EDIT

/**

* Copyright (C) 2009 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 java.io.IOException;

import java.util.Collection;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.lucene.index.CorruptIndexException;

import org.springframework.transaction.annotation.Transactional;

import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;

import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.api.service.pager.Pager;

import eu.etaxonomy.cdm.api.service.search.LuceneParseException;

import eu.etaxonomy.cdm.api.service.search.SearchResult;

import eu.etaxonomy.cdm.api.util.TaxonRelationshipEdge;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;

import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;

import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;

import eu.etaxonomy.cdm.persistence.query.OrderHint;

/**

 * @author a.babadshanjan

 * @since 01.09.2008

 */

public interface IOccurrenceService

        extends IIdentifiableEntityService<SpecimenOrObservationBase> {

    /**

     * Returns a paged list of occurrences that have been determined to belong

     * to the taxon concept determinedAs, optionally restricted to objects

     * belonging to a class that that extends SpecimenOrObservationBase. This

     * will also consider specimens that are determined as a taxon concept

     * belonging to the synonymy of the given taxon concept.

     * <p>

     * In contrast to {@link #listByAnyAssociation(Class, Taxon, List)} this

     * method only takes SpecimenOrObservationBase instances into account which

     * are actually determined as the taxon specified by

     * <code>determinedAs</code>.

     *

     * @param type

     *            The type of entities to return (can be null to count all

     *            entities of type <T>)

     * @param determinedAs

     *            the taxon concept that the occurrences have been determined to

     *            belong to

     * @param pageSize

     *            The maximum number of objects returned (can be null for all

     *            matching objects)

     * @param pageNumber

     *            The offset (in pageSize chunks) from the start of the result

     *            set (0 - based, can be null, equivalent of starting at the

     *            beginning of the recordset)

     * @param orderHints

     *            Supports path like <code>orderHints.propertyNames</code> which

     *            include *-to-one properties like createdBy.username or

     *            authorTeam.persistentTitleCache

     * @param propertyPaths

     *            properties to be initialized

     * @return

     */

    public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * Returns a paged list of occurrences that have been determined to belong

     * to the taxon name determinedAs, optionally restricted to objects

     * belonging to a class that that extends SpecimenOrObservationBase.

     * <p>

     * In contrast to {@link #listByAnyAssociation(Class, Taxon, List)} this

     * method only takes SpecimenOrObservationBase instances into account which

     * are actually determined as the taxon specified by

     * <code>determinedAs</code>.

     *

     * @param type

     *            The type of entities to return (can be null to count all

     *            entities of type <T>)

     * @param determinedAs

     *            the taxon name that the occurrences have been determined to

     *            belong to

     * @param pageSize

     *            The maximum number of objects returned (can be null for all

     *            matching objects)

     * @param pageNumber

     *            The offset (in pageSize chunks) from the start of the result

     *            set (0 - based, can be null, equivalent of starting at the

     *            beginning of the recordset)

     * @param orderHints

     *            Supports path like <code>orderHints.propertyNames</code> which

     *            include *-to-one properties like createdBy.username or

     *            authorTeam.persistentTitleCache

     * @param propertyPaths

     *            properties to be initialized

     * @return

     */

    public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonName determinedAs, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * Returns a List of Media that are associated with a given occurence

     *

     * @param occurence the occurence associated with these media

     * @param pageSize The maximum number of media returned (can be null for all related media)

     * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)

     * @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}

     * @return a Pager of media instances

     */

    public Pager<Media> getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths);

    /**

     * Returns all media attached to this occurence and its children. Also takes

     * {@link MediaSpecimen} and molecular images into account.

     *

     * @param occurence the occurence and its children from which the media to get

     * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)

     * @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}

     * @return a Pager of media instances

     */

    public Pager<Media> getMediaInHierarchy(SpecimenOrObservationBase<?> rootOccurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths);

    /**

     * Returns a count of determinations that have been made for a given occurence and for a given taxon concept

     *

     * @param occurence the occurence associated with these determinations (can be null for all occurrences)

     * @param taxonbase the taxon concept associated with these determinations (can be null for all taxon concepts)

     * @return a count of determination events

     */

    public long countDeterminations(SpecimenOrObservationBase occurence,TaxonBase taxonbase);

    /**

     * Returns a List of determinations that have been made for a given occurence

     *

     * @param occurence the occurence associated with these determinations (can be null for all occurrences)

     * @param taxonbase the taxon concept associated with these determinations (can be null for all taxon concepts)

     * @param pageSize The maximum number of determinations returned (can be null for all related determinations)

     * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)

     * @return a Pager of determination instances

     */

    public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonBase, Integer pageSize, Integer pageNumber, List<String> propertyPaths);

    /**

     * Returns a list of derivation events that have involved creating new DerivedUnits from this occurence

     *

     * @param occurence the occurence that was a source of these derivation events

     * @param pageSize The maximum number of derivation events returned (can be null for all related derivation events)

     * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)

     * @return a Pager of derivation events

     */

    public Pager<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths);

    /**

     * Returns a Paged List of SpecimenOrObservationBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)

     *

     * @param clazz filter the results by class (or pass null to return all SpecimenOrObservationBase instances)

     * @param queryString

     * @param pageSize The maximum number of occurrences returned (can be null for all matching occurrences)

     * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)

     * @param orderHints

     *            Supports path like <code>orderHints.propertyNames</code> which

     *            include *-to-one properties like createdBy.username or

     *            authorTeam.persistentTitleCache

     * @param propertyPaths properties to be initialized

     * @return a Pager SpecimenOrObservationBase instances

     * @see <a href="http://lucene.apache.org/java/2_4_0/queryparsersyntax.html">Apache Lucene - Query Parser Syntax</a>

     */

    @Override

    public Pager<SpecimenOrObservationBase> search(Class<? extends SpecimenOrObservationBase> clazz, String query, Integer pageSize,Integer pageNumber, List<OrderHint> orderHints,List<String> propertyPaths);

    /**

     * Retrieves the {@link UUID} and the string representation (title cache) of all

     * {@link FieldUnit}s found in the data base.

     * @return a list of {@link UuidAndTitleCache}

     */

    public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache();

    /**

     * Retrieves the {@link UUID} and the string representation (title cache) of all

     * {@link DerivedUnit}s found in the data base.

     * @return a list of {@link UuidAndTitleCache}

     */

    public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache(Integer limit, String pattern);

    public DerivedUnitFacade getDerivedUnitFacade(DerivedUnit derivedUnit, List<String> propertyPaths) throws DerivedUnitFacadeNotSupportedException;

    public List<DerivedUnitFacade> listDerivedUnitFacades(DescriptionBase description, List<String> propertyPaths);

    /**

     * Lists all instances of {@link SpecimenOrObservationBase} which are

     * associated with the <code>taxon</code> specified as parameter.

     * SpecimenOrObservationBase instances can be associated to taxa in multiple

     * ways, all these possible relations are taken into account:

     * <ul>

     * <li>The {@link IndividualsAssociation} elements in a

     * {@link TaxonDescription} contain {@link DerivedUnit}s</li>

     * <li>{@link SpecimenTypeDesignation}s may be associated with any

     * {@link HomotypicalGroup} related to the specific {@link Taxon}.</li>

     * <li>A {@link Taxon} may be referenced by the {@link DeterminationEvent}

     * of the {@link SpecimenOrObservationBase}</li>

     * </ul>

     * Further more there also can be taxa which are associated with the taxon

     * in question (parameter associatedTaxon) by {@link TaxonRelationship}s. If

     * the parameter <code>includeRelationships</code> is containing elements,

     * these according {@TaxonRelationshipType}s and

     * directional information will be used to collect further

     * {@link SpecimenOrObservationBase} instances found this way.

     *

     * @param <T>

     * @param type

     * @param associatedTaxon

     * @param Set<TaxonRelationshipVector> includeRelationships. TaxonRelationships will not be taken into account if this is <code>NULL</code>.

     * @param maxDepth TODO

     * @param pageSize

     * @param pageNumber

     * @param orderHints

     * @param propertyPaths

     * @return

     */

    public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,

            Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * The method will search for specimen associated with the taxon nodes.<br>

     * It will search for 3 possible association types: <br>

     * - via IndividualAssociations of the taxon<br>

     *  - via TypeDesignations of the taxon name<br>

     *  - via Determinations of the taxon or taxon name<br>

     * <br>

     * more are covered in

     * {@link IOccurrenceService#findByTitle(IIdentifiableEntityServiceConfigurator)}

     * @param taxonNodeUuids

     *            a list of {@link UUID}s of the taxon nodes

     * @param limit

     * @param start

     * @return a collection of {@link SpecimenNodeWrapper} containing the

     *         {@link TaxonNode} and the corresponding {@link UuidAndTitleCache}

     *         object for the specimen found for this taxon node

     */

    public Collection<SpecimenNodeWrapper> listUuidAndTitleCacheByAssociatedTaxon(List<UUID> taxonNodeUuids,

            Integer limit, Integer start);

    /**

     * @deprecated replace by {@link #listRootUnitsByAssociatedTaxon(Class, Taxon, List, List)}

     */

    @Deprecated

    public Collection<FieldUnit> listFieldUnitsByAssociatedTaxon(Taxon associatedTaxon, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * See {@link #listByAssociatedTaxon(Class, Set, Taxon, Integer, Integer, Integer, List, List)}

     *

     * @param type

     *  Restriction to subtype of <code>SpecimenOrObservationBase</code>, can be NULL.

     * @param includeRelationships

     * @param associatedTaxon

     * @param maxDepth

     * @param pageSize

     * @param pageNumber

     * @param orderHints

     * @param propertyPaths

     * @return a Pager

     */

    public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,

            Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * Retrieves all {@link FieldUnit}s for the {@link SpecimenOrObservationBase} with the given {@link UUID}.<br>

     * @param specimenUuid the UUID of the specimen

     * @param propertyPaths the property path

     * @return either a collection of FieldUnits this specimen was derived from, the FieldUnit itself

     * if this was a FieldUnit or an empty collection if no FieldUnits were found

     */

    public Collection<FieldUnit> findFieldUnits(UUID specimenUuid, List<String> propertyPaths);

    /**

     * Retrieves top most originals for a {@link SpecimenOrObservationBase} in the derivation graph by recursively

     * walking all {@link DerivationEvent}s.

     * In most cases item in the returned collection will be {@link FieldUnit FieldUnits} but also DerivedUnits are possible, in

     * cases where no FieledUnit exists.

     *

     * @param specimenUuid the UUID of the specimen

     * @param propertyPaths the property path

     * @return either a collection of root units

     */

    public Collection<SpecimenOrObservationBase> findRootUnits(UUID specimenUuid, List<String> propertyPaths);

    /**

     * @param clazz

     * @param queryString

     * @param languages

     * @param highlightFragments

     * @param pageSize

     * @param pageNumber

     * @param orderHints

     * @param propertyPaths

     * @return

     * @throws CorruptIndexException

     * @throws IOException

     * @throws ParseException

     */

    Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(Class<? extends SpecimenOrObservationBase> clazz,

            String queryString, RectangleDTO boundingBox, List<Language> languages, boolean highlightFragments,

            Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths)

            throws IOException, LuceneParseException;

    /**

     * See {@link #listByAssociatedTaxon(Class, Set, String, Integer, Integer, Integer, List, List)}

     *

     * @param type

     * @param includeRelationships

     * @param associatedTaxon

     * @param maxDepth

     * @param pageSize

     * @param pageNumber

     * @param orderHints

     * @param propertyPaths

     * @return a Pager

     */

    public <T extends SpecimenOrObservationBase> Pager<T>  pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,

            String taxonUUID, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * Moves the given {@link Sequence} from one {@link DnaSample} to another

     * @param from the DnaSample from which the sequence will be removed

     * @param to the DnaSample which to which the sequence will be added

     * @param sequence the Sequence to move

     * @return <code>true</code> if successfully moved, <code>false</code> otherwise

     */

    public UpdateResult moveSequence(DnaSample from, DnaSample to, Sequence sequence);

    /**

     * @param fromUuid

     * @param toUuid

     * @param sequenceUuid

     * @return

     */

    public UpdateResult moveSequence(UUID fromUuid, UUID toUuid, UUID sequenceUuid);

    /**

     * Moves the given {@link DerivedUnit} from one {@link SpecimenOrObservationBase} to another.

     * @param from the SpecimenOrObservationBase from which the DerivedUnit will be removed

     * @param to the SpecimenOrObservationBase to which the DerivedUnit will be added

     * @param derivate the DerivedUnit to move

     * @return <code>true</code> if successfully moved, <code>false</code> otherwise

     */

    public UpdateResult moveDerivate(UUID specimenFromUuid, UUID specimenToUuid, UUID derivateUuid);

    /**

     * @param from

     * @param to

     * @param derivate

     * @return

     */

    public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate);

    /**

     * Assembles a {@link FieldUnitDTO} for the given field unit.<br>

     *

     * @param fieldUnit

     * @return a DTO with all the assembled information

     */

    public FieldUnitDTO assembleFieldUnitDTO(FieldUnit fieldUnit);

    /**

     * Assembles a {@link DerivedUnitDTO} for the given derived unit.

     * @param derivedUnit

     * @return a DTO with all the assembled information

     */

    public SpecimenOrObservationBaseDTO assembleDerivedUnitDTO(DerivedUnit derivedUnit);

    /**

     * Deletes the specified specimen according to the setting in the {@link SpecimenDeleteConfigurator}.<br>

     * @param specimen the specimen which shoul be deleted

     * @param config specifies options if and how the specimen should be deleted like e.g. including all

     * of its children

     * @return the {@link DeleteResult} which holds information about the outcome of this operation

     */

    public DeleteResult delete(SpecimenOrObservationBase<?> specimen, SpecimenDeleteConfigurator config);

    /**

     * Deletes the specified specimen belonging to the given {@link UUID}

     * according to the setting in the {@link SpecimenDeleteConfigurator}.

     *

     * @param specimen

     *            the specimen which shoul be deleted

     * @param config

     *            specifies options if and how the specimen should be deleted

     *            like e.g. including all of its children

     * @return the {@link DeleteResult} which holds information about the

     *         outcome of this operation

     */

    public DeleteResult delete(UUID specimenUuid, SpecimenDeleteConfigurator config);

    /**

     * Retrieves all {@link IndividualsAssociation} with the given specimen.<br>

     * @param specimen the specimen for which the associations are retrieved

     * @param limit

     * @param start

     * @param orderHints

     * @param propertyPaths

     * @return collection of all associations

     */

    public Collection<IndividualsAssociation> listIndividualsAssociations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * Retrieves all taxa linked via {@link IndividualsAssociation} with the given specimen.<br>

     * @param specimen the specimen which is linked to the taxa

     * @param limit

     * @param start

     * @param orderHints

     * @param propertyPaths

     * @return a collection of associated taxa

     */

    public Collection<TaxonBase<?>> listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen,

            Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

      * @see #listIndividualsAssociationTaxa(SpecimenOrObservationBase, Integer, Integer, List, List)

      */

    public Collection<TaxonBase<?>> listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen, boolean includeUnpublished,

            Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * Retrieves all associated taxa for the given specimen (via type designations, determination, individuals associations)

     * @param specimen

     * @param limit

     * @param start

     * @param orderHints

     * @param propertyPaths

     * @return

     */

    public Collection<TaxonBase<?>> listAssociatedTaxa(SpecimenOrObservationBase<?> specimen, boolean includeUnpublished,

            Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * @see #listAssociatedTaxa(SpecimenOrObservationBase, Integer, Integer, List, List)axa

     */

    public Collection<TaxonBase<?>> listAssociatedTaxa(SpecimenOrObservationBase<?> specimen,

            Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * Retrieves all taxa that the given specimen is determined as

     * @param specimen

     * @param limit

     * @param start

     * @param orderHints

     * @param propertyPaths

     * @return collection of all taxa the given specimen is determined as

     */

    public Collection<TaxonBase<?>> listDeterminedTaxa(SpecimenOrObservationBase<?> specimen, boolean includeUnpublished,

            Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * @see #listDeterminedTaxa(SpecimenOrObservationBase, Integer, Integer, List, List)

     */

    public Collection<TaxonBase<?>> listDeterminedTaxa(SpecimenOrObservationBase<?> specimen,

            Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * Retrieves all {@link DeterminationEvent}s which have the given specimen set as identified unit.

     * @param specimen

     * @param limit

     * @param start

     * @param orderHints

     * @param propertyPaths

     * @return collection of all determination events with the given specimen

     */

    public Collection<DeterminationEvent> listDeterminationEvents(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * Retrieves all taxa with a {@link SpecimenTypeDesignation} with the given specimen as a type specimen.

     * @param specimen the type specimen

     * @param specimen

     * @param limit

     * @param start

     * @param orderHints

     * @param propertyPaths

     * @return a collection of all taxa where the given specimen is the type specimen

     */

    public Collection<TaxonBase<?>> listTypeDesignationTaxa(DerivedUnit specimen,

            Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * @see #listTypeDesignationTaxa(DerivedUnit, Integer, Integer, List, List)a

     */

    public Collection<TaxonBase<?>> listTypeDesignationTaxa(DerivedUnit specimen, boolean includeUnpublished,

            Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * Retrieves all {@link SpecimenTypeDesignation}s which have the given specimens as a type specimen.

     * @param specimens the type specimens

     * @param limit

     * @param start

     * @param orderHints

     * @param propertyPaths

     * @return map of all designations with the given type specimens

     */

    public Map<DerivedUnit, Collection<SpecimenTypeDesignation>> listTypeDesignations(Collection<DerivedUnit> specimens, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * Retrieves all {@link SpecimenTypeDesignation}s which have the given specimen as a type specimen.

     * @param specimen the type specimen

     * @param limit

     * @param start

     * @param orderHints

     * @param propertyPaths

     * @return collection of all designations with the given type specimen

     */

    public Collection<SpecimenTypeDesignation> listTypeDesignations(DerivedUnit specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * Retrieves all {@link DescriptionBase}s that have the given specimen set as described specimen.

     * @param specimen the described specimen

     * @param limit

     * @param start

     * @param orderHints

     * @param propertyPaths

     * @return collection of all descriptions with the given described specimen

     */

    public Collection<DescriptionBase<?>> listDescriptionsWithDescriptionSpecimen(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * Gets all description elements that are used for describing the character

     * states of the given specimen

     *

     * @param specimenUuid

     *            the specimen {@link UUID} for which the character state description

     *            elements should be retrieved

     * @return a collection of all character state description elements for this

     *         specimen

     */

    public Collection<DescriptionElementBase> getCharacterDataForSpecimen(UUID specimenUuid);

    /**

     * Returns the most significant identifier for the given {@link DerivedUnit}.

     * @param derivedUnit the derived unit to check

     * @return the identifier string

     */

    public String getMostSignificantIdentifier(UUID derivedUnit);

    /**

     * Returns the number of specimens that match the given parameters

     * <br>

     * <b>NOTE - issue #6484:</b> the parameters {@link FindOccurrencesConfigurator#getAssignmentStatus()}

     * and {@link FindOccurrencesConfigurator#isRetrieveIndirectlyAssociatedSpecimens()} are not evaluated

     * in the count method

     * @param clazz the class to match

     * @param queryString the queryString to match

     * @param type the {@link SpecimenOrObservationType} to match

     * @param associatedTaxon the taxon these specimens are in any way associated to via

     * determination, type designations, individuals associations, etc.

     * @param matchmode determines how the query string should be matched

     * @param limit

     *            the maximum number of entities returned (can be null to return

     *            all entities)

     * @param start

     * @param orderHints

     *            Supports path like <code>orderHints.propertyNames</code> which

     *            include *-to-one properties like createdBy.username or

     *            authorTeam.persistentTitleCache

     * @return the number of found specimens

     */

    public long countOccurrences(IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config);

    /**

     * Return the all {@link SpecimenOrObservationBase}s of the complete

     * derivative hierarchy i.e. all parent and child derivatives and the given

     * specimen itself.

     *

     * @param specimen

     *            a specimen or observation

     * @return the derivative hierarchy as an unordered list of all specimens or observation

     */

    public List<SpecimenOrObservationBase<?>> getAllHierarchyDerivatives(SpecimenOrObservationBase<?> specimen);

    /**

     * Returns all child derivatives of the given specimen.

     * @param specimen a specimen or observation

     * @return an unordered list of all child derivatives

     */

    public List<DerivedUnit> getAllChildDerivatives(SpecimenOrObservationBase<?> specimen);

    /**

     * Returns all child derivatives of the given specimen.

     * @param specimen the UUID of a specimen or observation

     * @return an unordered list of all child derivatives

     */

    public List<DerivedUnit> getAllChildDerivatives(UUID specimenUuid);

    /**

     * Returns all {@link FieldUnit}s that are referencing this {@link GatheringEvent}

     * @param gatheringEventUuid the {@link UUID} of the gathering event

     * @return a list of field units referencing the gathering event

     */

    public List<FieldUnit> findFieldUnitsForGatheringEvent(UUID gatheringEventUuid);

    /**

     * Returns a list of {@link UuidAndTitleCache} for the specimens found with the

     * given configurator

     * @param config the configurator for the search

     * @return a list of UuidAndTitleCache object

     */

    @Transactional(readOnly = true)

    public Pager<UuidAndTitleCache<SpecimenOrObservationBase>> findByTitleUuidAndTitleCache(

            FindOccurrencesConfigurator config);

    /**

     * Returns a list of {@link DerivedUnitDTO} for the specimens found with the

     * given configurator

     * @param config the configurator for the search

     * @return a list of {@link DerivedUnitDTO} object

     */

    @Transactional(readOnly = true)

    public List<DerivedUnitDTO> findByTitleDerivedUnitDTO(

            FindOccurrencesConfigurator config);

    /**

     * Collects the <code>FieldUnits</code> which are at the root of the derivation event

     * graph in which the {@link DerivedUnit} with the specified <code>findByAccessionNumber</code>

     * is found.

     *

     * @deprecated method name unclear and thus replaced by {@link #findByGeneticAccessionNumber(String, List)}

     */

    @Deprecated

    SpecimenOrObservationBaseDTO findByAccessionNumber(String accessionNumberString, List<OrderHint> orderHints);

    /**

     * Collects the <code>FieldUnits</code> which are at the root of the derivation event

     * graph in which the {@link DnaSample} with the specified <code>accessionNumberString</code>

     * is found.

     */

    SpecimenOrObservationBaseDTO findByGeneticAccessionNumber(String dnaAccessionNumber, List<OrderHint> orderHints);

    /**

     * Recursively searches all {@link DerivationEvent}s to find all "originals" ({@link SpecimenOrObservationBase})

     * from which this DerivedUnit was derived until all FieldUnits are found.

     * <p>

     * <b>NOTE:</b> The recursive search still is a bit incomplete and may miss originals in the rare case where a

     * derivative has more than one original. (see https://dev.e-taxonomy.eu/redmine/issues/9253)

     *

     * @param derivedUnitDTO

     *      The DerivedUnitDTO to start the search from.

     * @param alreadyCollectedSpecimen

     *      A map to hold all originals that have been sees during the recursive walk.

     * @return

     *      The collection of all Field Units that are accessible from the derivative from where the search was started.

     */

    public Collection<SpecimenOrObservationBaseDTO> findRootUnitDTOs(UUID unitUUID);

    /**

     * Finds the units which are associated to a taxon

     * (<code>associatedTaxonUuid</code>) and returns all related root units

     * with the derivation branches up to the derivatives associated with the

     * taxon and the full derivation sub-tree of those.

     * <p>

     * Requirements as stated in the below linked tickets:

     * <ol>

     * <li>The derivation trees (derivatives, sub-derivatives,

     * sub-sub-derivatives, ....) of each of the root units will be included in

     * the result items in

     * ({@link SpecimenOrObservationBaseDTO#getDerivatives()})</li>

     * <li>.... should contain all derivates of a derivate determined to the

     * taxon or its name and all elements should be displayed only once.

     * ....</li>

     * <li>... also sollen beim DerivateTree eigentlich auch nur die Derivate

     * angezeigt werden, die über Taxon Association oder Determination an einem

     * Taxon oder Namen hängen und ihre direkten Eltern und Kinder (+

     * KindesKinder…).

     * <li>Also im Endeffekt muss man die Derivate raus suchen, die eine

     * Assoziation zu dem Taxon haben und dann die direkten Vorgänger und die

     * Nachfolger finden. Andere Derivate, die von Origin Derivaten abstammen

     * würden erstmal nicht dazugehören, außer sie sind ebenfalls mit dem Taxon

     * assoziiert....</li>

     * <ul>

     *

     * Related tickets:

     *

     * <ul>

     * <li>https://dev.e-taxonomy.eu/redmine/issues/7599</li>

     * <li>https://dev.e-taxonomy.eu/redmine/issues/9216</li>

     * </ul>

     *

     * @param includedRelationships

     *  TODO

     * @param associatedTaxonUuid

     *  The uuid of the taxon for which associated derivatives are to be found.

     * @param propertyPaths

     *  The bean initialization strategy

     * @return

     *  The list of root units with fully or partially assembled derivation graph.

     */

    List<SpecimenOrObservationBaseDTO> listRootUnitDTOsByAssociatedTaxon(Set<TaxonRelationshipEdge> includedRelationships,

            UUID associatedTaxonUuid, List<String> propertyPaths);

    /**

     * Lists all root units which are

     * associated <b>directly or indirectly</b>with the <code>taxon</code> specified

     * as parameter. "Indirectly" means that a sub derivate of the FieldUnit is

     * directly associated with the given taxon.

     * SpecimenOrObservationBase instances can be associated to taxa in multiple

     * ways, all these possible relations are taken into account:

     * <ul>

     * <li>The {@link IndividualsAssociation} elements in a

     * {@link TaxonDescription} contain {@link DerivedUnit}s</li>

     * <li>{@link SpecimenTypeDesignation}s may be associated with any

     * {@link HomotypicalGroup} related to the specific {@link Taxon}.</li>

     * <li>A {@link Taxon} may be referenced by the {@link DeterminationEvent}

     * of the {@link SpecimenOrObservationBase}</li>

     * </ul>

     * Further more there also can be taxa which are associated with the taxon

     * in question (parameter associatedTaxon) by {@link TaxonRelationship}s. If

     * the parameter <code>includeRelationships</code> is containing elements,

     * these according {@TaxonRelationshipType}s and

     * directional information will be used to collect further

     * {@link SpecimenOrObservationBase} instances found this way.

     *

     * @param <T>

     * @param type

     *  Restriction to a specific subtype, may be null.

     * @param associatedTaxon

     * @param Set<TaxonRelationshipVector> includeRelationships. TaxonRelationships will not be taken into account if this is <code>NULL</code>.

     * @param maxDepth TODO

     * @param pageSize

     * @param pageNumber

     * @param orderHints

     * @param propertyPaths

     * @return

     */

    public <T extends SpecimenOrObservationBase> Collection<T> listRootUnitsByAssociatedTaxon(Class<T> type, Taxon associatedTaxon, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * See {@link #listFieldUnitsByAssociatedTaxon(Set, Taxon, Integer, Integer, Integer, List, List)}

     */

    public <T extends SpecimenOrObservationBase> Pager<T> pageRootUnitsByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,

            Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);

    public List<Point> findPointsForFieldUnitList(List<UUID> fieldUnitUuids);

    /**

     * Load the FieldUnitDTO for the given <code>derivedUnitUuid</code> with all intermediate derivatives and {@link eu.etaxonomy.cdm.api.service.dto.GatheringEventDTO}

     * @param derivedUnitUuid

     * @return

     */

    FieldUnitDTO loadFieldUnitDTO(UUID derivedUnitUuid);

    Pager<MediaDTO> getMediaDTOs(SpecimenOrObservationBase<?> occurence, Integer pageSize, Integer pageNumber);

	Pager<Media> getMediaInHierarchy(SpecimenOrObservationBase<?> rootOccurence, boolean collectOriginalMedia, boolean collectDerivativeMedia,

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

}