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/**
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* Copyright (C) 2008 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*/
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package eu.etaxonomy.cdm.persistence.dao.occurrence;
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import java.util.Collection;
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import java.util.List;
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import java.util.UUID;
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import org.springframework.dao.DataAccessException;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.persistence.dao.common.IIdentifiableDao;
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import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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/**
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* @author a.babadshanjan
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* @created 01.09.2008
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*/
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public interface IOccurrenceDao extends IIdentifiableDao<SpecimenOrObservationBase> {
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/**
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* Returns the number of occurences belonging to a certain subclass - which must extend SpecimenOrObservationBase
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* @param clazz optionally restrict the counted occurrences to those of a certain subclass of SpecimenOrObservationBase
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* @param determinedAs the taxon name that these specimens are determined to belong to
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* @return
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*/
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public int count(Class<? extends SpecimenOrObservationBase> clazz,TaxonNameBase determinedAs);
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/**
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* Returns a sublist of SpecimenOrObservationBase instances stored in the database. A maximum
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* of 'limit' objects are returned, starting at object with index 'start'. Only occurrences which
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* have been determined to belong to the supplied name are returned.
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*
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* @param type
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* @param determinedAs the taxon name that these specimens are determined to belong to
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* @param limit
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* the maximum number of entities returned (can be null to return
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* all entities)
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* @param start
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* @param orderHints
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* Supports path like <code>orderHints.propertyNames</code> which
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* include *-to-one properties like createdBy.username or
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* authorTeam.persistentTitleCache
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* @return
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* @throws DataAccessException
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*/
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public List<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonNameBase determinedAs, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Returns the number of occurences belonging to a certain subclass - which must extend SpecimenOrObservationBase
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* @param clazz optionally restrict the counted occurrences to those of a certain subclass of SpecimenOrObservationBase
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* @param determinedAs the taxon concept that these specimens are determined to belong to
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* @return
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*/
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public int count(Class<? extends SpecimenOrObservationBase> clazz,TaxonBase determinedAs);
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/**
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* Returns a sublist of SpecimenOrObservationBase instances stored in the database. A maximum
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* of 'limit' objects are returned, starting at object with index 'start'. Only occurrences which
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* have been determined to belong to the supplied concept are returned.
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*
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* @param type
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* @param determinedAs the taxon concept that these specimens are determined to belong to
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* @param limit
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* the maximum number of entities returned (can be null to return
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* all entities)
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* @param start
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* @param orderHints
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* Supports path like <code>orderHints.propertyNames</code> which
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* include *-to-one properties like createdBy.username or
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* authorTeam.persistentTitleCache
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* @return
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* @throws DataAccessException
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*/
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public List<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Queries the database for specimens which match the given criteria<br>
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* <b>Note:</b> Specifying a taxon will already check the name of this
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* taxon, its synonymy and the synonym names for determinations of the
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* specimen. So specifying a taxon name is only necessary if it does not
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* belong to the before-mentioned group of names.
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*
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* @param clazz
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* the class to match
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* @param queryString
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* the queryString to match
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* @param type
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* the {@link SpecimenOrObservationType} to match
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* @param associatedTaxon
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* the taxon these specimens are in any way associated to via
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* determination, type designations, individuals associations,
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* etc.
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* @param associatedTaxonName
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* the taxon name that the specimens have been determined as
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* @param matchmode
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* determines how the query string should be matched
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* @param limit
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* the maximum number of entities returned (can be null to return
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* all entities)
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* @param start
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* @param orderHints
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* Supports path like <code>orderHints.propertyNames</code> which
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* include *-to-one properties like createdBy.username or
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* authorTeam.persistentTitleCache
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* @param propertyPaths
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* @return a list of specimens that match the given parameters
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*/
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public <T extends SpecimenOrObservationBase> List<T> findOccurrences(Class<T> clazz, String queryString,
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String significantIdentifier, SpecimenOrObservationType type, Taxon determinedAs,
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TaxonNameBase associatedTaxonName, MatchMode matchmode, Integer limit, Integer start,
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List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Returns the number of specimens that match the given parameters
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* <b>Note:</b> Specifying a taxon will already check the name of this
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* taxon, its synonymy and the synonym names for determinations of the
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* specimen. So specifying a taxon name is only necessary if it does not
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* belong to the before-mentioned group of names.
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*
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* @param clazz
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* the class to match
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* @param queryString
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* the queryString to match
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* @param type
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* the {@link SpecimenOrObservationType} to match
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* @param associatedTaxon
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* the taxon these specimens are in any way associated to via
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* determination, type designations, individuals associations,
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* etc.
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* @param associatedTaxonName
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* the taxon name that the specimens have been determined as
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* @param matchmode
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* determines how the query string should be matched
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* @param limit
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* the maximum number of entities returned (can be null to return
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* all entities)
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* @param start
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* @param orderHints
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* Supports path like <code>orderHints.propertyNames</code> which
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* include *-to-one properties like createdBy.username or
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* authorTeam.persistentTitleCache
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* @return the number of found specimens
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*/
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public <T extends SpecimenOrObservationBase> int countOccurrences(Class<T> clazz, String queryString,
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String significantIdentifier, SpecimenOrObservationType recordBasis, Taxon associatedTaxon,
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TaxonNameBase associatedTaxonName, MatchMode matchmode, Integer limit, Integer start,
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List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Returns a count of Media that are associated with a given occurence
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*
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* @param occurence the occurence associated with these media
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* @return a count of media instances
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*/
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public int countMedia(SpecimenOrObservationBase occurence);
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/**
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* Returns a List of Media that are associated with a given occurence
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*
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* @param occurence the occurence associated with these media
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* @param pageSize The maximum number of media returned (can be null for all related media)
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* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
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* @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
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* @return a List of media instances
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*/
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public List<Media> getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths);
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/**
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* Returns a count of determinations that have been made for a given occurence and for a given taxon concept
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*
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* @param occurence the occurence associated with these determinations (can be null for all occurrences)
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* @param taxonbase the taxon concept associated with these determinations (can be null for all taxon concepts)
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* @return a count of determination events
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*/
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public int countDeterminations(SpecimenOrObservationBase occurence,TaxonBase taxonbase);
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/**
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* Returns a List of determinations that have been made for a given occurence and for a given taxon concept
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*
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* @param occurence the occurence associated with these determinations (can be null for all occurrences)
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* @param taxonbase the taxon concept associated with these determinations (can be null for all taxon concepts)
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* @param pageSize The maximum number of determinations returned (can be null for all related determinations)
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* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
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* @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
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* @return a List of determination instances
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*/
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public List<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurence,TaxonBase taxonbase, Integer pageSize, Integer pageNumber, List<String> propertyPaths);
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/**
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* Returns a count of derivation events that have involved creating new DerivedUnits from this occurence
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*
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* @param occurence the occurence that was a source of these derivation events
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* @return a count of derivation events
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*/
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public int countDerivationEvents(SpecimenOrObservationBase occurence);
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/**
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* Returns a list of derivation events that have involved creating new DerivedUnits from this occurence
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*
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* @param occurence the occurence that was a source of these derivation events
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* @param pageSize The maximum number of derivation events returned (can be null for all related derivation events)
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* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
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* @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
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* @return a List of derivation events
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*/
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public List<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths);
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/**
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* Retrieves the {@link UUID} and the string representation (title cache) of all
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* {@link FieldUnit}s found in the data base.
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* @return a list of {@link UuidAndTitleCache}
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*/
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public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache();
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/**
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* Retrieves the {@link UUID} and the string representation (title cache) of all
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* {@link DerivedUnit}s found in the data base.
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* @return a list of {@link UuidAndTitleCache}
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*/
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public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache();
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/**
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* Lists all instances of {@link SpecimenOrObservationBase} which are determined as the <code>taxon name</code> specified as parameter.
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*
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* @param <T>
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* @param type
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* @param associatedTaxonName
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* @param limit
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* @param start
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* @param orderHints
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* @param propertyPaths
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* @return
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*/
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public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxonName(Class<T> type,
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TaxonNameBase associatedTaxonName, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Lists all instances of {@link SpecimenOrObservationBase} which are associated with the <code>taxon</code> specified as parameter.
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* SpecimenOrObservationBase instances can be associated to taxa in multiple ways, all these possible relations are taken into account:
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* <ul>
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* <li>The {@link IndividualsAssociation} elements in a {@link TaxonDescription} contain {@link DerivedUnit}s</li>
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* <li>{@link SpecimenTypeDesignation}s may be associated with any {@link HomotypicalGroup} related to the specific {@link Taxon}.</li>
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* <li>A {@link Taxon} or a {@link TaxonNameBase} may be referenced by the {@link DeterminationEvent} of the {@link SpecimenOrObservationBase}</li>
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* </ul>
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*
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* @param <T>
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* @param type
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* @param associatedTaxon
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* @param limit
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* @param start
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* @param orderHints
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* @param propertyPaths
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* @return
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*/
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public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Taxon associatedTaxon,
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Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Retrieves all {@link IndividualsAssociation} with the given specimen.<br>
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* @param specimen the specimen for which the associations are retrieved
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* @param limit
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* @param start
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* @param orderHints
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* @param propertyPaths
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* @return collection of all associations
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*/
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public Collection<IndividualsAssociation> listIndividualsAssociations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Retrieves all {@link SpecimenTypeDesignation}s which have the given specimen as a type specimen.
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* @param specimen the type specimen
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* @param limit
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* @param start
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* @param orderHints
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* @param propertyPaths
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* @return collection of all designations with the given type specimen
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*/
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/**
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* Retrieves all {@link DeterminationEvent}s which have the given specimen set as identified unit.
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* @param specimen
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* @param limit
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* @param start
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* @param orderHints
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* @param propertyPaths
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* @return collection of all determinations with the given specimen
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*/
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public Collection<DeterminationEvent> listDeterminationEvents(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Retrieves all {@link SpecimenTypeDesignation}s which have the given specimen as a type specimen.
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* @param specimen the type specimen
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* @param limit
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* @param start
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* @param orderHints
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* @param propertyPaths
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* @return collection of all designations with the given type specimen
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*/
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public Collection<SpecimenTypeDesignation> listTypeDesignations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Retrieves all {@link DescriptionBase}s that have the given specimen set as described specimen.
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* @param specimen the described specimen
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* @param limit
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* @param start
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* @param orderHints
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* @param propertyPaths
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* @return collection of all descriptions with the given described specimen
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*/
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public Collection<DescriptionBase<?>> listDescriptionsWithDescriptionSpecimen(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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335
|
* Retrieves all {@link SpecimenOrObservationBase}s that have the given {@link SpecimenOrObservationType}.
|
|
336
|
* @param type
|
|
337
|
* @param limit
|
|
338
|
* @param start
|
|
339
|
* @param orderHints
|
|
340
|
* @param propertyPaths
|
|
341
|
* @return collection of specimen with the given type
|
|
342
|
*/
|
|
343
|
public Collection<SpecimenOrObservationBase> listBySpecimenOrObservationType(SpecimenOrObservationType type, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
|
|
344
|
}
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