EDIT

/**

* Copyright (C) 2008 EDIT

* European Distributed Institute of Taxonomy

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

*/

package eu.etaxonomy.cdm.persistence.dao.occurrence;

import java.util.Collection;

import java.util.List;

import java.util.UUID;

import org.springframework.dao.DataAccessException;

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

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.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.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.persistence.dao.common.IIdentifiableDao;

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.MatchMode;

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

/**

 * @author a.babadshanjan

 * @since 01.09.2008

 */

public interface IOccurrenceDao extends IIdentifiableDao<SpecimenOrObservationBase> {

    /**

     * Returns the number of occurences belonging to a certain subclass - which must extend SpecimenOrObservationBase

     * @param clazz optionally restrict the counted occurrences to those of a certain subclass of SpecimenOrObservationBase

     * @param determinedAs the taxon name that these specimens are determined to belong to

     * @return

     */

    public long count(Class<? extends SpecimenOrObservationBase> clazz,TaxonName determinedAs);

    /**

     * Returns a sublist of SpecimenOrObservationBase instances stored in the database. A maximum

     * of 'limit' objects are returned, starting at object with index 'start'. Only occurrences which

     * have been determined to belong to the supplied name are returned.

     *

     * @param type

     * @param determinedAs the taxon name that these specimens are determined to belong to

     * @param orderHints

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

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

     *            authorTeam.persistentTitleCache

     * @return

     * @throws DataAccessException

     */

    public List<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonName determinedAs,

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

    /**

	 * Returns the number of occurences belonging to a certain subclass - which must extend SpecimenOrObservationBase

	 * @param clazz optionally restrict the counted occurrences to those of a certain subclass of SpecimenOrObservationBase

	 * @param determinedAs the taxon concept that these specimens are determined to belong to

	 * @return

	 */

	public long count(Class<? extends SpecimenOrObservationBase> clazz,TaxonBase determinedAs);

	/**

	 * Returns a sublist of SpecimenOrObservationBase instances stored in the database. A maximum

	 * of 'limit' objects are returned, starting at object with index 'start'. Only occurrences which

	 * have been determined to belong to the supplied concept are returned.

	 *

	 * @param type

	 * @param determinedAs the taxon concept that these specimens are determined to belong to

	 * @param orderHints

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

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

	 *            authorTeam.persistentTitleCache

	 * @return

	 * @throws DataAccessException

	 */

	public List<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs,

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

	/**

     * Queries the database for specimens which match the given criteria<br>

     * <b>Note:</b> Specifying a taxon will already check the name of this

     * taxon, its synonymy and the synonym names for determinations of the

     * specimen. So specifying a taxon name is only necessary if it does not

     * belong to the before-mentioned group of names.

     *

     * @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 associatedTaxonName

     *            the taxon name that the specimens have been determined as

     * @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

     * @param propertyPaths

     * @return a list of specimens that match the given parameters

     */

    public <T extends SpecimenOrObservationBase> List<T> findOccurrences(Class<T> clazz, String queryString,

            String significantIdentifier, SpecimenOrObservationType type, Taxon determinedAs,

            TaxonName associatedTaxonName, MatchMode matchmode, Integer limit, Integer start,

            List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     * @see IOccurrenceDao#findOccurrences(Class, String, String, SpecimenOrObservationType, Taxon, TaxonName, MatchMode, Integer, Integer, List, List)

     * @param clazz

     * @param queryString

     * @param significantIdentifier

     * @param type

     * @param determinedAs

     * @param associatedTaxonName

     * @param matchmode

     * @param limit

     * @param start

     * @param orderHints

     * @param propertyPaths

     * @return

     */

    public <T extends SpecimenOrObservationBase> List<UuidAndTitleCache<SpecimenOrObservationBase>> findOccurrencesUuidAndTitleCache(

            Class<T> clazz, String queryString,

            String significantIdentifier, SpecimenOrObservationType type, Taxon determinedAs,

            TaxonName associatedTaxonName, MatchMode matchmode, Integer limit, Integer start,

            List<OrderHint> orderHints);

    /**

     * Returns the number of specimens that match the given parameters

     * <b>Note:</b> Specifying a taxon will already check the name of this

     * taxon, its synonymy and the synonym names for determinations of the

     * specimen. So specifying a taxon name is only necessary if it does not

     * belong to the before-mentioned group of names.

     *

     * @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 associatedTaxonName

     *            the taxon name that the specimens have been determined as

     * @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 <T extends SpecimenOrObservationBase> long countOccurrences(Class<T> clazz, String queryString,

            String significantIdentifier, SpecimenOrObservationType recordBasis, Taxon associatedTaxon,

            TaxonName associatedTaxonName, MatchMode matchmode, Integer limit, Integer start,

            List<OrderHint> orderHints, List<String> propertyPaths);

	/**

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

     *

	 * @param occurence the occurence associated with these media

     * @return a count of media instances

     */

	public long countMedia(SpecimenOrObservationBase occurence);

    /**

     * 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 List of media instances

     */

	public List<Media> getMedia(SpecimenOrObservationBase occurence, 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 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)

	 * @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)

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

     * @return a List of determination instances

     */

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

	/**

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

     *

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

     * @return a count of derivation events

     */

    public long countDerivationEvents(SpecimenOrObservationBase occurence);

    /**

     * 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)

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

     * @return a List of derivation events

     */

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

	/**

	 * Lists all instances of {@link SpecimenOrObservationBase} which are determined as the <code>taxon name</code> specified as parameter.

	 *

	 * @param <T>

	 * @param type

	 * @param associatedTaxonName

	 * @param limit

	 * @param start

	 * @param orderHints

	 * @param propertyPaths

	 * @return

	 */

	public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxonName(Class<T> type,

            TaxonName associatedTaxonName, Integer limit, Integer start, List<OrderHint> orderHints, 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} or a {@link TaxonName} may be referenced by the {@link DeterminationEvent} of the {@link SpecimenOrObservationBase}</li>

	 * </ul>

	 *

	 * @param <T>

	 * @param type

	 * @param associatedTaxon

	 * @param limit

	 * @param start

	 * @param orderHints

	 * @param propertyPaths

	 * @return

	 */

	public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Taxon associatedTaxon,

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

	/**

	 * @see IOccurrenceDao#listByAssociatedTaxon(Class, Taxon, Integer, Integer, List, List)

	 * @param type

	 * @param associatedTaxon

	 * @param limit

	 * @param start

	 * @param orderHints

	 * @param propertyPaths

	 * @return

	 */

	public <T extends SpecimenOrObservationBase> List<UuidAndTitleCache<SpecimenOrObservationBase>> listUuidAndTitleCacheByAssociatedTaxon(Class<T> type, Taxon associatedTaxon,

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

    /**

     * 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 IOccurrenceDao#findOccurrences(Class, String, String, SpecimenOrObservationType, Taxon, TaxonName, MatchMode, Integer, Integer, List, List)}

     * @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);

    /**

     * 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 {@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

	 */

	/**

     * 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 determinations with the given specimen

	 */

    public Collection<DeterminationEvent> listDeterminationEvents(SpecimenOrObservationBase<?> specimen, 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(SpecimenOrObservationBase<?> 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);

    /**

     * Retrieves all {@link SpecimenOrObservationBase}s that have the given {@link SpecimenOrObservationType}.

     * @param type

     * @param limit

     * @param start

     * @param orderHints

     * @param propertyPaths

     * @return collection of specimen with the given type

     */

    public Collection<SpecimenOrObservationBase> listBySpecimenOrObservationType(SpecimenOrObservationType type, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

     *

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

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

     * @param limit

     * @param start

     * @param orderHints

     * @param propertyPaths

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

     */

    public List<FieldUnit> findFieldUnitsForGatheringEvent(UUID gatheringEventUuid, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);

    /**

    *

    * Returns {@link DerivedUnit} that has the accession number and is determined to a taxon

    * @param accessionNumber

    * @param propertyPaths

    * @return a derived unit

    */

   public List<DerivedUnit> findByGeneticAccessionNumber(String accessionNumberString, List<String> propertyPaths);

    /**

     * @param derivedUnitUuid

     * @return

     */

    public List<SpecimenOrObservationBase> findOriginalsForDerivedUnit(UUID derivedUnitUuid, List<String> propertyPaths);

    /**

     * @param fieldUnitUuids

     * @return

     */

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

}