }

        if (logger.isDebugEnabled()){logger.info("doFindByMarker [subtreeUuid]  : " + request.getRequestURI() + "?" + request.getQueryString() );}

        PagerParameters pagerParams = new PagerParameters(pageSize, pageNumber).normalizeAndValidate(response);

        return service.findByMarker(type, markerType, value, subTree, includeEntity, pagerParams.getPageSize(), pagerParams.getPageIndex(), initializationStrategy);

    }

import eu.etaxonomy.cdm.api.service.dto.FindByMarkerDTO;

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

     * @return all {@link IdentifiableEntity identifiable entities} which have the according

     * identifier attached

    public <S extends T> Pager<FindByIdentifierDTO<S>> findByIdentifier(

            Class<S> clazz, String identifier, DefinedTerm identifierType,

            MatchMode matchmode, boolean includeCdmEntity,

            Integer pageSize, Integer pageNumber, List<String> propertyPaths);

    /**

     * Returns a Pager for {@link FindByMarkerDTO DTOs} that hold the marker including type, title and uuid

     * and the according CDM object information (uuid, title and the object itself (optional)).

     *

     * @param clazz

     * @param markerType

     * @param markerValue

     * @param includeEntity

     * @param pageSize

     * @param pageNumber

     * @param propertyPaths

     * @return all {@link IdentifiableEntity identifiable entities} which have the according

     * marker with the given flag value attached

     */

    public <S extends T> Pager<FindByMarkerDTO<S>> findByMarker(

            Class<S> clazz, MarkerType markerType, Boolean markerValue,

            boolean includeEntity, Integer pageSize,

            Integer pageNumber, List<String> propertyPaths);

import eu.etaxonomy.cdm.api.service.dto.FindByMarkerDTO;

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

    /**

     * @param clazz the optional {@link TaxonBase} subclass

     * @param identifier the identifier string

     * @param identifierType the identifier type

     * @param subtreeFilter filter on a classification subtree (TaxonNode)

     * @param matchmode the match mode for the identifier string

     * @param includeEntity should the taxon as an object be included in the result

     * @param pageSize page size

     * @param pageNumber page number

     * @param propertyPaths property path for initializing the returned taxon object (requires includeEntity=true)

     * @return the resulting {@link FindByIdentifierDTO} pager

     * @see IIdentifiableEntityService#findByIdentifier(Class, String, DefinedTerm, MatchMode, boolean, Integer, Integer, List)

     */

    /**

     * Returns a pager for {@link FindByMarkerDTO DTOs} that hold the marker including type, title and uuid

     * and the according {@link TaxonBase} information (uuid, title and the taxon object itself (optional)).

     *

     * @param clazz The optional {@link TaxonBase} subclass

     * @param markerType the obligatory marker type, if not given, the results will always be empty

     * @param markerValue the optional

     * @param subtreeFilter filter on a classification subtree (TaxonNode)

     * @param includeEntity should the taxon as an object be included in the result

     * @param pageSize page size

     * @param pageNumber page number

     * @param propertyPaths property path for initializing the returned taxon object (requires includeEntity=true)

     * @return the resulting {@link FindByMarkerDTO} pager

     * @see IIdentifiableEntityService#findByMarker(Class, MarkerType, Boolean, boolean, Integer, Integer, List)

     */

    public <S extends TaxonBase> Pager<FindByMarkerDTO<S>> findByMarker(

            Class<S> clazz, MarkerType markerType, Boolean markerValue,

            TaxonNode subtreeFilter, boolean includeEntity, Integer pageSize,

            Integer pageNumber, List<String> propertyPaths);

import eu.etaxonomy.cdm.api.service.dto.FindByMarkerDTO;

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

    @Override

    @Transactional(readOnly = true)

    public <S extends T> Pager<FindByMarkerDTO<S>> findByMarker(

            Class<S> clazz, MarkerType markerType, Boolean markerValue,

            boolean includeEntity, Integer pageSize,

            Integer pageNumber, List<String> propertyPaths) {

        Long numberOfResults = dao.countByMarker(clazz, markerType, markerValue);

        List<Object[]> daoResults = new ArrayList<>();

        if(numberOfResults > 0) { // no point checking again

            daoResults = dao.findByMarker(clazz, markerType, markerValue, includeEntity,

                    pageSize, pageNumber, propertyPaths);

        }

        List<FindByMarkerDTO<S>> result = new ArrayList<>();

        for (Object[] daoObj : daoResults){

            if (includeEntity){

                result.add(new FindByMarkerDTO<S>((MarkerType)daoObj[0], (Boolean)daoObj[1], (S)daoObj[2]));

            }else{

                result.add(new FindByMarkerDTO<S>((MarkerType)daoObj[0], (Boolean)daoObj[1], (UUID)daoObj[2], (String)daoObj[3]));

            }

        }

        return new DefaultPagerImpl<FindByMarkerDTO<S>>(pageNumber, numberOfResults, pageSize, result);

    }

import eu.etaxonomy.cdm.api.service.dto.FindByMarkerDTO;

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

    @Transactional(readOnly = true)

    public <S extends TaxonBase> Pager<FindByMarkerDTO<S>> findByMarker(

            Class<S> clazz, MarkerType markerType, Boolean markerValue,

            TaxonNode subtreeFilter, boolean includeEntity, Integer pageSize,

            Integer pageNumber, List<String> propertyPaths) {

        if (subtreeFilter == null){

            return super.findByMarker (clazz, markerType, markerValue, includeEntity, pageSize, pageNumber, propertyPaths);

        }

        Long numberOfResults = dao.countByMarker(clazz, markerType, markerValue, subtreeFilter);

        List<Object[]> daoResults = new ArrayList<Object[]>();

        if(numberOfResults > 0) { // no point checking again

            daoResults = dao.findByMarker(clazz, markerType, markerValue, subtreeFilter,

                    includeEntity, pageSize, pageNumber, propertyPaths);

        }

        List<FindByMarkerDTO<S>> result = new ArrayList<>();

        for (Object[] daoObj : daoResults){

            if (includeEntity){

                result.add(new FindByMarkerDTO<S>((MarkerType)daoObj[0], (Boolean)daoObj[1], (S)daoObj[2]));

            }else{

                result.add(new FindByMarkerDTO<S>((MarkerType)daoObj[0], (Boolean)daoObj[1], (UUID)daoObj[2], (String)daoObj[3]));

            }

        }

        return new DefaultPagerImpl<FindByMarkerDTO<S>>(pageNumber, numberOfResults, pageSize, result);

    }

    @Override

// $Id$

/**

* Copyright (C) 2014 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.dto;

import java.util.UUID;

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

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

/**

 * DTO for IdentifiableEntities matching a certain marker.

 *

 * @author a.mueller

 * @date 2016-09-16

 *

 */

public class FindByMarkerDTO<T extends IdentifiableEntity<?>> {

	public class Marker{

		UUID typeUuid;

		String typeLabel;

		Boolean flag;

		public Marker(MarkerType markerType, Boolean flag) {

			this.typeUuid = markerType.getUuid();

			this.typeLabel = markerType.getTitleCache();

			this.flag = flag;

		}

		public UUID getTypeUuid() {return typeUuid;}

		public String getTypeLabel() {return typeLabel;}

		public Boolean getFlag() {return flag;}

	}

	public class CdmEntity{

		UUID cdmUuid;

		String titleCache;

		T entity;

		public CdmEntity(UUID cdmUuid, String titleCache, T entity) {

			this.cdmUuid = cdmUuid;

			this.titleCache = titleCache;

			this.entity = entity;

		}

		public UUID getCdmUuid() {return cdmUuid;}

		public String getTitleCache() {return titleCache;}

		public T getEntity() {return entity;}

	}

	private Marker marker;

	private CdmEntity cdmEntity;

	public FindByMarkerDTO(MarkerType markerType, Boolean flag, T entity){

		this.marker = new Marker(markerType, flag);

		this.cdmEntity = new CdmEntity(entity.getUuid(), entity.getTitleCache(), entity);

	}

	public FindByMarkerDTO(MarkerType markerType, Boolean flag, UUID entityUuid, String titleCache){

		this.marker = new Marker(markerType, flag);

		this.cdmEntity = new CdmEntity(entityUuid, titleCache, null);

	}

	public Marker getMarker() {

		return marker;

	}

	public CdmEntity getCdmEntity() {

		return cdmEntity;

	}

    /**

     * {@inheritDoc}

     */

    @Override

    public String toString() {

        return "(" + marker.typeLabel + "; "  + cdmEntity.getTitleCache() + "; " + cdmEntity.cdmUuid +  ")";

    }

}

    private static final long serialVersionUID = -1869488482336439083L;

    protected static Integer MAX_PAGE_LABELS = 3;

import eu.etaxonomy.cdm.api.service.dto.FindByMarkerDTO;

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

	@DataSet(value="IdentifiableServiceBaseTest.testFindByIdentifierOrMarker.xml")

	public final void testFindByIdentifier(){

	@DataSet(value="IdentifiableServiceBaseTest.testFindByIdentifierOrMarker.xml")

	public final void testFindByIdentifierClassification(){

    @Test

    @DataSet(value="IdentifiableServiceBaseTest.testFindByIdentifierOrMarker.xml")

    public final void testFindByMarker(){

        //classification Filter

        Classification classification = classificationService.find(5000);

        TaxonNode rootNode = classification.getRootNode();

        Boolean markerValue = true;

        UUID uuidMarkerTypeCompleted = MarkerType.uuidComplete;

        UUID uuidMarkerTypeDoubtful = UUID.fromString("b51325c8-05fe-421a-832b-d86fc249ef6e");

        MarkerType markerType1 = (MarkerType)termService.find(uuidMarkerTypeCompleted);

        MarkerType noMarkerType = null;

        MarkerType markerType2 = (MarkerType)termService.find(uuidMarkerTypeDoubtful);

        Assert.assertNotNull(markerType2);

        MarkerType markerType = markerType1;

        Pager<FindByMarkerDTO<Taxon>> taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue,

                rootNode, true, null, null, null);

        Assert.assertEquals("Result size for 'marker1=true' should be 1", Long.valueOf(1), taxonPager.getCount());

        Assert.assertEquals("Result size for 'marker1=true' should be 1", 1, taxonPager.getRecords().size());

        FindByMarkerDTO<Taxon> dto = taxonPager.getRecords().get(0);

        FindByMarkerDTO<Taxon>.Marker marker = dto.getMarker();

        Assert.assertTrue("Flag must be true", marker.getFlag());

        Assert.assertEquals("Flag must be true", uuidMarkerTypeCompleted, marker.getTypeUuid());

        Assert.assertNotNull("the CDM entity in the dto must not be empty if includeEntity=true", dto.getCdmEntity().getEntity());

        Assert.assertEquals(5000, dto.getCdmEntity().getEntity().getId());

        markerValue = false;

        taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue, rootNode, false, null, null, null);

        Assert.assertEquals("Result size for 'marker1=false' should be 0", Long.valueOf(0), taxonPager.getCount());

        markerValue = true;

        markerType = noMarkerType;

        taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue, rootNode, false, null, null, null);

        Assert.assertEquals("Result size for not existing marker type should be 0", Long.valueOf(0), taxonPager.getCount());

        markerType = markerType2;

        taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue, rootNode, false, null, null, null);

        Assert.assertEquals("Result size for markerType2 should be 0", Long.valueOf(0), taxonPager.getCount());

        rootNode = null;

        markerType = markerType1;

        taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue, rootNode, false, null, null, null);

        Assert.assertEquals("Result size for no subtree should be 2", Long.valueOf(2), taxonPager.getCount());

        Pager<FindByMarkerDTO<TaxonBase>> taxonBasePager = taxonService.findByMarker(TaxonBase.class, markerType, markerValue, rootNode, false, null, null, null);

        Assert.assertEquals("Result size for taxa and synonyms without subtree filter with flag = true should be 3", Long.valueOf(3), taxonBasePager.getCount());

        markerValue = null;

        taxonBasePager = taxonService.findByMarker(TaxonBase.class, markerType, markerValue, rootNode, false, null, null, null);

        Assert.assertEquals("Result size for taxa and synonyms without subtree filter with any flag value should be 4", Long.valueOf(4), taxonBasePager.getCount());

        markerValue = true;

        Pager<FindByMarkerDTO<TaxonNameBase>> namePager = nameService.findByMarker(TaxonNameBase.class, markerType, markerValue, false, null, null, null);

        Assert.assertEquals("Result size for names with flag = true should be 1", Long.valueOf(1), namePager.getCount());

    }

<?xml version='1.0' encoding='UTF-8'?>

<dataset>

  <TAXONBASE DTYPE="Taxon" ID="5000" CREATED="2015-01-07 21:54:20.0" UUID="888cded1-cadc-48de-8629-e32927919879" UPDATED="2015-01-07 21:54:20.76" LSID_AUTHORITY="[null]" LSID_LSID="[null]" LSID_NAMESPACE="[null]" LSID_OBJECT="[null]" LSID_REVISION="[null]" PROTECTEDTITLECACHE="false" TITLECACHE="Abies alba sec. ???" APPENDEDPHRASE="[null]" DOUBTFUL="false" PUBLISH="true" USENAMECACHE="false" EXCLUDED="false" TAXONSTATUSUNKNOWN="false" TAXONOMICCHILDRENCOUNT="0" UNPLACED="false" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]" NAME_ID="5000" SEC_ID="[null]" TAXONOMICPARENTCACHE_ID="[null]"/>

  <TAXONBASE DTYPE="Taxon" ID="5001" CREATED="2015-01-07 21:54:20.0" UUID="00f3ab3d-b8a7-4a28-95c1-e654f548bf7e" UPDATED="2015-01-07 21:54:20.76" LSID_AUTHORITY="[null]" LSID_LSID="[null]" LSID_NAMESPACE="[null]" LSID_OBJECT="[null]" LSID_REVISION="[null]" PROTECTEDTITLECACHE="true" TITLECACHE="Cached taxon" APPENDEDPHRASE="[null]" DOUBTFUL="false" PUBLISH="true" USENAMECACHE="false" EXCLUDED="false" TAXONSTATUSUNKNOWN="false" TAXONOMICCHILDRENCOUNT="0" UNPLACED="false" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]" NAME_ID="[null]" SEC_ID="[null]" TAXONOMICPARENTCACHE_ID="[null]"/>

  <TAXONBASE DTYPE="Synonym" ID="5002" CREATED="2015-01-22 01:56:08.0" UUID="b92f77bc-c61d-44e1-b44e-f3f4ba4e6ade" UPDATED="2015-01-22 01:56:08.134" LSID_AUTHORITY="[null]" LSID_LSID="[null]" LSID_NAMESPACE="[null]" LSID_OBJECT="[null]" LSID_REVISION="[null]" PROTECTEDTITLECACHE="false" TITLECACHE="Synonym#0&lt;b92f77bc-c61d-44e1-b44e-f3f4ba4e6ade&gt;" APPENDEDPHRASE="[null]" DOUBTFUL="false" PUBLISH="true" USENAMECACHE="false" EXCLUDED="[null]" TAXONSTATUSUNKNOWN="[null]" TAXONOMICCHILDRENCOUNT="[null]" UNPLACED="[null]" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]" NAME_ID="[null]" SEC_ID="[null]" TAXONOMICPARENTCACHE_ID="[null]"/>

  <TAXONBASE DTYPE="Synonym" ID="5003" CREATED="2015-01-22 01:56:08.0" UUID="d9f9a849-d75b-4a37-8434-df191ea083c3" UPDATED="2015-01-22 01:56:08.134" LSID_AUTHORITY="[null]" LSID_LSID="[null]" LSID_NAMESPACE="[null]" LSID_OBJECT="[null]" LSID_REVISION="[null]" PROTECTEDTITLECACHE="false" TITLECACHE="Synonym#0&lt;b92f77bc-c61d-44e1-b44e-f3f4ba4e6ade&gt;" APPENDEDPHRASE="[null]" DOUBTFUL="false" PUBLISH="true" USENAMECACHE="false" EXCLUDED="[null]" TAXONSTATUSUNKNOWN="[null]" TAXONOMICCHILDRENCOUNT="[null]" UNPLACED="[null]" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]" NAME_ID="[null]" SEC_ID="[null]" TAXONOMICPARENTCACHE_ID="[null]"/>

  <TAXONNAMEBASE DTYPE="BotanicalName" ID="5000" CREATED="2015-01-07 21:54:20.0" UUID="14697dc1-7786-4c21-b56d-1e6601327417" UPDATED="2015-01-07 21:54:20.76" LSID_AUTHORITY="[null]" LSID_LSID="[null]" LSID_NAMESPACE="[null]" LSID_OBJECT="[null]" LSID_REVISION="[null]" PROTECTEDTITLECACHE="true" TITLECACHE="Abies alba" APPENDEDPHRASE="[null]" FULLTITLECACHE="" NOMENCLATURALMICROREFERENCE="[null]" PARSINGPROBLEM="0" PROBLEMENDS="-1" PROBLEMSTARTS="-1" PROTECTEDFULLTITLECACHE="false" AUTHORSHIPCACHE="" BINOMHYBRID="false" GENUSORUNINOMIAL="[null]" HYBRIDFORMULA="false" INFRAGENERICEPITHET="[null]" INFRASPECIFICEPITHET="[null]" MONOMHYBRID="false" NAMECACHE="" PROTECTEDAUTHORSHIPCACHE="false" PROTECTEDNAMECACHE="false" SPECIFICEPITHET="[null]" TRINOMHYBRID="false" NAMEAPPROBATION="[null]" SUBGENUSAUTHORSHIP="[null]" ANAMORPHIC="false" CULTIVARNAME="[null]" ACRONYM="[null]" BREED="[null]" ORIGINALPUBLICATIONYEAR="[null]" PUBLICATIONYEAR="[null]" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]" HOMOTYPICALGROUP_ID="5000" NOMENCLATURALREFERENCE_ID="[null]" RANK_ID="765" BASIONYMAUTHORSHIP_ID="[null]" COMBINATIONAUTHORSHIP_ID="[null]" EXBASIONYMAUTHORSHIP_ID="[null]" EXCOMBINATIONAUTHORSHIP_ID="[null]"/>

  <IDENTIFIER ID="5000" UUID="f27ece3f-a94a-4748-b9a6-dc6ca3e9b589" CREATED="2015-01-07 21:54:20.0" IDENTIFIER="ext-name12" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]" TYPE_ID="2062"/>

  <IDENTIFIER ID="5001" UUID="9f42987a-0cc3-49f8-a0df-83fafc1247f8" CREATED="2015-01-07 21:54:20.0" IDENTIFIER="ext-1234" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]" TYPE_ID="2061"/>

  <IDENTIFIER ID="5002" UUID="433ad739-b62c-451f-bde9-f0c7ffa3d829" CREATED="2015-01-07 21:54:20.0" IDENTIFIER="ext-cache1" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]" TYPE_ID="2062"/>

  <IDENTIFIER ID="5003" UUID="b08d005f-a1f1-41bb-a8bc-448bde2569dc" CREATED="2015-01-07 21:54:20.0" IDENTIFIER="ext-syn1" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]" TYPE_ID="2062"/>

  <IDENTIFIER ID="5004" UUID="2d1fb00b-51fa-441a-81e7-79577bef4e2d" CREATED="2015-01-07 21:54:20.0" IDENTIFIER="ext-syn2" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]" TYPE_ID="2062"/>

  <MARKER ID="5000" UUID="2aecee45-4930-4f16-bdc6-8e41d657b74f" CREATED="2016-09-16 21:54:20.0" FLAG="true" MARKERTYPE_ID="890"/>

  <MARKER ID="5001" UUID="5cf0d264-48f3-4ad1-8294-6649dba4d259" CREATED="2016-09-16 21:54:20.0" FLAG="true" MARKERTYPE_ID="890"/>

  <MARKER ID="5002" UUID="f7064d00-3d29-45f1-8188-c132cb701b7b" CREATED="2016-09-16 21:54:20.0" FLAG="true" MARKERTYPE_ID="890"/>

  <MARKER ID="5003" UUID="ae683ce1-cbef-425e-9b0b-6bfffcf912d1" CREATED="2016-09-16 21:54:20.0" FLAG="true" MARKERTYPE_ID="890"/>

  <MARKER ID="5004" UUID="dc011c6c-345c-4042-9cca-ee22af29ffea" CREATED="2016-09-16 21:54:20.0" FLAG="false" MARKERTYPE_ID="890"/>

  <TAXONBASE_IDENTIFIER TAXONBASE_ID="5000" IDENTIFIERS_ID="5001" SORTINDEX="0"/>

  <TAXONBASE_IDENTIFIER TAXONBASE_ID="5001" IDENTIFIERS_ID="5002" SORTINDEX="0"/>

  <TAXONBASE_IDENTIFIER TAXONBASE_ID="5002" IDENTIFIERS_ID="5003" SORTINDEX="0"/>

  <TAXONBASE_IDENTIFIER TAXONBASE_ID="5003" IDENTIFIERS_ID="5004" SORTINDEX="0"/>

  <TAXONBASE_MARKER TAXONBASE_ID="5000" MARKERS_ID="5001"/>

  <TAXONBASE_MARKER TAXONBASE_ID="5001" MARKERS_ID="5002"/>

  <TAXONBASE_MARKER TAXONBASE_ID="5002" MARKERS_ID="5003"/>

  <TAXONBASE_MARKER TAXONBASE_ID="5003" MARKERS_ID="5004"/>

  <TAXONNAMEBASE_IDENTIFIER TAXONNAMEBASE_ID="5000" IDENTIFIERS_ID="5000" SORTINDEX="0"/>

  <TAXONNAMEBASE_MARKER TAXONNAMEBASE_ID="5000" MARKERS_ID="5000"/>

  <CLASSIFICATION ID="5000" CREATED="2015-01-07 21:54:20.0" UUID="277ac532-b670-4a1b-927a-61063ecfeb5b" UPDATED="2015-01-07 21:54:20.76" LSID_AUTHORITY="[null]" LSID_LSID="[null]" LSID_NAMESPACE="[null]" LSID_OBJECT="[null]" LSID_REVISION="[null]" PROTECTEDTITLECACHE="true" TITLECACHE="My classification" MICROREFERENCE="[null]" TIMEPERIOD_START="[null]" TIMEPERIOD_FREETEXT="[null]" TIMEPERIOD_END="[null]" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]" NAME_ID="[null]" REFERENCE_ID="[null]" ROOTNODE_ID="5000"/>

  <TAXONNODE ID="5000" CREATED="2015-01-07 21:54:20.0" UUID="cf00cde1-efc8-4d3b-8c5c-71c3d6e692d9" UPDATED="2015-01-07 21:54:20.76" SORTINDEX="-1" TREEINDEX="#t5000#5000#" COUNTCHILDREN="1" MICROREFERENCEFORPARENTCHILDRELATION="[null]" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]" CLASSIFICATION_ID="5000" PARENT_ID="[null]" REFERENCEFORPARENTCHILDRELATION_ID="[null]" SYNONYMTOBEUSED_ID="[null]" TAXON_ID="[null]"/>

  <TAXONNODE ID="5001" CREATED="2015-01-07 21:54:20.0" UUID="73d8ece1-c511-48b7-9a1f-f6fab3149bf1" UPDATED="2015-01-07 21:54:20.76" SORTINDEX="0" TREEINDEX="#t5000#5000#5001#" COUNTCHILDREN="0" MICROREFERENCEFORPARENTCHILDRELATION="[null]" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]" CLASSIFICATION_ID="5000" PARENT_ID="5000" REFERENCEFORPARENTCHILDRELATION_ID="[null]" SYNONYMTOBEUSED_ID="[null]" TAXON_ID="5000"/>

  <HOMOTYPICALGROUP ID="5000" CREATED="2015-01-07 21:54:20.0" UUID="599e8459-4302-47d5-aa0b-9b69a0f329e4" UPDATED="2015-01-07 21:54:20.76" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]"/>

  <SYNONYMRELATIONSHIP ID="5000" CREATED="2015-01-22 01:56:08.0" UUID="946836b6-7b57-4d40-8abf-33f3ea0e1b4d" UPDATED="2015-01-22 01:56:08.134" CITATIONMICROREFERENCE="[null]" ORIGINALNAMESTRING="[null]" DOUBTFUL="false" PARTIAL="false" PROPARTE="false" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]" CITATION_ID="[null]" RELATEDFROM_ID="5002" RELATEDTO_ID="5000" TYPE_ID="847"/>

  <SYNONYMRELATIONSHIP ID="5001" CREATED="2015-01-22 01:56:08.0" UUID="38824018-4a6d-42af-8c97-8a10f94999cd" UPDATED="2015-01-22 01:56:08.134" CITATIONMICROREFERENCE="[null]" ORIGINALNAMESTRING="[null]" DOUBTFUL="false" PARTIAL="false" PROPARTE="false" CREATEDBY_ID="[null]" UPDATEDBY_ID="[null]" CITATION_ID="[null]" RELATEDFROM_ID="5003" RELATEDTO_ID="5001" TYPE_ID="847"/>

</dataset>