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/**
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* Copyright (C) 2009 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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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.api.service;
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import java.io.IOException;
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import java.util.Collection;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.lucene.index.CorruptIndexException;
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import org.hibernate.search.spatial.impl.Rectangle;
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import org.springframework.transaction.annotation.Transactional;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
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import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;
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import eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator;
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import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;
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import eu.etaxonomy.cdm.api.service.dto.DerivedUnitDTO;
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import eu.etaxonomy.cdm.api.service.dto.FieldUnitDTO;
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import eu.etaxonomy.cdm.api.service.dto.MediaDTO;
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import eu.etaxonomy.cdm.api.service.dto.SpecimenOrObservationBaseDTO;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.api.service.search.LuceneParseException;
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import eu.etaxonomy.cdm.api.service.search.SearchResult;
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import eu.etaxonomy.cdm.api.util.TaxonRelationshipEdge;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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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.location.Point;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.molecular.DnaSample;
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import eu.etaxonomy.cdm.model.molecular.Sequence;
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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.TaxonName;
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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.GatheringEvent;
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import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
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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.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
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import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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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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* @since 01.09.2008
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*/
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public interface IOccurrenceService
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extends IIdentifiableEntityService<SpecimenOrObservationBase> {
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/**
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* Returns a paged list of occurrences that have been determined to belong
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* to the taxon concept determinedAs, optionally restricted to objects
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* belonging to a class that that extends SpecimenOrObservationBase. This
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* will also consider specimens that are determined as a taxon concept
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* belonging to the synonymy of the given taxon concept.
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* <p>
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* In contrast to {@link #listByAnyAssociation(Class, Taxon, List)} this
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* method only takes SpecimenOrObservationBase instances into account which
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* are actually determined as the taxon specified by
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* <code>determinedAs</code>.
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*
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* @param type
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* The type of entities to return (can be null to count all
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* entities of type <T>)
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* @param determinedAs
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* the taxon concept that the occurrences have been determined to
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* belong to
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* @param pageSize
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* The maximum number of objects returned (can be null for all
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* matching objects)
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* @param pageNumber
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* The offset (in pageSize chunks) from the start of the result
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* set (0 - based, can be null, equivalent of starting at the
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* beginning of the recordset)
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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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* properties to be initialized
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* @return
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*/
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public Pager<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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* Returns a paged list of occurrences that have been determined to belong
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* to the taxon name determinedAs, optionally restricted to objects
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* belonging to a class that that extends SpecimenOrObservationBase.
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* <p>
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* In contrast to {@link #listByAnyAssociation(Class, Taxon, List)} this
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* method only takes SpecimenOrObservationBase instances into account which
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* are actually determined as the taxon specified by
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* <code>determinedAs</code>.
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*
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* @param type
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* The type of entities to return (can be null to count all
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* entities of type <T>)
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* @param determinedAs
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* the taxon name that the occurrences have been determined to
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* belong to
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* @param pageSize
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* The maximum number of objects returned (can be null for all
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* matching objects)
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* @param pageNumber
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* The offset (in pageSize chunks) from the start of the result
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* set (0 - based, can be null, equivalent of starting at the
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* beginning of the recordset)
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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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* properties to be initialized
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* @return
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*/
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public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonName determinedAs, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
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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 Pager of media instances
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*/
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public Pager<Media> getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths);
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/**
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* Returns all media attached to this occurence and its children. Also takes
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* {@link MediaSpecimen} and molecular images into account.
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*
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* @param occurence the occurence and its children from which the media to get
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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 Pager of media instances
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*/
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public Pager<Media> getMediainHierarchy(SpecimenOrObservationBase rootOccurence, 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 long 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
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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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* @return a Pager of determination instances
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*/
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public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonBase, Integer pageSize, Integer pageNumber, List<String> propertyPaths);
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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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* @return a Pager of derivation events
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*/
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public Pager<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths);
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/**
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* Returns a Paged List of SpecimenOrObservationBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
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*
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* @param clazz filter the results by class (or pass null to return all SpecimenOrObservationBase instances)
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* @param queryString
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* @param pageSize The maximum number of occurrences returned (can be null for all matching occurrences)
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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 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 properties to be initialized
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* @return a Pager SpecimenOrObservationBase instances
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* @see <a href="http://lucene.apache.org/java/2_4_0/queryparsersyntax.html">Apache Lucene - Query Parser Syntax</a>
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*/
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@Override
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public Pager<SpecimenOrObservationBase> search(Class<? extends SpecimenOrObservationBase> clazz, String query, Integer pageSize,Integer pageNumber, List<OrderHint> orderHints,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(Integer limit, String pattern);
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public DerivedUnitFacade getDerivedUnitFacade(DerivedUnit derivedUnit, List<String> propertyPaths) throws DerivedUnitFacadeNotSupportedException;
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public List<DerivedUnitFacade> listDerivedUnitFacades(DescriptionBase description, List<String> propertyPaths);
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/**
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* Lists all instances of {@link SpecimenOrObservationBase} which are
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* associated with the <code>taxon</code> specified as parameter.
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* SpecimenOrObservationBase instances can be associated to taxa in multiple
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* 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
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* {@link TaxonDescription} contain {@link DerivedUnit}s</li>
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* <li>{@link SpecimenTypeDesignation}s may be associated with any
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* {@link HomotypicalGroup} related to the specific {@link Taxon}.</li>
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* <li>A {@link Taxon} may be referenced by the {@link DeterminationEvent}
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* of the {@link SpecimenOrObservationBase}</li>
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* </ul>
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* Further more there also can be taxa which are associated with the taxon
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* in question (parameter associatedTaxon) by {@link TaxonRelationship}s. If
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* the parameter <code>includeRelationships</code> is containing elements,
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* these according {@TaxonRelationshipType}s and
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* directional information will be used to collect further
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* {@link SpecimenOrObservationBase} instances found this way.
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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 Set<TaxonRelationshipVector> includeRelationships. TaxonRelationships will not be taken into account if this is <code>NULL</code>.
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* @param maxDepth TODO
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* @param pageSize
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* @param pageNumber
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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, Set<TaxonRelationshipEdge> includeRelationships,
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Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* The method will search for specimen associated with the taxon nodes.<br>
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* It will search for 3 possible association types: <br>
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* - via IndividualAssociations of the taxon<br>
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* - via TypeDesignations of the taxon name<br>
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* - via Determinations of the taxon or taxon name<br>
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* <br>
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* more are covered in
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* {@link IOccurrenceService#findByTitle(IIdentifiableEntityServiceConfigurator)}
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* @param taxonNodeUuids
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* a list of {@link UUID}s of the taxon nodes
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* @param limit
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* @param start
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* @return a collection of {@link SpecimenNodeWrapper} containing the
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* {@link TaxonNode} and the corresponding {@link UuidAndTitleCache}
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* object for the specimen found for this taxon node
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*/
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public Collection<SpecimenNodeWrapper> listUuidAndTitleCacheByAssociatedTaxon(List<UUID> taxonNodeUuids,
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Integer limit, Integer start);
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/**
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* @deprecated replace by {@link #listRootUnitsByAssociatedTaxon(Class, Taxon, List, List)}
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*/
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@Deprecated
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public Collection<FieldUnit> listFieldUnitsByAssociatedTaxon(Taxon associatedTaxon, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* See {@link #listByAssociatedTaxon(Class, Set, Taxon, Integer, Integer, Integer, List, List)}
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*
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* @param type
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* Restriction to subtype of <code>SpecimenOrObservationBase</code>, can be NULL.
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* @param includeRelationships
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* @param associatedTaxon
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* @param maxDepth
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* @param pageSize
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* @param pageNumber
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* @param orderHints
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* @param propertyPaths
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* @return a Pager
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*/
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public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
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Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Retrieves all {@link FieldUnit}s for the {@link SpecimenOrObservationBase} with the given {@link UUID}.<br>
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* @param specimenUuid the UUID of the specimen
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* @param propertyPaths the property path
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* @return either a collection of FieldUnits this specimen was derived from, the FieldUnit itself
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* if this was a FieldUnit or an empty collection if no FieldUnits were found
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*/
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public Collection<FieldUnit> findFieldUnits(UUID specimenUuid, List<String> propertyPaths);
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/**
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* Retrieves top most originals for a {@link SpecimenOrObservationBase} in the derivation graph by recursively
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* walking all {@link DerivationEvent}s.
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* In most cases item in the returned collection will be {@link FieldUnit FieldUnits} but also DerivedUnits are possible, in
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* cases where no FieledUnit exists.
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*
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* @param specimenUuid the UUID of the specimen
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* @param propertyPaths the property path
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* @return either a collection of root units
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*/
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public Collection<SpecimenOrObservationBase> findRootUnits(UUID specimenUuid, List<String> propertyPaths);
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/**
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* @param clazz
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* @param queryString
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* @param languages
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* @param highlightFragments
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* @param pageSize
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* @param pageNumber
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* @param orderHints
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* @param propertyPaths
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* @return
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* @throws CorruptIndexException
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* @throws IOException
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* @throws ParseException
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*/
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Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(Class<? extends SpecimenOrObservationBase> clazz,
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String queryString, Rectangle boundingBox, List<Language> languages, boolean highlightFragments,
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Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths)
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throws IOException, LuceneParseException;
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/**
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* See {@link #listByAssociatedTaxon(Class, Set, String, Integer, Integer, Integer, List, List)}
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*
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* @param type
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* @param includeRelationships
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* @param associatedTaxon
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* @param maxDepth
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* @param pageSize
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* @param pageNumber
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* @param orderHints
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* @param propertyPaths
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* @return a Pager
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*/
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public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
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String taxonUUID, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
361
|
|
362
|
/**
|
363
|
* Moves the given {@link Sequence} from one {@link DnaSample} to another
|
364
|
* @param from the DnaSample from which the sequence will be removed
|
365
|
* @param to the DnaSample which to which the sequence will be added
|
366
|
* @param sequence the Sequence to move
|
367
|
* @return <code>true</code> if successfully moved, <code>false</code> otherwise
|
368
|
*/
|
369
|
public UpdateResult moveSequence(DnaSample from, DnaSample to, Sequence sequence);
|
370
|
|
371
|
|
372
|
/**
|
373
|
* @param fromUuid
|
374
|
* @param toUuid
|
375
|
* @param sequenceUuid
|
376
|
* @return
|
377
|
*/
|
378
|
public UpdateResult moveSequence(UUID fromUuid, UUID toUuid, UUID sequenceUuid);
|
379
|
|
380
|
/**
|
381
|
* Moves the given {@link DerivedUnit} from one {@link SpecimenOrObservationBase} to another.
|
382
|
* @param from the SpecimenOrObservationBase from which the DerivedUnit will be removed
|
383
|
* @param to the SpecimenOrObservationBase to which the DerivedUnit will be added
|
384
|
* @param derivate the DerivedUnit to move
|
385
|
* @return <code>true</code> if successfully moved, <code>false</code> otherwise
|
386
|
*/
|
387
|
public UpdateResult moveDerivate(UUID specimenFromUuid, UUID specimenToUuid, UUID derivateUuid);
|
388
|
|
389
|
/**
|
390
|
* @param from
|
391
|
* @param to
|
392
|
* @param derivate
|
393
|
* @return
|
394
|
*/
|
395
|
public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate);
|
396
|
|
397
|
/**
|
398
|
* Assembles a {@link FieldUnitDTO} for the given field unit.<br>
|
399
|
*
|
400
|
* @param fieldUnit
|
401
|
* @return a DTO with all the assembled information
|
402
|
*/
|
403
|
public FieldUnitDTO assembleFieldUnitDTO(FieldUnit fieldUnit);
|
404
|
|
405
|
/**
|
406
|
* Assembles a {@link DerivedUnitDTO} for the given derived unit.
|
407
|
* @param derivedUnit
|
408
|
* @return a DTO with all the assembled information
|
409
|
*/
|
410
|
public SpecimenOrObservationBaseDTO assembleDerivedUnitDTO(DerivedUnit derivedUnit);
|
411
|
|
412
|
/**
|
413
|
* Deletes the specified specimen according to the setting in the {@link SpecimenDeleteConfigurator}.<br>
|
414
|
* @param specimen the specimen which shoul be deleted
|
415
|
* @param config specifies options if and how the specimen should be deleted like e.g. including all
|
416
|
* of its children
|
417
|
* @return the {@link DeleteResult} which holds information about the outcome of this operation
|
418
|
*/
|
419
|
public DeleteResult delete(SpecimenOrObservationBase<?> specimen, SpecimenDeleteConfigurator config);
|
420
|
|
421
|
/**
|
422
|
* Deletes the specified specimen belonging to the given {@link UUID}
|
423
|
* according to the setting in the {@link SpecimenDeleteConfigurator}.
|
424
|
*
|
425
|
* @param specimen
|
426
|
* the specimen which shoul be deleted
|
427
|
* @param config
|
428
|
* specifies options if and how the specimen should be deleted
|
429
|
* like e.g. including all of its children
|
430
|
* @return the {@link DeleteResult} which holds information about the
|
431
|
* outcome of this operation
|
432
|
*/
|
433
|
public DeleteResult delete(UUID specimenUuid, SpecimenDeleteConfigurator config);
|
434
|
|
435
|
/**
|
436
|
* Retrieves all {@link IndividualsAssociation} with the given specimen.<br>
|
437
|
* @param specimen the specimen for which the associations are retrieved
|
438
|
* @param limit
|
439
|
* @param start
|
440
|
* @param orderHints
|
441
|
* @param propertyPaths
|
442
|
* @return collection of all associations
|
443
|
*/
|
444
|
public Collection<IndividualsAssociation> listIndividualsAssociations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
|
445
|
|
446
|
|
447
|
/**
|
448
|
* Retrieves all taxa linked via {@link IndividualsAssociation} with the given specimen.<br>
|
449
|
* @param specimen the specimen which is linked to the taxa
|
450
|
* @param limit
|
451
|
* @param start
|
452
|
* @param orderHints
|
453
|
* @param propertyPaths
|
454
|
* @return a collection of associated taxa
|
455
|
*/
|
456
|
public Collection<TaxonBase<?>> listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen,
|
457
|
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
|
458
|
/**
|
459
|
* @see #listIndividualsAssociationTaxa(SpecimenOrObservationBase, Integer, Integer, List, List)
|
460
|
*/
|
461
|
public Collection<TaxonBase<?>> listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen, boolean includeUnpublished,
|
462
|
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
|
463
|
|
464
|
/**
|
465
|
* Retrieves all associated taxa for the given specimen (via type designations, determination, individuals associations)
|
466
|
* @param specimen
|
467
|
* @param limit
|
468
|
* @param start
|
469
|
* @param orderHints
|
470
|
* @param propertyPaths
|
471
|
* @return
|
472
|
*/
|
473
|
public Collection<TaxonBase<?>> listAssociatedTaxa(SpecimenOrObservationBase<?> specimen, boolean includeUnpublished,
|
474
|
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
|
475
|
/**
|
476
|
* @see #listAssociatedTaxa(SpecimenOrObservationBase, Integer, Integer, List, List)axa
|
477
|
*/
|
478
|
public Collection<TaxonBase<?>> listAssociatedTaxa(SpecimenOrObservationBase<?> specimen,
|
479
|
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
|
480
|
|
481
|
/**
|
482
|
* Retrieves all taxa that the given specimen is determined as
|
483
|
* @param specimen
|
484
|
* @param limit
|
485
|
* @param start
|
486
|
* @param orderHints
|
487
|
* @param propertyPaths
|
488
|
* @return collection of all taxa the given specimen is determined as
|
489
|
*/
|
490
|
public Collection<TaxonBase<?>> listDeterminedTaxa(SpecimenOrObservationBase<?> specimen, boolean includeUnpublished,
|
491
|
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
|
492
|
/**
|
493
|
* @see #listDeterminedTaxa(SpecimenOrObservationBase, Integer, Integer, List, List)
|
494
|
*/
|
495
|
public Collection<TaxonBase<?>> listDeterminedTaxa(SpecimenOrObservationBase<?> specimen,
|
496
|
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
|
497
|
|
498
|
/**
|
499
|
* Retrieves all {@link DeterminationEvent}s which have the given specimen set as identified unit.
|
500
|
* @param specimen
|
501
|
* @param limit
|
502
|
* @param start
|
503
|
* @param orderHints
|
504
|
* @param propertyPaths
|
505
|
* @return collection of all determination events with the given specimen
|
506
|
*/
|
507
|
public Collection<DeterminationEvent> listDeterminationEvents(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
|
508
|
|
509
|
/**
|
510
|
* Retrieves all taxa with a {@link SpecimenTypeDesignation} with the given specimen as a type specimen.
|
511
|
* @param specimen the type specimen
|
512
|
* @param specimen
|
513
|
* @param limit
|
514
|
* @param start
|
515
|
* @param orderHints
|
516
|
* @param propertyPaths
|
517
|
* @return a collection of all taxa where the given specimen is the type specimen
|
518
|
*/
|
519
|
public Collection<TaxonBase<?>> listTypeDesignationTaxa(DerivedUnit specimen,
|
520
|
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
|
521
|
/**
|
522
|
* @see #listTypeDesignationTaxa(DerivedUnit, Integer, Integer, List, List)a
|
523
|
*/
|
524
|
public Collection<TaxonBase<?>> listTypeDesignationTaxa(DerivedUnit specimen, boolean includeUnpublished,
|
525
|
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
|
526
|
|
527
|
/**
|
528
|
* Retrieves all {@link SpecimenTypeDesignation}s which have the given specimens as a type specimen.
|
529
|
* @param specimens the type specimens
|
530
|
* @param limit
|
531
|
* @param start
|
532
|
* @param orderHints
|
533
|
* @param propertyPaths
|
534
|
* @return map of all designations with the given type specimens
|
535
|
*/
|
536
|
public Map<DerivedUnit, Collection<SpecimenTypeDesignation>> listTypeDesignations(Collection<DerivedUnit> specimens, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
|
537
|
|
538
|
/**
|
539
|
* Retrieves all {@link SpecimenTypeDesignation}s which have the given specimen as a type specimen.
|
540
|
* @param specimen the type specimen
|
541
|
* @param limit
|
542
|
* @param start
|
543
|
* @param orderHints
|
544
|
* @param propertyPaths
|
545
|
* @return collection of all designations with the given type specimen
|
546
|
*/
|
547
|
public Collection<SpecimenTypeDesignation> listTypeDesignations(DerivedUnit specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
|
548
|
|
549
|
/**
|
550
|
* Retrieves all {@link DescriptionBase}s that have the given specimen set as described specimen.
|
551
|
* @param specimen the described specimen
|
552
|
* @param limit
|
553
|
* @param start
|
554
|
* @param orderHints
|
555
|
* @param propertyPaths
|
556
|
* @return collection of all descriptions with the given described specimen
|
557
|
*/
|
558
|
public Collection<DescriptionBase<?>> listDescriptionsWithDescriptionSpecimen(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
|
559
|
|
560
|
/**
|
561
|
* Gets all description elements that are used for describing the character
|
562
|
* states of the given specimen
|
563
|
*
|
564
|
* @param specimenUuid
|
565
|
* the specimen {@link UUID} for which the character state description
|
566
|
* elements should be retrieved
|
567
|
* @return a collection of all character state description elements for this
|
568
|
* specimen
|
569
|
*/
|
570
|
public Collection<DescriptionElementBase> getCharacterDataForSpecimen(UUID specimenUuid);
|
571
|
|
572
|
/**
|
573
|
* Returns the most significant identifier for the given {@link DerivedUnit}.
|
574
|
* @param derivedUnit the derived unit to check
|
575
|
* @return the identifier string
|
576
|
* @deprecated use {@link DerivedUnit#getMostSignificantIdentifier()} instead
|
577
|
*/
|
578
|
@Deprecated
|
579
|
public String getMostSignificantIdentifier(DerivedUnit derivedUnit);
|
580
|
|
581
|
/**
|
582
|
* Returns the number of specimens that match the given parameters
|
583
|
* <br>
|
584
|
* <b>NOTE - issue #6484:</b> the parameters {@link FindOccurrencesConfigurator#getAssignmentStatus()}
|
585
|
* and {@link FindOccurrencesConfigurator#isRetrieveIndirectlyAssociatedSpecimens()} are not evaluated
|
586
|
* in the count method
|
587
|
* @param clazz the class to match
|
588
|
* @param queryString the queryString to match
|
589
|
* @param type the {@link SpecimenOrObservationType} to match
|
590
|
* @param associatedTaxon the taxon these specimens are in any way associated to via
|
591
|
* determination, type designations, individuals associations, etc.
|
592
|
* @param matchmode determines how the query string should be matched
|
593
|
* @param limit
|
594
|
* the maximum number of entities returned (can be null to return
|
595
|
* all entities)
|
596
|
* @param start
|
597
|
* @param orderHints
|
598
|
* Supports path like <code>orderHints.propertyNames</code> which
|
599
|
* include *-to-one properties like createdBy.username or
|
600
|
* authorTeam.persistentTitleCache
|
601
|
* @return the number of found specimens
|
602
|
*/
|
603
|
public long countOccurrences(IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config);
|
604
|
|
605
|
/**
|
606
|
* Return the all {@link SpecimenOrObservationBase}s of the complete
|
607
|
* derivative hierarchy i.e. all parent and child derivatives and the given
|
608
|
* specimen itself.
|
609
|
*
|
610
|
* @param specimen
|
611
|
* a specimen or observation
|
612
|
* @return the derivative hierarchy as an unordered list of all specimens or observation
|
613
|
*/
|
614
|
public List<SpecimenOrObservationBase<?>> getAllHierarchyDerivatives(SpecimenOrObservationBase<?> specimen);
|
615
|
|
616
|
/**
|
617
|
* Returns all child derivatives of the given specimen.
|
618
|
* @param specimen a specimen or observation
|
619
|
* @return an unordered list of all child derivatives
|
620
|
*/
|
621
|
public List<DerivedUnit> getAllChildDerivatives(SpecimenOrObservationBase<?> specimen);
|
622
|
|
623
|
/**
|
624
|
* Returns all child derivatives of the given specimen.
|
625
|
* @param specimen the UUID of a specimen or observation
|
626
|
* @return an unordered list of all child derivatives
|
627
|
*/
|
628
|
public List<DerivedUnit> getAllChildDerivatives(UUID specimenUuid);
|
629
|
|
630
|
/**
|
631
|
* Returns all {@link FieldUnit}s that are referencing this {@link GatheringEvent}
|
632
|
* @param gatheringEventUuid the {@link UUID} of the gathering event
|
633
|
* @return a list of field units referencing the gathering event
|
634
|
*/
|
635
|
public List<FieldUnit> findFieldUnitsForGatheringEvent(UUID gatheringEventUuid);
|
636
|
|
637
|
|
638
|
/**
|
639
|
* Returns a list of {@link UuidAndTitleCache} for the specimens found with the
|
640
|
* given configurator
|
641
|
* @param config the configurator for the search
|
642
|
* @return a list of UuidAndTitleCache object
|
643
|
*/
|
644
|
@Transactional(readOnly = true)
|
645
|
public Pager<UuidAndTitleCache<SpecimenOrObservationBase>> findByTitleUuidAndTitleCache(
|
646
|
FindOccurrencesConfigurator config);
|
647
|
|
648
|
/**
|
649
|
* Returns a list of {@link DerivedUnitDTO} for the specimens found with the
|
650
|
* given configurator
|
651
|
* @param config the configurator for the search
|
652
|
* @return a list of {@link DerivedUnitDTO} object
|
653
|
*/
|
654
|
@Transactional(readOnly = true)
|
655
|
public List<DerivedUnitDTO> findByTitleDerivedUnitDTO(
|
656
|
FindOccurrencesConfigurator config);
|
657
|
|
658
|
|
659
|
/**
|
660
|
* Collects the <code>FieldUnits</code> which are at the root of the derivation event
|
661
|
* graph in which the {@link DerivedUnit} with the specified <code>findByAccessionNumber</code>
|
662
|
* is found.
|
663
|
*
|
664
|
* @deprecated method name unclear and thus replaced by {@link #findByGeneticAccessionNumber(String, List)}
|
665
|
*/
|
666
|
@Deprecated
|
667
|
SpecimenOrObservationBaseDTO findByAccessionNumber(String accessionNumberString, List<OrderHint> orderHints);
|
668
|
|
669
|
/**
|
670
|
* Collects the <code>FieldUnits</code> which are at the root of the derivation event
|
671
|
* graph in which the {@link DnaSample} with the specified <code>accessionNumberString</code>
|
672
|
* is found.
|
673
|
*/
|
674
|
SpecimenOrObservationBaseDTO findByGeneticAccessionNumber(String dnaAccessionNumber, List<OrderHint> orderHints);
|
675
|
|
676
|
/**
|
677
|
* Recursively searches all {@link DerivationEvent}s to find all "originals" ({@link SpecimenOrObservationBase})
|
678
|
* from which this DerivedUnit was derived until all FieldUnits are found.
|
679
|
* <p>
|
680
|
* <b>NOTE:</b> The recursive search still is a bit incomplete and may miss originals in the rare case where a
|
681
|
* derivative has more than one original. (see https://dev.e-taxonomy.eu/redmine/issues/9253)
|
682
|
*
|
683
|
* @param derivedUnitDTO
|
684
|
* The DerivedUnitDTO to start the search from.
|
685
|
* @param alreadyCollectedSpecimen
|
686
|
* A map to hold all originals that have been sees during the recursive walk.
|
687
|
* @return
|
688
|
* The collection of all Field Units that are accessible from the derivative from where the search was started.
|
689
|
*/
|
690
|
public Collection<SpecimenOrObservationBaseDTO> findRootUnitDTOs(UUID unitUUID);
|
691
|
|
692
|
/**
|
693
|
* Finds the units which are associated to a taxon
|
694
|
* (<code>associatedTaxonUuid</code>) and returns all related root units
|
695
|
* with the derivation branches up to the derivatives associated with the
|
696
|
* taxon and the full derivation sub-tree of those.
|
697
|
* <p>
|
698
|
* Requirements as stated in the below linked tickets:
|
699
|
* <ol>
|
700
|
* <li>The derivation trees (derivatives, sub-derivatives,
|
701
|
* sub-sub-derivatives, ....) of each of the root units will be included in
|
702
|
* the result items in
|
703
|
* ({@link SpecimenOrObservationBaseDTO#getDerivatives()})</li>
|
704
|
* <li>.... should contain all derivates of a derivate determined to the
|
705
|
* taxon or its name and all elements should be displayed only once.
|
706
|
* ....</li>
|
707
|
* <li>... also sollen beim DerivateTree eigentlich auch nur die Derivate
|
708
|
* angezeigt werden, die über Taxon Association oder Determination an einem
|
709
|
* Taxon oder Namen hängen und ihre direkten Eltern und Kinder (+
|
710
|
* KindesKinder…).
|
711
|
* <li>Also im Endeffekt muss man die Derivate raus suchen, die eine
|
712
|
* Assoziation zu dem Taxon haben und dann die direkten Vorgänger und die
|
713
|
* Nachfolger finden. Andere Derivate, die von Origin Derivaten abstammen
|
714
|
* würden erstmal nicht dazugehören, außer sie sind ebenfalls mit dem Taxon
|
715
|
* assoziiert....</li>
|
716
|
* <ul>
|
717
|
*
|
718
|
* Related tickets:
|
719
|
*
|
720
|
* <ul>
|
721
|
* <li>https://dev.e-taxonomy.eu/redmine/issues/7599</li>
|
722
|
* <li>https://dev.e-taxonomy.eu/redmine/issues/9216</li>
|
723
|
* </ul>
|
724
|
*
|
725
|
* @param includedRelationships
|
726
|
* TODO
|
727
|
* @param associatedTaxonUuid
|
728
|
* The uuid of the taxon for which associated derivatives are to be found.
|
729
|
* @param propertyPaths
|
730
|
* The bean initialization strategy
|
731
|
* @return
|
732
|
* The list of root units with fully or partially assembled derivation graph.
|
733
|
*/
|
734
|
List<SpecimenOrObservationBaseDTO> listRootUnitDTOsByAssociatedTaxon(Set<TaxonRelationshipEdge> includedRelationships,
|
735
|
UUID associatedTaxonUuid, List<String> propertyPaths);
|
736
|
|
737
|
|
738
|
/**
|
739
|
* Lists all root units which are
|
740
|
* associated <b>directly or indirectly</b>with the <code>taxon</code> specified
|
741
|
* as parameter. "Indirectly" means that a sub derivate of the FieldUnit is
|
742
|
* directly associated with the given taxon.
|
743
|
* SpecimenOrObservationBase instances can be associated to taxa in multiple
|
744
|
* ways, all these possible relations are taken into account:
|
745
|
* <ul>
|
746
|
* <li>The {@link IndividualsAssociation} elements in a
|
747
|
* {@link TaxonDescription} contain {@link DerivedUnit}s</li>
|
748
|
* <li>{@link SpecimenTypeDesignation}s may be associated with any
|
749
|
* {@link HomotypicalGroup} related to the specific {@link Taxon}.</li>
|
750
|
* <li>A {@link Taxon} may be referenced by the {@link DeterminationEvent}
|
751
|
* of the {@link SpecimenOrObservationBase}</li>
|
752
|
* </ul>
|
753
|
* Further more there also can be taxa which are associated with the taxon
|
754
|
* in question (parameter associatedTaxon) by {@link TaxonRelationship}s. If
|
755
|
* the parameter <code>includeRelationships</code> is containing elements,
|
756
|
* these according {@TaxonRelationshipType}s and
|
757
|
* directional information will be used to collect further
|
758
|
* {@link SpecimenOrObservationBase} instances found this way.
|
759
|
*
|
760
|
* @param <T>
|
761
|
* @param type
|
762
|
* Restriction to a specific subtype, may be null.
|
763
|
* @param associatedTaxon
|
764
|
* @param Set<TaxonRelationshipVector> includeRelationships. TaxonRelationships will not be taken into account if this is <code>NULL</code>.
|
765
|
* @param maxDepth TODO
|
766
|
* @param pageSize
|
767
|
* @param pageNumber
|
768
|
* @param orderHints
|
769
|
* @param propertyPaths
|
770
|
* @return
|
771
|
*/
|
772
|
public <T extends SpecimenOrObservationBase> Collection<T> listRootUnitsByAssociatedTaxon(Class<T> type, Taxon associatedTaxon, List<OrderHint> orderHints, List<String> propertyPaths);
|
773
|
|
774
|
|
775
|
/**
|
776
|
* See {@link #listFieldUnitsByAssociatedTaxon(Set, Taxon, Integer, Integer, Integer, List, List)}
|
777
|
*/
|
778
|
public <T extends SpecimenOrObservationBase> Pager<T> pageRootUnitsByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
|
779
|
Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
780
|
|
781
|
|
782
|
|
783
|
public List<Point> findPointsForFieldUnitList(List<UUID> fieldUnitUuids);
|
784
|
|
785
|
/**
|
786
|
* Load the FieldUnitDTO for the given <code>derivedUnitUuid</code> with all intermediate derivatives and {@link eu.etaxonomy.cdm.api.service.dto.GatheringEventDTO}
|
787
|
|
788
|
* @param derivedUnitUuid
|
789
|
* @return
|
790
|
*/
|
791
|
FieldUnitDTO loadFieldUnitDTO(UUID derivedUnitUuid);
|
792
|
|
793
|
Pager<MediaDTO> getMediaDTOs(SpecimenOrObservationBase<?> occurence, Integer pageSize, Integer pageNumber);
|
794
|
|
795
|
}
|