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887126ca
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Andreas Müller
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/**
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* Copyright (C) 2007 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.net.URI;
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import java.net.URISyntaxException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.HashSet;
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09a260bb
|
Katja Luther
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import java.util.Iterator;
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887126ca
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Andreas Müller
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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2622a38b
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Andreas Müller
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import org.apache.lucene.queryparser.classic.ParseException;
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887126ca
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Andreas Müller
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import org.apache.lucene.search.BooleanClause.Occur;
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f6b282fc
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Andreas Kohlbecker
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import org.apache.lucene.search.BooleanQuery.Builder;
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887126ca
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Andreas Müller
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import org.apache.lucene.search.SortField;
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57ea8a3a
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Andreas Kohlbecker
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import org.apache.lucene.search.grouping.TopGroups;
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import org.apache.lucene.util.BytesRef;
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887126ca
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Andreas Müller
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import org.hibernate.TransientObjectException;
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import org.hibernate.search.spatial.impl.Rectangle;
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import org.joda.time.Partial;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.dao.DataRetrievalFailureException;
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import org.springframework.stereotype.Service;
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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.DerivedUnitFacadeConfigurator;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
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import eu.etaxonomy.cdm.api.service.UpdateResult.Status;
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import eu.etaxonomy.cdm.api.service.config.DeleteConfiguratorBase;
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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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a7e45124
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Katja Luther
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import eu.etaxonomy.cdm.api.service.dto.DNASampleDTO;
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887126ca
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Andreas Müller
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import eu.etaxonomy.cdm.api.service.dto.DerivateDTO;
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import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO;
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import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO.ContigFile;
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91cdf81a
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Patrick Plitzner
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import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO.Link;
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887126ca
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Andreas Müller
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import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO.MolecularData;
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import eu.etaxonomy.cdm.api.service.dto.FieldUnitDTO;
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import eu.etaxonomy.cdm.api.service.dto.PreservedSpecimenDTO;
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import eu.etaxonomy.cdm.api.service.exception.ReferencedObjectUndeletableException;
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import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
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import eu.etaxonomy.cdm.api.service.search.ILuceneIndexToolProvider;
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import eu.etaxonomy.cdm.api.service.search.ISearchResultBuilder;
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3ca8a283
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Patrick Plitzner
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import eu.etaxonomy.cdm.api.service.search.LuceneParseException;
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887126ca
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Andreas Müller
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import eu.etaxonomy.cdm.api.service.search.LuceneSearch;
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import eu.etaxonomy.cdm.api.service.search.QueryFactory;
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import eu.etaxonomy.cdm.api.service.search.SearchResult;
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import eu.etaxonomy.cdm.api.service.search.SearchResultBuilder;
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import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
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3c8d638c
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Patrick Plitzner
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import eu.etaxonomy.cdm.common.CdmUtils;
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887126ca
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Andreas Müller
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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6557bce4
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Patrick Plitzner
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import eu.etaxonomy.cdm.format.CdmFormatterFactory;
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import eu.etaxonomy.cdm.format.ICdmFormatter.FormatKey;
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887126ca
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Andreas Müller
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.CdmBaseType;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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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.QuantitativeData;
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import eu.etaxonomy.cdm.model.description.SpecimenDescription;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.location.Country;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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6b53ead8
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Katja Luther
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import eu.etaxonomy.cdm.model.location.Point;
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887126ca
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Andreas Müller
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.media.MediaRepresentation;
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import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
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import eu.etaxonomy.cdm.model.media.MediaUtils;
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import eu.etaxonomy.cdm.model.molecular.AmplificationResult;
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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.molecular.SingleRead;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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9dc896c9
|
Andreas Müller
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import eu.etaxonomy.cdm.model.name.TaxonName;
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887126ca
|
Andreas Müller
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import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
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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.persistence.dao.common.IDefinedTermDao;
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import eu.etaxonomy.cdm.persistence.dao.initializer.AbstractBeanInitializer;
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import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;
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| 116 |
edfed701
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Patrick Plitzner
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import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;
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887126ca
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Andreas Müller
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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1cfc76cb
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Patrick Plitzner
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import eu.etaxonomy.cdm.persistence.query.AssignmentStatus;
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887126ca
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Andreas Müller
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
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9c61a32b
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Patrick Plitzner
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import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;
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887126ca
|
Andreas Müller
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/**
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* @author a.babadshanjan
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a88578ce
|
Andreas Müller
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* @since 01.09.2008
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887126ca
|
Andreas Müller
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*/
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@Service
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@Transactional(readOnly = true)
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public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObservationBase, IOccurrenceDao> implements IOccurrenceService {
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static private final Logger logger = Logger.getLogger(OccurrenceServiceImpl.class);
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@Autowired
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private IDefinedTermDao definedTermDao;
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@Autowired
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private IDescriptionService descriptionService;
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e6e5ebdc
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Patrick Plitzner
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@Autowired
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private INameService nameService;
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a9c2b3c3
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Katja Luther
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@Autowired
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private IEventBaseService eventService;
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887126ca
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Andreas Müller
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@Autowired
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private ITaxonService taxonService;
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@Autowired
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private ISequenceService sequenceService;
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@Autowired
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private AbstractBeanInitializer beanInitializer;
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@Autowired
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private ILuceneIndexToolProvider luceneIndexToolProvider;
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private static final String SEPARATOR_STRING = ", ";
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| 159 |
ee6e05c9
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Katja Luther
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private static final List<String> DERIVED_UNIT_INIT_STRATEGY = Arrays.asList(new String []{
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"derivedFrom.derivatives",
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"derivedFrom.originals",
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"specimenTypeDesignations.*",
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"specimenTypeDesignations.citation.*",
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"specimenTypeDesignations.homotypicalGroup.*",
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"specimenTypeDesignations.typifiedNames",
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"collection.$"
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});
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887126ca
|
Andreas Müller
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public OccurrenceServiceImpl() {
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logger.debug("Load OccurrenceService Bean");
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}
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@Override
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@Transactional(readOnly = false)
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public void updateTitleCache(Class<? extends SpecimenOrObservationBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<SpecimenOrObservationBase> cacheStrategy, IProgressMonitor monitor) {
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if (clazz == null) {
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clazz = SpecimenOrObservationBase.class;
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}
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super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
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}
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/**
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* FIXME Candidate for harmonization
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* move to termService
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*/
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@Override
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public Country getCountryByIso(String iso639) {
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return this.definedTermDao.getCountryByIso(iso639);
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}
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/**
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* FIXME Candidate for harmonization
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* move to termService
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*/
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@Override
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public List<Country> getCountryByName(String name) {
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024d9b21
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Andreas Kohlbecker
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List<? extends DefinedTermBase> terms = this.definedTermDao.findByTitleWithRestrictions(Country.class, name, null, null, null, null, null, null);
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7e7e032e
|
Andreas Müller
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List<Country> countries = new ArrayList<>();
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887126ca
|
Andreas Müller
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for (int i = 0; i < terms.size(); i++) {
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countries.add((Country) terms.get(i));
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}
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return countries;
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}
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@Override
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@Autowired
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protected void setDao(IOccurrenceDao dao) {
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this.dao = dao;
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}
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@Override
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public Pager<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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| 215 |
9a21de1f
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Andreas Müller
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long numberOfResults = dao.countDerivationEvents(occurence);
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| 216 |
887126ca
|
Andreas Müller
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7e7e032e
|
Andreas Müller
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List<DerivationEvent> results = new ArrayList<>();
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| 218 |
887126ca
|
Andreas Müller
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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results = dao.getDerivationEvents(occurence, pageSize, pageNumber, propertyPaths);
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}
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9a21de1f
|
Andreas Müller
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return new DefaultPagerImpl<DerivationEvent>(pageNumber, numberOfResults, pageSize, results);
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| 223 |
887126ca
|
Andreas Müller
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}
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@Override
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| 226 |
9a21de1f
|
Andreas Müller
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public long countDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonbase) {
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| 227 |
887126ca
|
Andreas Müller
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return dao.countDeterminations(occurence, taxonbase);
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}
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@Override
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| 231 |
2a4c4dd0
|
Andreas Müller
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public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase,
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Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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| 233 |
9a21de1f
|
Andreas Müller
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long numberOfResults = dao.countDeterminations(occurrence, taxonBase);
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| 234 |
887126ca
|
Andreas Müller
|
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| 235 |
7e7e032e
|
Andreas Müller
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List<DeterminationEvent> results = new ArrayList<>();
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| 236 |
887126ca
|
Andreas Müller
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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results = dao.getDeterminations(occurrence, taxonBase, pageSize, pageNumber, propertyPaths);
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}
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| 240 |
9a21de1f
|
Andreas Müller
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return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
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| 241 |
887126ca
|
Andreas Müller
|
}
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@Override
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| 244 |
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public Pager<Media> getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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| 245 |
9a21de1f
|
Andreas Müller
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long numberOfResults = dao.countMedia(occurence);
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| 246 |
887126ca
|
Andreas Müller
|
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| 247 |
7e7e032e
|
Andreas Müller
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List<Media> results = new ArrayList<>();
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| 248 |
887126ca
|
Andreas Müller
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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results = dao.getMedia(occurence, pageSize, pageNumber, propertyPaths);
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}
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| 252 |
9a21de1f
|
Andreas Müller
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return new DefaultPagerImpl<Media>(pageNumber, numberOfResults, pageSize, results);
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| 253 |
887126ca
|
Andreas Müller
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}
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| 254 |
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| 255 |
6eccaa42
|
Patrick Plitzner
|
@Override
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| 256 |
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public Pager<Media> getMediainHierarchy(SpecimenOrObservationBase rootOccurence, Integer pageSize,
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Integer pageNumber, List<String> propertyPaths) {
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| 258 |
7e7e032e
|
Andreas Müller
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List<Media> media = new ArrayList<>();
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| 259 |
6eccaa42
|
Patrick Plitzner
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//media specimens
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| 260 |
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if(rootOccurence.isInstanceOf(MediaSpecimen.class)){
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MediaSpecimen mediaSpecimen = HibernateProxyHelper.deproxy(rootOccurence, MediaSpecimen.class);
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media.add(mediaSpecimen.getMediaSpecimen());
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}
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| 264 |
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// pherograms & gelPhotos
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if (rootOccurence.isInstanceOf(DnaSample.class)) {
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|
|
DnaSample dnaSample = CdmBase.deproxy(rootOccurence, DnaSample.class);
|
| 267 |
|
|
Set<Sequence> sequences = dnaSample.getSequences();
|
| 268 |
|
|
//we do show only those gelPhotos which lead to a consensus sequence
|
| 269 |
|
|
for (Sequence sequence : sequences) {
|
| 270 |
7e7e032e
|
Andreas Müller
|
Set<Media> dnaRelatedMedia = new HashSet<>();
|
| 271 |
6eccaa42
|
Patrick Plitzner
|
for (SingleRead singleRead : sequence.getSingleReads()){
|
| 272 |
|
|
AmplificationResult amplification = singleRead.getAmplificationResult();
|
| 273 |
|
|
dnaRelatedMedia.add(amplification.getGelPhoto());
|
| 274 |
|
|
dnaRelatedMedia.add(singleRead.getPherogram());
|
| 275 |
|
|
dnaRelatedMedia.remove(null);
|
| 276 |
|
|
}
|
| 277 |
|
|
media.addAll(dnaRelatedMedia);
|
| 278 |
|
|
}
|
| 279 |
|
|
}
|
| 280 |
|
|
if(rootOccurence.isInstanceOf(DerivedUnit.class)){
|
| 281 |
|
|
DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(rootOccurence, DerivedUnit.class);
|
| 282 |
|
|
for (DerivationEvent derivationEvent : derivedUnit.getDerivationEvents()) {
|
| 283 |
|
|
for (DerivedUnit childDerivative : derivationEvent.getDerivatives()) {
|
| 284 |
|
|
media.addAll(getMediainHierarchy(childDerivative, pageSize, pageNumber, propertyPaths).getRecords());
|
| 285 |
|
|
}
|
| 286 |
|
|
}
|
| 287 |
|
|
}
|
| 288 |
2a4c4dd0
|
Andreas Müller
|
return new DefaultPagerImpl<Media>(pageNumber, Long.valueOf(media.size()), pageSize, media);
|
| 289 |
6eccaa42
|
Patrick Plitzner
|
}
|
| 290 |
|
|
|
| 291 |
e6e5ebdc
|
Patrick Plitzner
|
@Override
|
| 292 |
2a4c4dd0
|
Andreas Müller
|
public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonName determinedAs,
|
| 293 |
|
|
Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 294 |
9a21de1f
|
Andreas Müller
|
long numberOfResults = dao.count(type, determinedAs);
|
| 295 |
2a4c4dd0
|
Andreas Müller
|
@SuppressWarnings("rawtypes")
|
| 296 |
7e7e032e
|
Andreas Müller
|
List<SpecimenOrObservationBase> results = new ArrayList<>();
|
| 297 |
e6e5ebdc
|
Patrick Plitzner
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
| 298 |
2a4c4dd0
|
Andreas Müller
|
results = dao.list(type, determinedAs, pageSize, pageNumber, orderHints, propertyPaths);
|
| 299 |
e6e5ebdc
|
Patrick Plitzner
|
}
|
| 300 |
9a21de1f
|
Andreas Müller
|
return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
|
| 301 |
e6e5ebdc
|
Patrick Plitzner
|
}
|
| 302 |
|
|
|
| 303 |
887126ca
|
Andreas Müller
|
@Override
|
| 304 |
2a4c4dd0
|
Andreas Müller
|
public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs,
|
| 305 |
|
|
Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 306 |
9a21de1f
|
Andreas Müller
|
long numberOfResults = dao.count(type, determinedAs);
|
| 307 |
2a4c4dd0
|
Andreas Müller
|
@SuppressWarnings("rawtypes")
|
| 308 |
7e7e032e
|
Andreas Müller
|
List<SpecimenOrObservationBase> results = new ArrayList<>();
|
| 309 |
887126ca
|
Andreas Müller
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
| 310 |
2a4c4dd0
|
Andreas Müller
|
results = dao.list(type, determinedAs, pageSize, pageNumber, orderHints, propertyPaths);
|
| 311 |
887126ca
|
Andreas Müller
|
}
|
| 312 |
9a21de1f
|
Andreas Müller
|
return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
|
| 313 |
887126ca
|
Andreas Müller
|
}
|
| 314 |
|
|
|
| 315 |
|
|
@Override
|
| 316 |
a9c2b3c3
|
Katja Luther
|
public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache(Integer limit, String pattern) {
|
| 317 |
|
|
return dao.getDerivedUnitUuidAndTitleCache(limit, pattern);
|
| 318 |
887126ca
|
Andreas Müller
|
}
|
| 319 |
|
|
|
| 320 |
|
|
@Override
|
| 321 |
|
|
public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {
|
| 322 |
|
|
return dao.getFieldUnitUuidAndTitleCache();
|
| 323 |
|
|
}
|
| 324 |
|
|
|
| 325 |
|
|
@Override
|
| 326 |
|
|
public DerivedUnitFacade getDerivedUnitFacade(DerivedUnit derivedUnit, List<String> propertyPaths) throws DerivedUnitFacadeNotSupportedException {
|
| 327 |
|
|
derivedUnit = (DerivedUnit) dao.load(derivedUnit.getUuid(), null);
|
| 328 |
|
|
DerivedUnitFacadeConfigurator config = DerivedUnitFacadeConfigurator.NewInstance();
|
| 329 |
|
|
config.setThrowExceptionForNonSpecimenPreservationMethodRequest(false);
|
| 330 |
|
|
DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit, config);
|
| 331 |
|
|
beanInitializer.initialize(derivedUnitFacade, propertyPaths);
|
| 332 |
|
|
return derivedUnitFacade;
|
| 333 |
|
|
}
|
| 334 |
|
|
|
| 335 |
|
|
@Override
|
| 336 |
|
|
public List<DerivedUnitFacade> listDerivedUnitFacades(
|
| 337 |
|
|
DescriptionBase description, List<String> propertyPaths) {
|
| 338 |
|
|
|
| 339 |
7e7e032e
|
Andreas Müller
|
List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<>();
|
| 340 |
887126ca
|
Andreas Müller
|
IndividualsAssociation tempIndividualsAssociation;
|
| 341 |
|
|
SpecimenOrObservationBase tempSpecimenOrObservationBase;
|
| 342 |
a1439def
|
Andreas Müller
|
List<IndividualsAssociation> elements = descriptionService.listDescriptionElements(description, null, IndividualsAssociation.class, null, 0, Arrays.asList(new String []{"associatedSpecimenOrObservation"}));
|
| 343 |
|
|
for (IndividualsAssociation element : elements) {
|
| 344 |
|
|
tempIndividualsAssociation = HibernateProxyHelper.deproxy(element, IndividualsAssociation.class);
|
| 345 |
|
|
if (tempIndividualsAssociation.getAssociatedSpecimenOrObservation() != null) {
|
| 346 |
|
|
tempSpecimenOrObservationBase = HibernateProxyHelper.deproxy(tempIndividualsAssociation.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase.class);
|
| 347 |
|
|
if (tempSpecimenOrObservationBase.isInstanceOf(DerivedUnit.class)) {
|
| 348 |
|
|
try {
|
| 349 |
|
|
derivedUnitFacadeList.add(DerivedUnitFacade.NewInstance(HibernateProxyHelper.deproxy(tempSpecimenOrObservationBase, DerivedUnit.class)));
|
| 350 |
|
|
} catch (DerivedUnitFacadeNotSupportedException e) {
|
| 351 |
|
|
logger.warn(tempIndividualsAssociation.getAssociatedSpecimenOrObservation().getTitleCache() + " : " + e.getMessage());
|
| 352 |
887126ca
|
Andreas Müller
|
}
|
| 353 |
|
|
}
|
| 354 |
|
|
}
|
| 355 |
|
|
}
|
| 356 |
|
|
|
| 357 |
|
|
beanInitializer.initializeAll(derivedUnitFacadeList, propertyPaths);
|
| 358 |
|
|
|
| 359 |
|
|
return derivedUnitFacadeList;
|
| 360 |
|
|
}
|
| 361 |
|
|
|
| 362 |
|
|
|
| 363 |
|
|
@Override
|
| 364 |
|
|
public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
|
| 365 |
|
|
Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 366 |
|
|
|
| 367 |
|
|
return pageByAssociatedTaxon(type, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
|
| 368 |
|
|
}
|
| 369 |
|
|
|
| 370 |
edfed701
|
Patrick Plitzner
|
@Override
|
| 371 |
d9b27602
|
Patrick Plitzner
|
public Collection<SpecimenNodeWrapper> listUuidAndTitleCacheByAssociatedTaxon(List<UUID> taxonNodeUuids,
|
| 372 |
b27b3345
|
Patrick Plitzner
|
Integer limit, Integer start) {
|
| 373 |
|
|
return dao.listUuidAndTitleCacheByAssociatedTaxon(taxonNodeUuids, limit, start);
|
| 374 |
edfed701
|
Patrick Plitzner
|
}
|
| 375 |
|
|
|
| 376 |
887126ca
|
Andreas Müller
|
@Override
|
| 377 |
|
|
public Collection<SpecimenOrObservationBase> listFieldUnitsByAssociatedTaxon(Taxon associatedTaxon, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 378 |
|
|
return pageFieldUnitsByAssociatedTaxon(null, associatedTaxon, null, null, null, null, propertyPaths).getRecords();
|
| 379 |
|
|
}
|
| 380 |
|
|
|
| 381 |
|
|
@Override
|
| 382 |
|
|
public Pager<SpecimenOrObservationBase> pageFieldUnitsByAssociatedTaxon(Set<TaxonRelationshipEdge> includeRelationships,
|
| 383 |
|
|
Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
|
| 384 |
|
|
List<String> propertyPaths) {
|
| 385 |
|
|
|
| 386 |
|
|
if (!getSession().contains(associatedTaxon)) {
|
| 387 |
|
|
associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
|
| 388 |
|
|
}
|
| 389 |
|
|
|
| 390 |
|
|
// gather the IDs of all relevant field units
|
| 391 |
7e7e032e
|
Andreas Müller
|
Set<UUID> fieldUnitUuids = new HashSet<>();
|
| 392 |
887126ca
|
Andreas Müller
|
List<SpecimenOrObservationBase> records = listByAssociatedTaxon(null, includeRelationships, associatedTaxon, maxDepth, null, null, orderHints, propertyPaths);
|
| 393 |
|
|
for (SpecimenOrObservationBase<?> specimen : records) {
|
| 394 |
6b53ead8
|
Katja Luther
|
for (FieldUnit fieldUnit : findFieldUnits(specimen.getUuid(), null)) {
|
| 395 |
88d0b58a
|
Patrick Plitzner
|
fieldUnitUuids.add(fieldUnit.getUuid());
|
| 396 |
887126ca
|
Andreas Müller
|
}
|
| 397 |
|
|
}
|
| 398 |
88d0b58a
|
Patrick Plitzner
|
//dao.list() does the paging of the field units. Passing the field units directly to the Pager would not work
|
| 399 |
|
|
List<SpecimenOrObservationBase> fieldUnits = dao.list(fieldUnitUuids, pageSize, pageNumber, orderHints, propertyPaths);
|
| 400 |
ea33ac4f
|
Andreas Müller
|
return new DefaultPagerImpl<>(pageNumber, fieldUnitUuids.size(), pageSize, fieldUnits);
|
| 401 |
887126ca
|
Andreas Müller
|
}
|
| 402 |
|
|
|
| 403 |
|
|
@Override
|
| 404 |
eec520d3
|
Andreas Kohlbecker
|
public FieldUnitDTO assembleFieldUnitDTO(FieldUnit fieldUnit) {
|
| 405 |
887126ca
|
Andreas Müller
|
|
| 406 |
|
|
if (!getSession().contains(fieldUnit)) {
|
| 407 |
|
|
fieldUnit = (FieldUnit) load(fieldUnit.getUuid());
|
| 408 |
|
|
}
|
| 409 |
|
|
|
| 410 |
d70a126f
|
Katja Luther
|
FieldUnitDTO fieldUnitDTO = new FieldUnitDTO(fieldUnit);
|
| 411 |
887126ca
|
Andreas Müller
|
|
| 412 |
|
|
if (fieldUnit.getGatheringEvent() != null) {
|
| 413 |
|
|
GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
|
| 414 |
|
|
// Country
|
| 415 |
|
|
NamedArea country = gatheringEvent.getCountry();
|
| 416 |
4103e3d4
|
Patrick Plitzner
|
fieldUnitDTO.setCountry(country != null ? country.getLabel() : null);
|
| 417 |
887126ca
|
Andreas Müller
|
// Collection
|
| 418 |
|
|
AgentBase collector = gatheringEvent.getCollector();
|
| 419 |
|
|
String fieldNumber = fieldUnit.getFieldNumber();
|
| 420 |
|
|
String collectionString = "";
|
| 421 |
|
|
if (collector != null || fieldNumber != null) {
|
| 422 |
|
|
collectionString += collector != null ? collector : "";
|
| 423 |
|
|
if (!collectionString.isEmpty()) {
|
| 424 |
|
|
collectionString += " ";
|
| 425 |
|
|
}
|
| 426 |
|
|
collectionString += (fieldNumber != null ? fieldNumber : "");
|
| 427 |
|
|
collectionString.trim();
|
| 428 |
|
|
}
|
| 429 |
|
|
fieldUnitDTO.setCollection(collectionString);
|
| 430 |
|
|
// Date
|
| 431 |
|
|
Partial gatheringDate = gatheringEvent.getGatheringDate();
|
| 432 |
|
|
String dateString = null;
|
| 433 |
|
|
if (gatheringDate != null) {
|
| 434 |
6557bce4
|
Patrick Plitzner
|
dateString = gatheringDate.toString();
|
| 435 |
887126ca
|
Andreas Müller
|
}
|
| 436 |
|
|
else if(gatheringEvent.getTimeperiod()!=null && gatheringEvent.getTimeperiod().getFreeText()!=null){
|
| 437 |
|
|
dateString = gatheringEvent.getTimeperiod().getFreeText();
|
| 438 |
|
|
}
|
| 439 |
|
|
fieldUnitDTO.setDate(dateString);
|
| 440 |
|
|
}
|
| 441 |
|
|
|
| 442 |
|
|
// Herbaria map
|
| 443 |
7e7e032e
|
Andreas Müller
|
Map<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> collectionToCountMap = new HashMap<>();
|
| 444 |
887126ca
|
Andreas Müller
|
// List of accession numbers for citation
|
| 445 |
7e7e032e
|
Andreas Müller
|
List<String> preservedSpecimenAccessionNumbers = new ArrayList<>();
|
| 446 |
887126ca
|
Andreas Müller
|
|
| 447 |
|
|
// assemble preserved specimen DTOs
|
| 448 |
|
|
Set<DerivationEvent> derivationEvents = fieldUnit.getDerivationEvents();
|
| 449 |
|
|
for (DerivationEvent derivationEvent : derivationEvents) {
|
| 450 |
|
|
Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
|
| 451 |
|
|
for (DerivedUnit derivedUnit : derivatives) {
|
| 452 |
612d9ce9
|
Patrick Plitzner
|
if(!derivedUnit.isPublish()){
|
| 453 |
|
|
continue;
|
| 454 |
|
|
}
|
| 455 |
887126ca
|
Andreas Müller
|
// collect accession numbers for citation
|
| 456 |
5a143666
|
Patrick Plitzner
|
String identifier = getMostSignificantIdentifier(derivedUnit);
|
| 457 |
887126ca
|
Andreas Müller
|
// collect collections for herbaria column
|
| 458 |
5a143666
|
Patrick Plitzner
|
eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
|
| 459 |
|
|
if (collection != null) {
|
| 460 |
|
|
//combine collection with identifier
|
| 461 |
|
|
if (identifier != null) {
|
| 462 |
|
|
if(collection.getCode()!=null){
|
| 463 |
|
|
identifier = (collection.getCode()!=null?collection.getCode():"[no collection]")+" "+identifier;
|
| 464 |
|
|
}
|
| 465 |
|
|
preservedSpecimenAccessionNumbers.add(identifier);
|
| 466 |
|
|
}
|
| 467 |
|
|
|
| 468 |
|
|
Integer herbariumCount = collectionToCountMap.get(collection);
|
| 469 |
887126ca
|
Andreas Müller
|
if (herbariumCount == null) {
|
| 470 |
|
|
herbariumCount = 0;
|
| 471 |
|
|
}
|
| 472 |
5a143666
|
Patrick Plitzner
|
collectionToCountMap.put(collection, herbariumCount + 1);
|
| 473 |
887126ca
|
Andreas Müller
|
}
|
| 474 |
|
|
if (derivedUnit.getRecordBasis().equals(SpecimenOrObservationType.PreservedSpecimen)) {
|
| 475 |
|
|
PreservedSpecimenDTO preservedSpecimenDTO = assemblePreservedSpecimenDTO(derivedUnit, fieldUnitDTO);
|
| 476 |
77993547
|
Katja Luther
|
fieldUnitDTO.addDerivate(preservedSpecimenDTO);
|
| 477 |
887126ca
|
Andreas Müller
|
fieldUnitDTO.setHasCharacterData(fieldUnitDTO.isHasCharacterData() || preservedSpecimenDTO.isHasCharacterData());
|
| 478 |
|
|
fieldUnitDTO.setHasDetailImage(fieldUnitDTO.isHasDetailImage() || preservedSpecimenDTO.isHasDetailImage());
|
| 479 |
|
|
fieldUnitDTO.setHasDna(fieldUnitDTO.isHasDna() || preservedSpecimenDTO.isHasDna());
|
| 480 |
|
|
fieldUnitDTO.setHasSpecimenScan(fieldUnitDTO.isHasSpecimenScan() || preservedSpecimenDTO.isHasSpecimenScan());
|
| 481 |
|
|
}
|
| 482 |
|
|
}
|
| 483 |
|
|
}
|
| 484 |
|
|
// assemble derivate data DTO
|
| 485 |
|
|
assembleDerivateDataDTO(fieldUnitDTO, fieldUnit);
|
| 486 |
|
|
|
| 487 |
|
|
// assemble citation
|
| 488 |
|
|
String citation = fieldUnit.getTitleCache();
|
| 489 |
9c61a32b
|
Patrick Plitzner
|
if((CdmUtils.isBlank(citation) || citation.equals(IdentifiableEntityDefaultCacheStrategy.TITLE_CACHE_GENERATION_NOT_IMPLEMENTED))
|
| 490 |
4fd26794
|
Patrick Plitzner
|
&& !fieldUnit.isProtectedTitleCache()){
|
| 491 |
|
|
fieldUnit.setTitleCache(null);
|
| 492 |
|
|
citation = fieldUnit.getTitleCache();
|
| 493 |
|
|
}
|
| 494 |
887126ca
|
Andreas Müller
|
if (!preservedSpecimenAccessionNumbers.isEmpty()) {
|
| 495 |
|
|
citation += " (";
|
| 496 |
|
|
for (String accessionNumber : preservedSpecimenAccessionNumbers) {
|
| 497 |
|
|
if (!accessionNumber.isEmpty()) {
|
| 498 |
|
|
citation += accessionNumber + SEPARATOR_STRING;
|
| 499 |
|
|
}
|
| 500 |
|
|
}
|
| 501 |
|
|
citation = removeTail(citation, SEPARATOR_STRING);
|
| 502 |
|
|
citation += ")";
|
| 503 |
|
|
}
|
| 504 |
|
|
fieldUnitDTO.setCitation(citation);
|
| 505 |
|
|
|
| 506 |
|
|
// assemble herbaria string
|
| 507 |
|
|
String herbariaString = "";
|
| 508 |
|
|
for (Entry<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> e : collectionToCountMap.entrySet()) {
|
| 509 |
|
|
eu.etaxonomy.cdm.model.occurrence.Collection collection = e.getKey();
|
| 510 |
|
|
if (collection.getCode() != null) {
|
| 511 |
|
|
herbariaString += collection.getCode();
|
| 512 |
|
|
}
|
| 513 |
|
|
if (e.getValue() > 1) {
|
| 514 |
|
|
herbariaString += "(" + e.getValue() + ")";
|
| 515 |
|
|
}
|
| 516 |
|
|
herbariaString += SEPARATOR_STRING;
|
| 517 |
|
|
}
|
| 518 |
|
|
herbariaString = removeTail(herbariaString, SEPARATOR_STRING);
|
| 519 |
cb9801c1
|
Katja Luther
|
fieldUnitDTO.setCollection(herbariaString);
|
| 520 |
887126ca
|
Andreas Müller
|
|
| 521 |
|
|
return fieldUnitDTO;
|
| 522 |
|
|
}
|
| 523 |
|
|
|
| 524 |
|
|
@Override
|
| 525 |
|
|
public PreservedSpecimenDTO assemblePreservedSpecimenDTO(DerivedUnit derivedUnit) {
|
| 526 |
|
|
return assemblePreservedSpecimenDTO(derivedUnit, null);
|
| 527 |
|
|
}
|
| 528 |
|
|
|
| 529 |
|
|
@Override
|
| 530 |
|
|
public String getMostSignificantIdentifier(DerivedUnit derivedUnit) {
|
| 531 |
|
|
if (derivedUnit.getAccessionNumber() != null && !derivedUnit.getAccessionNumber().isEmpty()) {
|
| 532 |
|
|
return derivedUnit.getAccessionNumber();
|
| 533 |
|
|
}
|
| 534 |
|
|
else if(derivedUnit.getBarcode()!=null && !derivedUnit.getBarcode().isEmpty()){
|
| 535 |
|
|
return derivedUnit.getBarcode();
|
| 536 |
|
|
}
|
| 537 |
|
|
else if(derivedUnit.getCatalogNumber()!=null && !derivedUnit.getCatalogNumber().isEmpty()){
|
| 538 |
|
|
return derivedUnit.getCatalogNumber();
|
| 539 |
|
|
}
|
| 540 |
|
|
return null;
|
| 541 |
|
|
}
|
| 542 |
|
|
|
| 543 |
|
|
public PreservedSpecimenDTO assemblePreservedSpecimenDTO(DerivedUnit derivedUnit, FieldUnitDTO fieldUnitDTO) {
|
| 544 |
|
|
if (!getSession().contains(derivedUnit)) {
|
| 545 |
|
|
derivedUnit = (DerivedUnit) load(derivedUnit.getUuid());
|
| 546 |
|
|
}
|
| 547 |
d70a126f
|
Katja Luther
|
PreservedSpecimenDTO preservedSpecimenDTO = new PreservedSpecimenDTO(derivedUnit);
|
| 548 |
887126ca
|
Andreas Müller
|
|
| 549 |
6557bce4
|
Patrick Plitzner
|
//specimen identifier
|
| 550 |
|
|
FormatKey collectionKey = FormatKey.COLLECTION_CODE;
|
| 551 |
2837fda6
|
Andreas Müller
|
String specimenIdentifier = CdmFormatterFactory.format(derivedUnit, collectionKey);
|
| 552 |
6557bce4
|
Patrick Plitzner
|
if (CdmUtils.isBlank(specimenIdentifier)) {
|
| 553 |
|
|
collectionKey = FormatKey.COLLECTION_NAME;
|
| 554 |
887126ca
|
Andreas Müller
|
}
|
| 555 |
6557bce4
|
Patrick Plitzner
|
specimenIdentifier = CdmFormatterFactory.format(derivedUnit, new FormatKey[] {
|
| 556 |
|
|
collectionKey, FormatKey.SPACE,
|
| 557 |
|
|
FormatKey.MOST_SIGNIFICANT_IDENTIFIER, FormatKey.SPACE });
|
| 558 |
01371d61
|
Patrick Plitzner
|
if(CdmUtils.isBlank(specimenIdentifier)){
|
| 559 |
|
|
specimenIdentifier = derivedUnit.getTitleCache();
|
| 560 |
|
|
}
|
| 561 |
6557bce4
|
Patrick Plitzner
|
if(CdmUtils.isBlank(specimenIdentifier)){
|
| 562 |
|
|
specimenIdentifier = derivedUnit.getUuid().toString();
|
| 563 |
e1207484
|
Patrick Plitzner
|
}
|
| 564 |
6557bce4
|
Patrick Plitzner
|
preservedSpecimenDTO.setAccessionNumber(specimenIdentifier);
|
| 565 |
77993547
|
Katja Luther
|
|
| 566 |
887126ca
|
Andreas Müller
|
|
| 567 |
4a39cd98
|
Patrick Plitzner
|
//preferred stable URI
|
| 568 |
|
|
preservedSpecimenDTO.setPreferredStableUri(derivedUnit.getPreferredStableUri());
|
| 569 |
|
|
|
| 570 |
887126ca
|
Andreas Müller
|
// citation
|
| 571 |
42002c0a
|
Patrick Plitzner
|
Collection<FieldUnit> fieldUnits = getFieldUnits(derivedUnit, null);
|
| 572 |
887126ca
|
Andreas Müller
|
if (fieldUnits.size() == 1) {
|
| 573 |
|
|
preservedSpecimenDTO.setCitation(fieldUnits.iterator().next().getTitleCache());
|
| 574 |
|
|
}
|
| 575 |
|
|
else{
|
| 576 |
|
|
preservedSpecimenDTO.setCitation("No Citation available. This specimen either has no or multiple field units.");
|
| 577 |
|
|
}
|
| 578 |
|
|
|
| 579 |
|
|
// character state data
|
| 580 |
|
|
Collection<DescriptionElementBase> characterDataForSpecimen = getCharacterDataForSpecimen(derivedUnit);
|
| 581 |
|
|
if (!characterDataForSpecimen.isEmpty()) {
|
| 582 |
|
|
if (fieldUnitDTO != null) {
|
| 583 |
|
|
fieldUnitDTO.setHasCharacterData(true);
|
| 584 |
|
|
}
|
| 585 |
|
|
}
|
| 586 |
|
|
for (DescriptionElementBase descriptionElementBase : characterDataForSpecimen) {
|
| 587 |
|
|
String character = descriptionElementBase.getFeature().getLabel();
|
| 588 |
7e7e032e
|
Andreas Müller
|
ArrayList<Language> languages = new ArrayList<>(Collections.singleton(Language.DEFAULT()));
|
| 589 |
887126ca
|
Andreas Müller
|
if (descriptionElementBase instanceof QuantitativeData) {
|
| 590 |
|
|
QuantitativeData quantitativeData = (QuantitativeData) descriptionElementBase;
|
| 591 |
|
|
DefaultQuantitativeDescriptionBuilder builder = new DefaultQuantitativeDescriptionBuilder();
|
| 592 |
|
|
String state = builder.build(quantitativeData, languages).getText(Language.DEFAULT());
|
| 593 |
|
|
preservedSpecimenDTO.addCharacterData(character, state);
|
| 594 |
|
|
}
|
| 595 |
|
|
else if(descriptionElementBase instanceof CategoricalData){
|
| 596 |
|
|
CategoricalData categoricalData = (CategoricalData) descriptionElementBase;
|
| 597 |
|
|
DefaultCategoricalDescriptionBuilder builder = new DefaultCategoricalDescriptionBuilder();
|
| 598 |
|
|
String state = builder.build(categoricalData, languages).getText(Language.DEFAULT());
|
| 599 |
|
|
preservedSpecimenDTO.addCharacterData(character, state);
|
| 600 |
|
|
}
|
| 601 |
|
|
}
|
| 602 |
|
|
// check type designations
|
| 603 |
|
|
Collection<SpecimenTypeDesignation> specimenTypeDesignations = listTypeDesignations(derivedUnit, null, null, null, null);
|
| 604 |
|
|
for (SpecimenTypeDesignation specimenTypeDesignation : specimenTypeDesignations) {
|
| 605 |
|
|
if (fieldUnitDTO != null) {
|
| 606 |
|
|
fieldUnitDTO.setHasType(true);
|
| 607 |
|
|
}
|
| 608 |
|
|
TypeDesignationStatusBase<?> typeStatus = specimenTypeDesignation.getTypeStatus();
|
| 609 |
cd175378
|
Patrick Plitzner
|
Set<TaxonName> typifiedNames = specimenTypeDesignation.getTypifiedNames();
|
| 610 |
|
|
List<String> typedTaxaNames = new ArrayList<>();
|
| 611 |
|
|
for (TaxonName taxonName : typifiedNames) {
|
| 612 |
9657122e
|
Patrick Plitzner
|
typedTaxaNames.add(taxonName.getTitleCache());
|
| 613 |
887126ca
|
Andreas Müller
|
}
|
| 614 |
64688697
|
Patrick Plitzner
|
preservedSpecimenDTO.addTypes(typeStatus!=null?typeStatus.getLabel():"", typedTaxaNames);
|
| 615 |
887126ca
|
Andreas Müller
|
}
|
| 616 |
|
|
|
| 617 |
|
|
// individuals associations
|
| 618 |
|
|
Collection<IndividualsAssociation> individualsAssociations = listIndividualsAssociations(derivedUnit, null, null, null, null);
|
| 619 |
|
|
for (IndividualsAssociation individualsAssociation : individualsAssociations) {
|
| 620 |
|
|
if (individualsAssociation.getInDescription() != null) {
|
| 621 |
|
|
if (individualsAssociation.getInDescription().isInstanceOf(TaxonDescription.class)) {
|
| 622 |
|
|
TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(individualsAssociation.getInDescription(), TaxonDescription.class);
|
| 623 |
|
|
Taxon taxon = taxonDescription.getTaxon();
|
| 624 |
172def0a
|
Patrick Plitzner
|
if (taxon != null) {
|
| 625 |
|
|
preservedSpecimenDTO.addAssociatedTaxon(taxon);
|
| 626 |
887126ca
|
Andreas Müller
|
}
|
| 627 |
|
|
}
|
| 628 |
|
|
}
|
| 629 |
|
|
}
|
| 630 |
|
|
// assemble sub derivates
|
| 631 |
|
|
preservedSpecimenDTO.setDerivateDataDTO(assembleDerivateDataDTO(preservedSpecimenDTO, derivedUnit));
|
| 632 |
|
|
return preservedSpecimenDTO;
|
| 633 |
|
|
}
|
| 634 |
|
|
|
| 635 |
|
|
private DerivateDataDTO assembleDerivateDataDTO(DerivateDTO derivateDTO, SpecimenOrObservationBase<?> specimenOrObservation) {
|
| 636 |
|
|
DerivateDataDTO derivateDataDTO = new DerivateDataDTO();
|
| 637 |
|
|
Collection<DerivedUnit> childDerivates = getDerivedUnitsFor(specimenOrObservation);
|
| 638 |
|
|
for (DerivedUnit childDerivate : childDerivates) {
|
| 639 |
|
|
// assemble molecular data
|
| 640 |
|
|
//pattern: DNAMarker [contig1, primer1_1, primer1_2, ...][contig2, primer2_1, ...]...
|
| 641 |
|
|
if (childDerivate.isInstanceOf(DnaSample.class)) {
|
| 642 |
|
|
if (childDerivate.getRecordBasis() == SpecimenOrObservationType.TissueSample) {
|
| 643 |
|
|
// TODO implement TissueSample assembly for web service
|
| 644 |
|
|
}
|
| 645 |
|
|
if (childDerivate.getRecordBasis() == SpecimenOrObservationType.DnaSample) {
|
| 646 |
|
|
|
| 647 |
|
|
DnaSample dna = HibernateProxyHelper.deproxy(childDerivate, DnaSample.class);
|
| 648 |
|
|
if (!dna.getSequences().isEmpty()) {
|
| 649 |
|
|
derivateDTO.setHasDna(true);
|
| 650 |
|
|
}
|
| 651 |
|
|
for (Sequence sequence : dna.getSequences()) {
|
| 652 |
|
|
URI boldUri = null;
|
| 653 |
|
|
try {
|
| 654 |
|
|
boldUri = sequence.getBoldUri();
|
| 655 |
|
|
} catch (URISyntaxException e1) {
|
| 656 |
|
|
logger.error("Could not create BOLD URI", e1);
|
| 657 |
|
|
}
|
| 658 |
|
|
final DefinedTerm dnaMarker = sequence.getDnaMarker();
|
| 659 |
91cdf81a
|
Patrick Plitzner
|
Link providerLink = null;
|
| 660 |
|
|
if(boldUri!=null && dnaMarker!=null){
|
| 661 |
|
|
providerLink = new DerivateDataDTO.Link(boldUri, dnaMarker.getLabel());
|
| 662 |
|
|
}
|
| 663 |
|
|
MolecularData molecularData = derivateDataDTO.addProviderLink(providerLink);
|
| 664 |
887126ca
|
Andreas Müller
|
|
| 665 |
|
|
//contig file
|
| 666 |
|
|
ContigFile contigFile = null;
|
| 667 |
|
|
if (sequence.getContigFile() != null) {
|
| 668 |
|
|
MediaRepresentationPart contigMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile());
|
| 669 |
|
|
if (contigMediaRepresentationPart != null) {
|
| 670 |
91cdf81a
|
Patrick Plitzner
|
contigFile = molecularData.addContigFile(new Link(contigMediaRepresentationPart.getUri(), "contig"));
|
| 671 |
887126ca
|
Andreas Müller
|
}
|
| 672 |
|
|
}
|
| 673 |
91cdf81a
|
Patrick Plitzner
|
else{
|
| 674 |
|
|
contigFile = molecularData.addContigFile(null);
|
| 675 |
887126ca
|
Andreas Müller
|
}
|
| 676 |
|
|
// primer files
|
| 677 |
|
|
if (sequence.getSingleReads() != null) {
|
| 678 |
|
|
int readCount = 1;
|
| 679 |
|
|
for (SingleRead singleRead : sequence.getSingleReads()) {
|
| 680 |
|
|
MediaRepresentationPart pherogramMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram());
|
| 681 |
|
|
if (pherogramMediaRepresentationPart != null) {
|
| 682 |
|
|
contigFile.addPrimerLink(pherogramMediaRepresentationPart.getUri(), "read"+readCount++);
|
| 683 |
|
|
}
|
| 684 |
|
|
}
|
| 685 |
|
|
}
|
| 686 |
|
|
}
|
| 687 |
|
|
}
|
| 688 |
|
|
}
|
| 689 |
|
|
// assemble media data
|
| 690 |
|
|
else if (childDerivate.isInstanceOf(MediaSpecimen.class)) {
|
| 691 |
|
|
MediaSpecimen media = HibernateProxyHelper.deproxy(childDerivate, MediaSpecimen.class);
|
| 692 |
|
|
|
| 693 |
e1207484
|
Patrick Plitzner
|
URI mediaUri = getMediaUri(media);
|
| 694 |
887126ca
|
Andreas Müller
|
if (media.getKindOfUnit() != null) {
|
| 695 |
|
|
// specimen scan
|
| 696 |
91cdf81a
|
Patrick Plitzner
|
if (media.getKindOfUnit().getUuid().equals(DefinedTerm.uuidSpecimenScan)) {
|
| 697 |
887126ca
|
Andreas Müller
|
derivateDataDTO.addSpecimenScanUuid(media.getMediaSpecimen().getUuid());
|
| 698 |
|
|
derivateDTO.setHasSpecimenScan(true);
|
| 699 |
|
|
String imageLinkText = "scan";
|
| 700 |
|
|
if (derivateDTO instanceof PreservedSpecimenDTO && ((PreservedSpecimenDTO) derivateDTO).getAccessionNumber() != null) {
|
| 701 |
|
|
imageLinkText = ((PreservedSpecimenDTO) derivateDTO).getAccessionNumber();
|
| 702 |
|
|
}
|
| 703 |
e1207484
|
Patrick Plitzner
|
derivateDataDTO.addSpecimenScan(mediaUri, imageLinkText);
|
| 704 |
887126ca
|
Andreas Müller
|
}
|
| 705 |
|
|
// detail image
|
| 706 |
91cdf81a
|
Patrick Plitzner
|
else if (media.getKindOfUnit().getUuid().equals(DefinedTerm.uuidDetailImage)) {
|
| 707 |
887126ca
|
Andreas Müller
|
derivateDataDTO.addDetailImageUuid(media.getMediaSpecimen().getUuid());
|
| 708 |
|
|
derivateDTO.setHasDetailImage(true);
|
| 709 |
e1207484
|
Patrick Plitzner
|
String motif = "detail image";
|
| 710 |
|
|
if (media.getMediaSpecimen()!=null){
|
| 711 |
|
|
if(CdmUtils.isNotBlank(media.getMediaSpecimen().getTitleCache())) {
|
| 712 |
|
|
motif = media.getMediaSpecimen().getTitleCache();
|
| 713 |
|
|
}
|
| 714 |
887126ca
|
Andreas Müller
|
}
|
| 715 |
91cdf81a
|
Patrick Plitzner
|
derivateDataDTO.addDetailImage(mediaUri, motif);
|
| 716 |
887126ca
|
Andreas Müller
|
}
|
| 717 |
|
|
}
|
| 718 |
|
|
}
|
| 719 |
|
|
}
|
| 720 |
|
|
return derivateDataDTO;
|
| 721 |
|
|
}
|
| 722 |
|
|
|
| 723 |
|
|
private String removeTail(String string, final String tail) {
|
| 724 |
|
|
if (string.endsWith(tail)) {
|
| 725 |
|
|
string = string.substring(0, string.length() - tail.length());
|
| 726 |
|
|
}
|
| 727 |
|
|
return string;
|
| 728 |
|
|
}
|
| 729 |
|
|
|
| 730 |
e1207484
|
Patrick Plitzner
|
private URI getMediaUri(MediaSpecimen mediaSpecimen) {
|
| 731 |
|
|
URI mediaUri = null;
|
| 732 |
887126ca
|
Andreas Müller
|
Collection<MediaRepresentation> mediaRepresentations = mediaSpecimen.getMediaSpecimen().getRepresentations();
|
| 733 |
|
|
if (mediaRepresentations != null && !mediaRepresentations.isEmpty()) {
|
| 734 |
|
|
Collection<MediaRepresentationPart> mediaRepresentationParts = mediaRepresentations.iterator().next().getParts();
|
| 735 |
|
|
if (mediaRepresentationParts != null && !mediaRepresentationParts.isEmpty()) {
|
| 736 |
|
|
MediaRepresentationPart part = mediaRepresentationParts.iterator().next();
|
| 737 |
|
|
if (part.getUri() != null) {
|
| 738 |
e1207484
|
Patrick Plitzner
|
mediaUri = part.getUri();
|
| 739 |
887126ca
|
Andreas Müller
|
}
|
| 740 |
|
|
}
|
| 741 |
|
|
}
|
| 742 |
|
|
return mediaUri;
|
| 743 |
|
|
}
|
| 744 |
|
|
|
| 745 |
|
|
private Collection<DerivedUnit> getDerivedUnitsFor(SpecimenOrObservationBase<?> specimen) {
|
| 746 |
7e7e032e
|
Andreas Müller
|
Collection<DerivedUnit> derivedUnits = new ArrayList<>();
|
| 747 |
887126ca
|
Andreas Müller
|
for (DerivationEvent derivationEvent : specimen.getDerivationEvents()) {
|
| 748 |
|
|
for (DerivedUnit derivative : derivationEvent.getDerivatives()) {
|
| 749 |
|
|
derivedUnits.add(derivative);
|
| 750 |
|
|
derivedUnits.addAll(getDerivedUnitsFor(derivative));
|
| 751 |
|
|
}
|
| 752 |
|
|
}
|
| 753 |
|
|
return derivedUnits;
|
| 754 |
|
|
}
|
| 755 |
|
|
|
| 756 |
6b53ead8
|
Katja Luther
|
private Set<DerivateDTO> getDerivedUnitDTOsFor(DerivateDTO specimenDto, DerivedUnit specimen, HashMap<UUID, DerivateDTO> alreadyCollectedSpecimen) {
|
| 757 |
|
|
Set<DerivateDTO> derivedUnits = new HashSet<>();
|
| 758 |
|
|
// load
|
| 759 |
|
|
for (DerivationEvent derivationEvent : specimen.getDerivationEvents()) {
|
| 760 |
|
|
for (DerivedUnit derivative : derivationEvent.getDerivatives()) {
|
| 761 |
|
|
if (!alreadyCollectedSpecimen.containsKey(specimenDto.getUuid())){
|
| 762 |
a7e45124
|
Katja Luther
|
PreservedSpecimenDTO dto;
|
| 763 |
|
|
if (derivative instanceof DnaSample) {
|
| 764 |
|
|
dto = new DNASampleDTO(derivative);
|
| 765 |
|
|
} else {
|
| 766 |
484a120f
|
Katja Luther
|
dto = new PreservedSpecimenDTO(derivative);
|
| 767 |
a7e45124
|
Katja Luther
|
}
|
| 768 |
6b53ead8
|
Katja Luther
|
alreadyCollectedSpecimen.put(dto.getUuid(), dto);
|
| 769 |
|
|
dto.addAllDerivates(getDerivedUnitDTOsFor(dto, derivative, alreadyCollectedSpecimen));
|
| 770 |
|
|
derivedUnits.add(dto);
|
| 771 |
|
|
}
|
| 772 |
|
|
}
|
| 773 |
|
|
}
|
| 774 |
|
|
return derivedUnits;
|
| 775 |
|
|
}
|
| 776 |
887126ca
|
Andreas Müller
|
|
| 777 |
d70a126f
|
Katja Luther
|
// private Set<DerivateDTO> getDerivedUnitDTOsFor(DerivateDTO specimenDto, DerivedUnit specimen, HashMap<UUID, DerivateDTO> alreadyCollectedSpecimen) {
|
| 778 |
|
|
// Set<DerivateDTO> derivedUnits = new HashSet<>();
|
| 779 |
|
|
//// load
|
| 780 |
|
|
// for (DerivationEvent derivationEvent : specimen.getDerivationEvents()) {
|
| 781 |
|
|
// for (DerivedUnit derivative : derivationEvent.getDerivatives()) {
|
| 782 |
|
|
// if (!alreadyCollectedSpecimen.containsKey(specimenDto.getUuid())){
|
| 783 |
|
|
// PreservedSpecimenDTO dto;
|
| 784 |
|
|
// if (derivative instanceof DnaSample){
|
| 785 |
|
|
// dto = DNASampleDTO.newInstance(derivative);
|
| 786 |
|
|
// }else{
|
| 787 |
|
|
// dto = PreservedSpecimenDTO.newInstance(derivative);
|
| 788 |
|
|
// }
|
| 789 |
|
|
// alreadyCollectedSpecimen.put(dto.getUuid(), dto);
|
| 790 |
|
|
// dto.addAllDerivates(getDerivedUnitDTOsFor(dto, derivative, alreadyCollectedSpecimen));
|
| 791 |
|
|
// derivedUnits.add(dto);
|
| 792 |
|
|
// }
|
| 793 |
|
|
// }
|
| 794 |
|
|
// }
|
| 795 |
|
|
// return derivedUnits;
|
| 796 |
|
|
// }
|
| 797 |
|
|
|
| 798 |
|
|
|
| 799 |
887126ca
|
Andreas Müller
|
@SuppressWarnings("unchecked")
|
| 800 |
|
|
@Override
|
| 801 |
e08838f0
|
Andreas Müller
|
public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includedRelationships,
|
| 802 |
887126ca
|
Andreas Müller
|
Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 803 |
|
|
|
| 804 |
7e7e032e
|
Andreas Müller
|
Set<Taxon> taxa = new HashSet<>();
|
| 805 |
|
|
Set<Integer> occurrenceIds = new HashSet<>();
|
| 806 |
|
|
List<T> occurrences = new ArrayList<>();
|
| 807 |
e08838f0
|
Andreas Müller
|
boolean includeUnpublished = INCLUDE_UNPUBLISHED;
|
| 808 |
887126ca
|
Andreas Müller
|
|
| 809 |
|
|
// Integer limit = PagerUtils.limitFor(pageSize);
|
| 810 |
|
|
// Integer start = PagerUtils.startFor(pageSize, pageNumber);
|
| 811 |
|
|
|
| 812 |
|
|
if (!getSession().contains(associatedTaxon)) {
|
| 813 |
|
|
associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
|
| 814 |
|
|
}
|
| 815 |
|
|
|
| 816 |
e08838f0
|
Andreas Müller
|
if (includedRelationships != null) {
|
| 817 |
|
|
taxa = taxonService.listRelatedTaxa(associatedTaxon, includedRelationships, maxDepth, includeUnpublished, null, null, propertyPaths);
|
| 818 |
887126ca
|
Andreas Müller
|
}
|
| 819 |
|
|
|
| 820 |
|
|
taxa.add(associatedTaxon);
|
| 821 |
|
|
|
| 822 |
|
|
for (Taxon taxon : taxa) {
|
| 823 |
|
|
List<T> perTaxonOccurrences = dao.listByAssociatedTaxon(type, taxon, null, null, orderHints, propertyPaths);
|
| 824 |
11d3d7eb
|
Andreas Müller
|
for (SpecimenOrObservationBase<?> o : perTaxonOccurrences) {
|
| 825 |
887126ca
|
Andreas Müller
|
occurrenceIds.add(o.getId());
|
| 826 |
|
|
}
|
| 827 |
|
|
}
|
| 828 |
1ec74f53
|
Andreas Kohlbecker
|
occurrences = (List<T>) dao.loadList(occurrenceIds, propertyPaths);
|
| 829 |
887126ca
|
Andreas Müller
|
|
| 830 |
6b53ead8
|
Katja Luther
|
return new DefaultPagerImpl<T>(pageNumber, Long.valueOf(occurrences.size()), pageSize, occurrences);
|
| 831 |
887126ca
|
Andreas Müller
|
|
| 832 |
|
|
}
|
| 833 |
|
|
|
| 834 |
|
|
@Override
|
| 835 |
|
|
public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
|
| 836 |
|
|
String taxonUUID, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 837 |
|
|
|
| 838 |
|
|
UUID uuid = UUID.fromString(taxonUUID);
|
| 839 |
|
|
Taxon tax = (Taxon) taxonService.load(uuid);
|
| 840 |
|
|
// TODO REMOVE NULL STATEMENT
|
| 841 |
|
|
type = null;
|
| 842 |
|
|
return pageByAssociatedTaxon(type, includeRelationships, tax, maxDepth, pageSize, pageNumber, orderHints, propertyPaths);
|
| 843 |
|
|
|
| 844 |
|
|
}
|
| 845 |
|
|
|
| 846 |
6b53ead8
|
Katja Luther
|
@SuppressWarnings("unchecked")
|
| 847 |
|
|
@Override
|
| 848 |
|
|
public List<FieldUnitDTO> findFieldUnitDTOByAssociatedTaxon(Set<TaxonRelationshipEdge> includedRelationships,
|
| 849 |
|
|
UUID associatedTaxonUuid) {
|
| 850 |
|
|
|
| 851 |
|
|
Set<Taxon> taxa = new HashSet<>();
|
| 852 |
|
|
Set<Integer> occurrenceIds = new HashSet<>();
|
| 853 |
|
|
List<FieldUnitDTO> fieldUnitDTOs = new ArrayList<>();
|
| 854 |
|
|
HashMap<UUID, DerivateDTO> alreadyCollectedSpecimen = new HashMap<>();
|
| 855 |
|
|
List<SpecimenOrObservationBase> occurrences = new ArrayList<>();
|
| 856 |
|
|
boolean includeUnpublished = INCLUDE_UNPUBLISHED;
|
| 857 |
|
|
|
| 858 |
|
|
// Integer limit = PagerUtils.limitFor(pageSize);
|
| 859 |
|
|
// Integer start = PagerUtils.startFor(pageSize, pageNumber);
|
| 860 |
|
|
|
| 861 |
|
|
Taxon associatedTaxon = (Taxon) taxonService.load(associatedTaxonUuid);
|
| 862 |
|
|
|
| 863 |
|
|
|
| 864 |
|
|
if (includedRelationships != null) {
|
| 865 |
|
|
taxa = taxonService.listRelatedTaxa(associatedTaxon, includedRelationships, null, includeUnpublished, null, null, null);
|
| 866 |
|
|
}
|
| 867 |
|
|
|
| 868 |
|
|
taxa.add(associatedTaxon);
|
| 869 |
|
|
|
| 870 |
|
|
for (Taxon taxon : taxa) {
|
| 871 |
ee6e05c9
|
Katja Luther
|
List<SpecimenOrObservationBase> perTaxonOccurrences = dao.listByAssociatedTaxon(null,taxon, null, null, null, DERIVED_UNIT_INIT_STRATEGY);
|
| 872 |
6b53ead8
|
Katja Luther
|
for (SpecimenOrObservationBase<?> o : perTaxonOccurrences) {
|
| 873 |
|
|
if (o.isInstanceOf(DerivedUnit.class)){
|
| 874 |
a7e45124
|
Katja Luther
|
DerivedUnit derivedUnit;
|
| 875 |
|
|
DerivateDTO derivedUnitDTO;
|
| 876 |
|
|
if (o.isInstanceOf(DnaSample.class)) {
|
| 877 |
|
|
derivedUnit = HibernateProxyHelper.deproxy(o, DnaSample.class);
|
| 878 |
|
|
derivedUnitDTO = new DNASampleDTO(derivedUnit);
|
| 879 |
|
|
} else {
|
| 880 |
|
|
derivedUnit = HibernateProxyHelper.deproxy(o, DerivedUnit.class);
|
| 881 |
484a120f
|
Katja Luther
|
derivedUnitDTO = new PreservedSpecimenDTO(derivedUnit);
|
| 882 |
a7e45124
|
Katja Luther
|
}
|
| 883 |
6b53ead8
|
Katja Luther
|
if (alreadyCollectedSpecimen.get(derivedUnitDTO.getUuid()) == null){
|
| 884 |
|
|
alreadyCollectedSpecimen.put(derivedUnitDTO.getUuid(), derivedUnitDTO);
|
| 885 |
|
|
}
|
| 886 |
|
|
derivedUnitDTO.addAllDerivates(getDerivedUnitDTOsFor(derivedUnitDTO, derivedUnit, alreadyCollectedSpecimen));
|
| 887 |
|
|
this.findFieldUnitDTO(derivedUnitDTO, fieldUnitDTOs, alreadyCollectedSpecimen);
|
| 888 |
|
|
}
|
| 889 |
|
|
}
|
| 890 |
|
|
|
| 891 |
|
|
}
|
| 892 |
|
|
|
| 893 |
|
|
return fieldUnitDTOs;
|
| 894 |
|
|
|
| 895 |
|
|
}
|
| 896 |
|
|
|
| 897 |
a7e45124
|
Katja Luther
|
|
| 898 |
|
|
|
| 899 |
f2716206
|
Katja Luther
|
@Override
|
| 900 |
|
|
public List<DerivedUnit> findByAccessionNumber(
|
| 901 |
|
|
String accessionNumberString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
|
| 902 |
|
|
List<String> propertyPaths) {
|
| 903 |
|
|
|
| 904 |
|
|
List<DerivedUnit> records = new ArrayList<>();
|
| 905 |
6b53ead8
|
Katja Luther
|
records = dao.findByGeneticAccessionNumber(accessionNumberString, propertyPaths);
|
| 906 |
f2716206
|
Katja Luther
|
|
| 907 |
|
|
return records;
|
| 908 |
|
|
|
| 909 |
|
|
}
|
| 910 |
|
|
|
| 911 |
887126ca
|
Andreas Müller
|
@Override
|
| 912 |
|
|
public Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(
|
| 913 |
|
|
Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle boundingBox, List<Language> languages,
|
| 914 |
|
|
boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
|
| 915 |
3ca8a283
|
Patrick Plitzner
|
List<String> propertyPaths) throws IOException, LuceneParseException {
|
| 916 |
887126ca
|
Andreas Müller
|
|
| 917 |
|
|
LuceneSearch luceneSearch = prepareByFullTextSearch(clazz, queryString, boundingBox, languages, highlightFragments);
|
| 918 |
|
|
|
| 919 |
|
|
// --- execute search
|
| 920 |
3ca8a283
|
Patrick Plitzner
|
TopGroups<BytesRef> topDocsResultSet;
|
| 921 |
|
|
try {
|
| 922 |
|
|
topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);
|
| 923 |
|
|
} catch (ParseException e) {
|
| 924 |
|
|
LuceneParseException parseException = new LuceneParseException(e.getMessage());
|
| 925 |
|
|
parseException.setStackTrace(e.getStackTrace());
|
| 926 |
|
|
throw parseException;
|
| 927 |
|
|
}
|
| 928 |
887126ca
|
Andreas Müller
|
|
| 929 |
7e7e032e
|
Andreas Müller
|
Map<CdmBaseType, String> idFieldMap = new HashMap<>();
|
| 930 |
887126ca
|
Andreas Müller
|
idFieldMap.put(CdmBaseType.SPECIMEN_OR_OBSERVATIONBASE, "id");
|
| 931 |
|
|
|
| 932 |
|
|
// --- initialize taxa, highlight matches ....
|
| 933 |
|
|
ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
|
| 934 |
|
|
@SuppressWarnings("rawtypes")
|
| 935 |
|
|
List<SearchResult<SpecimenOrObservationBase>> searchResults = searchResultBuilder.createResultSet(
|
| 936 |
|
|
topDocsResultSet, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);
|
| 937 |
|
|
|
| 938 |
57ea8a3a
|
Andreas Kohlbecker
|
int totalHits = topDocsResultSet != null ? topDocsResultSet.totalGroupCount : 0;
|
| 939 |
887126ca
|
Andreas Müller
|
|
| 940 |
9a21de1f
|
Andreas Müller
|
return new DefaultPagerImpl<>(pageNumber, Long.valueOf(totalHits), pageSize, searchResults);
|
| 941 |
887126ca
|
Andreas Müller
|
|
| 942 |
|
|
}
|
| 943 |
|
|
|
| 944 |
|
|
private LuceneSearch prepareByFullTextSearch(Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle bbox,
|
| 945 |
|
|
List<Language> languages, boolean highlightFragments) {
|
| 946 |
|
|
|
| 947 |
f6b282fc
|
Andreas Kohlbecker
|
Builder finalQueryBuilder = new Builder();
|
| 948 |
|
|
Builder textQueryBuilder = new Builder();
|
| 949 |
887126ca
|
Andreas Müller
|
|
| 950 |
|
|
LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, FieldUnit.class);
|
| 951 |
|
|
QueryFactory queryFactory = luceneIndexToolProvider.newQueryFactoryFor(FieldUnit.class);
|
| 952 |
|
|
|
| 953 |
|
|
// --- criteria
|
| 954 |
|
|
luceneSearch.setCdmTypRestriction(clazz);
|
| 955 |
|
|
if (queryString != null) {
|
| 956 |
f6b282fc
|
Andreas Kohlbecker
|
textQueryBuilder.add(queryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);
|
| 957 |
|
|
finalQueryBuilder.add(textQueryBuilder.build(), Occur.MUST);
|
| 958 |
887126ca
|
Andreas Müller
|
}
|
| 959 |
|
|
|
| 960 |
|
|
// --- spacial query
|
| 961 |
|
|
if (bbox != null) {
|
| 962 |
f6b282fc
|
Andreas Kohlbecker
|
finalQueryBuilder.add(QueryFactory.buildSpatialQueryByRange(bbox, "gatheringEvent.exactLocation.point"), Occur.MUST);
|
| 963 |
887126ca
|
Andreas Müller
|
}
|
| 964 |
|
|
|
| 965 |
f6b282fc
|
Andreas Kohlbecker
|
luceneSearch.setQuery(finalQueryBuilder.build());
|
| 966 |
887126ca
|
Andreas Müller
|
|
| 967 |
|
|
// --- sorting
|
| 968 |
2622a38b
|
Andreas Müller
|
SortField[] sortFields = new SortField[] { SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.Type.STRING, false) };
|
| 969 |
887126ca
|
Andreas Müller
|
luceneSearch.setSortFields(sortFields);
|
| 970 |
|
|
|
| 971 |
|
|
if (highlightFragments) {
|
| 972 |
|
|
luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());
|
| 973 |
|
|
}
|
| 974 |
|
|
return luceneSearch;
|
| 975 |
|
|
}
|
| 976 |
|
|
|
| 977 |
|
|
|
| 978 |
|
|
@Override
|
| 979 |
6b53ead8
|
Katja Luther
|
public Collection<FieldUnit> findFieldUnits(UUID derivedUnitUuid, List<String> propertyPaths) {
|
| 980 |
887126ca
|
Andreas Müller
|
//It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})
|
| 981 |
|
|
//from which this DerivedUnit was derived until all FieldUnits are found.
|
| 982 |
|
|
|
| 983 |
|
|
// FIXME: use HQL queries to increase performance
|
| 984 |
42002c0a
|
Patrick Plitzner
|
SpecimenOrObservationBase<?> specimen = load(derivedUnitUuid, propertyPaths);
|
| 985 |
887126ca
|
Andreas Müller
|
// specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
|
| 986 |
7e7e032e
|
Andreas Müller
|
Collection<FieldUnit> fieldUnits = new ArrayList<>();
|
| 987 |
887126ca
|
Andreas Müller
|
|
| 988 |
|
|
if (specimen.isInstanceOf(FieldUnit.class)) {
|
| 989 |
|
|
fieldUnits.add(HibernateProxyHelper.deproxy(specimen, FieldUnit.class));
|
| 990 |
|
|
}
|
| 991 |
|
|
else if(specimen.isInstanceOf(DerivedUnit.class)){
|
| 992 |
42002c0a
|
Patrick Plitzner
|
fieldUnits.addAll(getFieldUnits(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class), propertyPaths));
|
| 993 |
887126ca
|
Andreas Müller
|
}
|
| 994 |
|
|
return fieldUnits;
|
| 995 |
|
|
}
|
| 996 |
|
|
|
| 997 |
42002c0a
|
Patrick Plitzner
|
private Collection<FieldUnit> getFieldUnits(DerivedUnit derivedUnit, List<String> propertyPaths) {
|
| 998 |
7e7e032e
|
Andreas Müller
|
Collection<FieldUnit> fieldUnits = new HashSet<>();
|
| 999 |
887126ca
|
Andreas Müller
|
Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
|
| 1000 |
|
|
if (originals != null && !originals.isEmpty()) {
|
| 1001 |
|
|
for (SpecimenOrObservationBase<?> original : originals) {
|
| 1002 |
|
|
if (original.isInstanceOf(FieldUnit.class)) {
|
| 1003 |
42002c0a
|
Patrick Plitzner
|
fieldUnits.add((FieldUnit) load(original.getUuid(), propertyPaths));
|
| 1004 |
887126ca
|
Andreas Müller
|
}
|
| 1005 |
|
|
else if(original.isInstanceOf(DerivedUnit.class)){
|
| 1006 |
42002c0a
|
Patrick Plitzner
|
fieldUnits.addAll(getFieldUnits(HibernateProxyHelper.deproxy(original, DerivedUnit.class), propertyPaths));
|
| 1007 |
887126ca
|
Andreas Müller
|
}
|
| 1008 |
|
|
}
|
| 1009 |
|
|
}
|
| 1010 |
|
|
return fieldUnits;
|
| 1011 |
|
|
}
|
| 1012 |
|
|
|
| 1013 |
abfe22d1
|
Katja Luther
|
|
| 1014 |
d70a126f
|
Katja Luther
|
|
| 1015 |
|
|
@Override
|
| 1016 |
6b53ead8
|
Katja Luther
|
public FieldUnitDTO findFieldUnitDTO(DerivateDTO derivedUnitDTO, Collection<FieldUnitDTO> fieldUnits, HashMap<UUID, DerivateDTO> alreadyCollectedSpecimen) {
|
| 1017 |
|
|
//It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})
|
| 1018 |
|
|
//from which this DerivedUnit was derived until all FieldUnits are found.
|
| 1019 |
|
|
List<SpecimenOrObservationBase> specimens = new ArrayList<>();
|
| 1020 |
|
|
List<String> propertyPaths = new ArrayList<>();
|
| 1021 |
c31ff29d
|
Katja Luther
|
|
| 1022 |
6b53ead8
|
Katja Luther
|
propertyPaths.add("descriptions.elements.media.title");
|
| 1023 |
c31ff29d
|
Katja Luther
|
propertyPaths.add("kindOfUnit");
|
| 1024 |
6b53ead8
|
Katja Luther
|
|
| 1025 |
|
|
specimens = dao.findOriginalsForDerivedUnit(derivedUnitDTO.getUuid(), propertyPaths);
|
| 1026 |
abfe22d1
|
Katja Luther
|
|
| 1027 |
6b53ead8
|
Katja Luther
|
if (specimens.size() > 1){
|
| 1028 |
|
|
logger.debug("The derived unit with uuid " + derivedUnitDTO.getUuid() + "has more than one orginal");
|
| 1029 |
|
|
}
|
| 1030 |
|
|
// for (SpecimenOrObservationBase specimen: specimens){
|
| 1031 |
|
|
SpecimenOrObservationBase specimen = null;
|
| 1032 |
|
|
if (specimens.size() > 0){
|
| 1033 |
|
|
specimen = specimens.get(0);
|
| 1034 |
|
|
}else{
|
| 1035 |
|
|
return null;
|
| 1036 |
|
|
}
|
| 1037 |
|
|
FieldUnitDTO fieldUnitDto = null;
|
| 1038 |
|
|
if (alreadyCollectedSpecimen.get(specimen.getUuid()) != null){
|
| 1039 |
|
|
alreadyCollectedSpecimen.get(specimen.getUuid()).addDerivate(derivedUnitDTO);
|
| 1040 |
|
|
if ( alreadyCollectedSpecimen.get(specimen.getUuid()) instanceof FieldUnitDTO){
|
| 1041 |
|
|
((FieldUnitDTO)alreadyCollectedSpecimen.get(specimen.getUuid())).getTaxonRelatedDerivedUnits().add(derivedUnitDTO.getUuid());
|
| 1042 |
|
|
}
|
| 1043 |
|
|
}else{
|
| 1044 |
|
|
if (specimen.isInstanceOf(FieldUnit.class)){
|
| 1045 |
|
|
fieldUnitDto = FieldUnitDTO.newInstance((FieldUnit)specimen);
|
| 1046 |
77993547
|
Katja Luther
|
fieldUnitDto.addDerivate(derivedUnitDTO);
|
| 1047 |
6b53ead8
|
Katja Luther
|
fieldUnits.add(fieldUnitDto);
|
| 1048 |
|
|
}else{
|
| 1049 |
a7e45124
|
Katja Luther
|
DerivateDTO originalDTO;
|
| 1050 |
|
|
if (specimen instanceof DnaSample){
|
| 1051 |
|
|
originalDTO = new DNASampleDTO((DnaSample)specimen);
|
| 1052 |
|
|
} else {
|
| 1053 |
484a120f
|
Katja Luther
|
originalDTO = new PreservedSpecimenDTO((DerivedUnit)specimen);
|
| 1054 |
a7e45124
|
Katja Luther
|
}
|
| 1055 |
6b53ead8
|
Katja Luther
|
originalDTO.addDerivate(derivedUnitDTO);
|
| 1056 |
|
|
fieldUnitDto = findFieldUnitDTO(originalDTO, fieldUnits, alreadyCollectedSpecimen);
|
| 1057 |
|
|
}
|
| 1058 |
|
|
|
| 1059 |
|
|
}
|
| 1060 |
|
|
// }
|
| 1061 |
|
|
alreadyCollectedSpecimen.put(derivedUnitDTO.getUuid(), derivedUnitDTO);
|
| 1062 |
abfe22d1
|
Katja Luther
|
if (fieldUnitDto != null){
|
| 1063 |
|
|
fieldUnitDto.addTaxonRelatedDerivedUnits(derivedUnitDTO);
|
| 1064 |
|
|
}
|
| 1065 |
6b53ead8
|
Katja Luther
|
return fieldUnitDto;
|
| 1066 |
abfe22d1
|
Katja Luther
|
|
| 1067 |
6b53ead8
|
Katja Luther
|
}
|
| 1068 |
|
|
|
| 1069 |
887126ca
|
Andreas Müller
|
@Override
|
| 1070 |
|
|
@Transactional(readOnly = false)
|
| 1071 |
|
|
public UpdateResult moveSequence(DnaSample from, DnaSample to, Sequence sequence) {
|
| 1072 |
|
|
return moveSequence(from.getUuid(), to.getUuid(), sequence.getUuid());
|
| 1073 |
|
|
}
|
| 1074 |
|
|
|
| 1075 |
|
|
@Override
|
| 1076 |
|
|
@Transactional(readOnly = false)
|
| 1077 |
|
|
public UpdateResult moveSequence(UUID fromUuid, UUID toUuid, UUID sequenceUuid) {
|
| 1078 |
|
|
// reload specimens to avoid session conflicts
|
| 1079 |
|
|
DnaSample from = (DnaSample) load(fromUuid);
|
| 1080 |
|
|
DnaSample to = (DnaSample) load(toUuid);
|
| 1081 |
|
|
Sequence sequence = sequenceService.load(sequenceUuid);
|
| 1082 |
|
|
|
| 1083 |
|
|
if (from == null || to == null || sequence == null) {
|
| 1084 |
|
|
throw new TransientObjectException("One of the CDM entities has not been saved to the data base yet. Moving only works for persisted/saved CDM entities.\n" +
|
| 1085 |
|
|
"Operation was move "+sequence+ " from "+from+" to "+to);
|
| 1086 |
|
|
}
|
| 1087 |
|
|
UpdateResult result = new UpdateResult();
|
| 1088 |
|
|
from.removeSequence(sequence);
|
| 1089 |
|
|
saveOrUpdate(from);
|
| 1090 |
|
|
to.addSequence(sequence);
|
| 1091 |
|
|
saveOrUpdate(to);
|
| 1092 |
|
|
result.setStatus(Status.OK);
|
| 1093 |
|
|
result.addUpdatedObject(from);
|
| 1094 |
|
|
result.addUpdatedObject(to);
|
| 1095 |
|
|
return result;
|
| 1096 |
|
|
}
|
| 1097 |
|
|
|
| 1098 |
|
|
@Override
|
| 1099 |
|
|
@Transactional(readOnly = false)
|
| 1100 |
|
|
public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate) {
|
| 1101 |
55e09b37
|
Patrick Plitzner
|
return moveDerivate(from!=null?from.getUuid():null, to.getUuid(), derivate.getUuid()).isOk();
|
| 1102 |
887126ca
|
Andreas Müller
|
}
|
| 1103 |
|
|
|
| 1104 |
|
|
@Override
|
| 1105 |
|
|
@Transactional(readOnly = false)
|
| 1106 |
|
|
public UpdateResult moveDerivate(UUID specimenFromUuid, UUID specimenToUuid, UUID derivateUuid) {
|
| 1107 |
|
|
// reload specimens to avoid session conflicts
|
| 1108 |
55e09b37
|
Patrick Plitzner
|
SpecimenOrObservationBase<?> from = null;
|
| 1109 |
|
|
if(specimenFromUuid!=null){
|
| 1110 |
|
|
from = load(specimenFromUuid);
|
| 1111 |
|
|
}
|
| 1112 |
887126ca
|
Andreas Müller
|
SpecimenOrObservationBase<?> to = load(specimenToUuid);
|
| 1113 |
|
|
DerivedUnit derivate = (DerivedUnit) load(derivateUuid);
|
| 1114 |
|
|
|
| 1115 |
55e09b37
|
Patrick Plitzner
|
if ((specimenFromUuid!=null && from == null) || to == null || derivate == null) {
|
| 1116 |
887126ca
|
Andreas Müller
|
throw new TransientObjectException("One of the CDM entities has not been saved to the data base yet. Moving only works for persisted/saved CDM entities.\n" +
|
| 1117 |
eec2d79d
|
Andreas Müller
|
"Operation was move "+derivate+ " from "+from+" to "+to);
|
| 1118 |
887126ca
|
Andreas Müller
|
}
|
| 1119 |
|
|
UpdateResult result = new UpdateResult();
|
| 1120 |
|
|
SpecimenOrObservationType derivateType = derivate.getRecordBasis();
|
| 1121 |
|
|
SpecimenOrObservationType toType = to.getRecordBasis();
|
| 1122 |
|
|
// check if type is a sub derivate type
|
| 1123 |
|
|
if(toType==SpecimenOrObservationType.FieldUnit //moving to FieldUnit always works
|
| 1124 |
|
|
|| derivateType==SpecimenOrObservationType.Media //moving media always works
|
| 1125 |
|
|
|| (derivateType.isKindOf(toType) && toType!=derivateType)){ //moving only to parent derivate type
|
| 1126 |
55e09b37
|
Patrick Plitzner
|
if(from!=null){
|
| 1127 |
|
|
// remove derivation event from parent specimen of dragged object
|
| 1128 |
|
|
DerivationEvent eventToRemove = null;
|
| 1129 |
|
|
for (DerivationEvent event : from.getDerivationEvents()) {
|
| 1130 |
|
|
if (event.getDerivatives().contains(derivate)) {
|
| 1131 |
|
|
eventToRemove = event;
|
| 1132 |
|
|
break;
|
| 1133 |
|
|
}
|
| 1134 |
|
|
}
|
| 1135 |
|
|
from.removeDerivationEvent(eventToRemove);
|
| 1136 |
|
|
if(eventToRemove!=null){
|
| 1137 |
|
|
// add new derivation event to target and copy the event parameters of the old one
|
| 1138 |
|
|
DerivationEvent derivedFromNewOriginalEvent = DerivationEvent.NewSimpleInstance(to, derivate, null);
|
| 1139 |
|
|
derivedFromNewOriginalEvent.setActor(eventToRemove.getActor());
|
| 1140 |
|
|
derivedFromNewOriginalEvent.setDescription(eventToRemove.getDescription());
|
| 1141 |
|
|
derivedFromNewOriginalEvent.setInstitution(eventToRemove.getInstitution());
|
| 1142 |
|
|
derivedFromNewOriginalEvent.setTimeperiod(eventToRemove.getTimeperiod());
|
| 1143 |
|
|
derivedFromNewOriginalEvent.setType(eventToRemove.getType());
|
| 1144 |
|
|
to.addDerivationEvent(derivedFromNewOriginalEvent);
|
| 1145 |
|
|
derivate.setDerivedFrom(derivedFromNewOriginalEvent);
|
| 1146 |
887126ca
|
Andreas Müller
|
}
|
| 1147 |
|
|
}
|
| 1148 |
55e09b37
|
Patrick Plitzner
|
else{
|
| 1149 |
|
|
//derivative had no parent before so we use empty derivation event
|
| 1150 |
887126ca
|
Andreas Müller
|
DerivationEvent derivedFromNewOriginalEvent = DerivationEvent.NewSimpleInstance(to, derivate, null);
|
| 1151 |
|
|
to.addDerivationEvent(derivedFromNewOriginalEvent);
|
| 1152 |
|
|
derivate.setDerivedFrom(derivedFromNewOriginalEvent);
|
| 1153 |
|
|
}
|
| 1154 |
|
|
|
| 1155 |
d11716c6
|
Patrick Plitzner
|
if(from!=null){
|
| 1156 |
|
|
saveOrUpdate(from);
|
| 1157 |
|
|
}
|
| 1158 |
887126ca
|
Andreas Müller
|
saveOrUpdate(to);
|
| 1159 |
|
|
result.setStatus(Status.OK);
|
| 1160 |
|
|
result.addUpdatedObject(from);
|
| 1161 |
|
|
result.addUpdatedObject(to);
|
| 1162 |
|
|
} else {
|
| 1163 |
|
|
result.setStatus(Status.ERROR);
|
| 1164 |
|
|
}
|
| 1165 |
|
|
return result;
|
| 1166 |
|
|
}
|
| 1167 |
|
|
|
| 1168 |
|
|
@Override
|
| 1169 |
645658b9
|
Katja Luther
|
public DeleteResult isDeletable(UUID specimenUuid, DeleteConfiguratorBase config) {
|
| 1170 |
887126ca
|
Andreas Müller
|
DeleteResult deleteResult = new DeleteResult();
|
| 1171 |
645658b9
|
Katja Luther
|
SpecimenOrObservationBase specimen = this.load(specimenUuid);
|
| 1172 |
887126ca
|
Andreas Müller
|
SpecimenDeleteConfigurator specimenDeleteConfigurator = (SpecimenDeleteConfigurator) config;
|
| 1173 |
|
|
|
| 1174 |
|
|
// check elements found by super method
|
| 1175 |
645658b9
|
Katja Luther
|
Set<CdmBase> relatedObjects = super.isDeletable(specimenUuid, config).getRelatedObjects();
|
| 1176 |
887126ca
|
Andreas Müller
|
for (CdmBase cdmBase : relatedObjects) {
|
| 1177 |
|
|
// check for type designation
|
| 1178 |
|
|
if (cdmBase.isInstanceOf(SpecimenTypeDesignation.class) && !specimenDeleteConfigurator.isDeleteFromTypeDesignation()) {
|
| 1179 |
|
|
deleteResult.setAbort();
|
| 1180 |
56897765
|
Patrick Plitzner
|
deleteResult.addException(new ReferencedObjectUndeletableException("Specimen or obeservation is a type specimen."));
|
| 1181 |
887126ca
|
Andreas Müller
|
deleteResult.addRelatedObject(cdmBase);
|
| 1182 |
|
|
break;
|
| 1183 |
|
|
}
|
| 1184 |
|
|
// check for IndividualsAssociations
|
| 1185 |
|
|
else if (cdmBase.isInstanceOf(IndividualsAssociation.class) && !specimenDeleteConfigurator.isDeleteFromIndividualsAssociation()) {
|
| 1186 |
|
|
deleteResult.setAbort();
|
| 1187 |
56897765
|
Patrick Plitzner
|
deleteResult.addException(new ReferencedObjectUndeletableException("Specimen or obeservation is still associated via IndividualsAssociations"));
|
| 1188 |
887126ca
|
Andreas Müller
|
deleteResult.addRelatedObject(cdmBase);
|
| 1189 |
|
|
break;
|
| 1190 |
|
|
}
|
| 1191 |
651c925a
|
Patrick Plitzner
|
// check for taxon description
|
| 1192 |
|
|
else if(cdmBase.isInstanceOf(TaxonDescription.class)
|
| 1193 |
|
|
&& HibernateProxyHelper.deproxy(cdmBase, TaxonDescription.class).getDescribedSpecimenOrObservation().equals(specimen)
|
| 1194 |
887126ca
|
Andreas Müller
|
&& !specimenDeleteConfigurator.isDeleteFromDescription()){
|
| 1195 |
|
|
deleteResult.setAbort();
|
| 1196 |
56897765
|
Patrick Plitzner
|
deleteResult.addException(new ReferencedObjectUndeletableException("Specimen or obeservation is still used as \"Described Specimen\" in a taxon description."));
|
| 1197 |
887126ca
|
Andreas Müller
|
deleteResult.addRelatedObject(cdmBase);
|
| 1198 |
|
|
break;
|
| 1199 |
|
|
}
|
| 1200 |
|
|
// check for children and parents (derivation events)
|
| 1201 |
|
|
else if (cdmBase.isInstanceOf(DerivationEvent.class)) {
|
| 1202 |
|
|
DerivationEvent derivationEvent = HibernateProxyHelper.deproxy(cdmBase, DerivationEvent.class);
|
| 1203 |
|
|
// check if derivation event is empty
|
| 1204 |
4a1ab701
|
Katja Luther
|
if (!derivationEvent.getDerivatives().isEmpty() && derivationEvent.getOriginals().contains(specimen)) {
|
| 1205 |
|
|
// if derivationEvent is the childEvent and contains derivations
|
| 1206 |
|
|
// if (derivationEvent.getDerivatives().contains(specimen)) {
|
| 1207 |
|
|
// //if it is the parent event the specimen is still deletable
|
| 1208 |
|
|
// continue;
|
| 1209 |
|
|
// }
|
| 1210 |
|
|
if(!specimenDeleteConfigurator.isDeleteChildren()){
|
| 1211 |
|
|
//if children should not be deleted then it is undeletable
|
| 1212 |
887126ca
|
Andreas Müller
|
deleteResult.setAbort();
|
| 1213 |
56897765
|
Patrick Plitzner
|
deleteResult.addException(new ReferencedObjectUndeletableException("Specimen or obeservation still has child derivatives."));
|
| 1214 |
887126ca
|
Andreas Müller
|
deleteResult.addRelatedObject(cdmBase);
|
| 1215 |
|
|
break;
|
| 1216 |
|
|
}
|
| 1217 |
|
|
else{
|
| 1218 |
|
|
// check all children if they can be deleted
|
| 1219 |
|
|
Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
|
| 1220 |
|
|
DeleteResult childResult = new DeleteResult();
|
| 1221 |
|
|
for (DerivedUnit derivedUnit : derivatives) {
|
| 1222 |
645658b9
|
Katja Luther
|
childResult.includeResult(isDeletable(derivedUnit.getUuid(), specimenDeleteConfigurator));
|
| 1223 |
887126ca
|
Andreas Müller
|
}
|
| 1224 |
|
|
if (!childResult.isOk()) {
|
| 1225 |
|
|
deleteResult.setAbort();
|
| 1226 |
|
|
deleteResult.includeResult(childResult);
|
| 1227 |
|
|
deleteResult.addRelatedObject(cdmBase);
|
| 1228 |
|
|
break;
|
| 1229 |
|
|
}
|
| 1230 |
|
|
}
|
| 1231 |
|
|
}
|
| 1232 |
|
|
}
|
| 1233 |
|
|
// check for amplification
|
| 1234 |
651c925a
|
Patrick Plitzner
|
else if (cdmBase.isInstanceOf(AmplificationResult.class)
|
| 1235 |
|
|
&& !specimenDeleteConfigurator.isDeleteMolecularData()
|
| 1236 |
|
|
&& !specimenDeleteConfigurator.isDeleteChildren()) {
|
| 1237 |
887126ca
|
Andreas Müller
|
deleteResult.setAbort();
|
| 1238 |
|
|
deleteResult.addException(new ReferencedObjectUndeletableException("DnaSample is used in amplification results."));
|
| 1239 |
|
|
deleteResult.addRelatedObject(cdmBase);
|
| 1240 |
|
|
break;
|
| 1241 |
|
|
}
|
| 1242 |
|
|
// check for sequence
|
| 1243 |
651c925a
|
Patrick Plitzner
|
else if (cdmBase.isInstanceOf(Sequence.class)
|
| 1244 |
|
|
&& !specimenDeleteConfigurator.isDeleteMolecularData()
|
| 1245 |
|
|
&& !specimenDeleteConfigurator.isDeleteChildren()) {
|
| 1246 |
887126ca
|
Andreas Müller
|
deleteResult.setAbort();
|
| 1247 |
|
|
deleteResult.addException(new ReferencedObjectUndeletableException("DnaSample is used in sequences."));
|
| 1248 |
|
|
deleteResult.addRelatedObject(cdmBase);
|
| 1249 |
|
|
break;
|
| 1250 |
|
|
}
|
| 1251 |
|
|
}
|
| 1252 |
|
|
if (deleteResult.isOk()) {
|
| 1253 |
|
|
//add all related object if deletion is OK so they can be handled by the delete() method
|
| 1254 |
|
|
deleteResult.addRelatedObjects(relatedObjects);
|
| 1255 |
|
|
}
|
| 1256 |
|
|
return deleteResult;
|
| 1257 |
|
|
}
|
| 1258 |
|
|
|
| 1259 |
f2fdced6
|
Patrick Plitzner
|
/**
|
| 1260 |
|
|
* {@inheritDoc}
|
| 1261 |
|
|
*/
|
| 1262 |
eb3c2286
|
Patrick Plitzner
|
@Transactional(readOnly = false)
|
| 1263 |
f2fdced6
|
Patrick Plitzner
|
@Override
|
| 1264 |
|
|
public DeleteResult delete(UUID specimenUuid, SpecimenDeleteConfigurator config) {
|
| 1265 |
|
|
return delete(load(specimenUuid), config);
|
| 1266 |
|
|
}
|
| 1267 |
|
|
|
| 1268 |
eb3c2286
|
Patrick Plitzner
|
|
| 1269 |
|
|
@Transactional(readOnly = false)
|
| 1270 |
887126ca
|
Andreas Müller
|
@Override
|
| 1271 |
|
|
public DeleteResult delete(SpecimenOrObservationBase<?> specimen, SpecimenDeleteConfigurator config) {
|
| 1272 |
|
|
specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
|
| 1273 |
|
|
|
| 1274 |
a9c2b3c3
|
Katja Luther
|
DeleteResult deleteResult = isDeletable(specimen.getUuid(), config);
|
| 1275 |
|
|
if (!deleteResult.isOk()) {
|
| 1276 |
|
|
return deleteResult;
|
| 1277 |
|
|
}
|
| 1278 |
|
|
|
| 1279 |
887126ca
|
Andreas Müller
|
if (config.isDeleteChildren()) {
|
| 1280 |
|
|
Set<DerivationEvent> derivationEvents = specimen.getDerivationEvents();
|
| 1281 |
|
|
//clone to avoid concurrent modification
|
| 1282 |
|
|
//can happen if the child is deleted and deleted its own derivedFrom event
|
| 1283 |
7e7e032e
|
Andreas Müller
|
Set<DerivationEvent> derivationEventsClone = new HashSet<>(derivationEvents);
|
| 1284 |
887126ca
|
Andreas Müller
|
for (DerivationEvent derivationEvent : derivationEventsClone) {
|
| 1285 |
|
|
Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
|
| 1286 |
09a260bb
|
Katja Luther
|
Iterator<DerivedUnit> it = derivatives.iterator();
|
| 1287 |
|
|
Set<DerivedUnit> derivativesToDelete = new HashSet<>();
|
| 1288 |
|
|
while (it.hasNext()) {
|
| 1289 |
|
|
DerivedUnit unit = it.next();
|
| 1290 |
|
|
derivativesToDelete.add(unit);
|
| 1291 |
|
|
}
|
| 1292 |
|
|
for (DerivedUnit unit:derivativesToDelete){
|
| 1293 |
bd1626d9
|
Patrick Plitzner
|
deleteResult.includeResult(delete(unit, config));
|
| 1294 |
887126ca
|
Andreas Müller
|
}
|
| 1295 |
|
|
}
|
| 1296 |
|
|
}
|
| 1297 |
|
|
|
| 1298 |
07dbf1bc
|
Katja Luther
|
|
| 1299 |
|
|
|
| 1300 |
887126ca
|
Andreas Müller
|
|
| 1301 |
|
|
// check related objects
|
| 1302 |
|
|
Set<CdmBase> relatedObjects = deleteResult.getRelatedObjects();
|
| 1303 |
|
|
|
| 1304 |
|
|
for (CdmBase relatedObject : relatedObjects) {
|
| 1305 |
|
|
// check for TypeDesignations
|
| 1306 |
|
|
if (relatedObject.isInstanceOf(SpecimenTypeDesignation.class)) {
|
| 1307 |
|
|
SpecimenTypeDesignation designation = HibernateProxyHelper.deproxy(relatedObject, SpecimenTypeDesignation.class);
|
| 1308 |
|
|
designation.setTypeSpecimen(null);
|
| 1309 |
9dc896c9
|
Andreas Müller
|
List<TaxonName> typifiedNames = new ArrayList<>();
|
| 1310 |
4a1ab701
|
Katja Luther
|
typifiedNames.addAll(designation.getTypifiedNames());
|
| 1311 |
9dc896c9
|
Andreas Müller
|
for (TaxonName taxonName : typifiedNames) {
|
| 1312 |
|
|
taxonName.removeTypeDesignation(designation);
|
| 1313 |
887126ca
|
Andreas Müller
|
}
|
| 1314 |
|
|
}
|
| 1315 |
|
|
// delete IndividualsAssociation
|
| 1316 |
|
|
if (relatedObject.isInstanceOf(IndividualsAssociation.class)) {
|
| 1317 |
4a1ab701
|
Katja Luther
|
IndividualsAssociation association = HibernateProxyHelper.deproxy(relatedObject, IndividualsAssociation.class);
|
| 1318 |
|
|
association.setAssociatedSpecimenOrObservation(null);
|
| 1319 |
|
|
association.getInDescription().removeElement(association);
|
| 1320 |
887126ca
|
Andreas Müller
|
}
|
| 1321 |
651c925a
|
Patrick Plitzner
|
// check for "described specimen" (deprecated)
|
| 1322 |
887126ca
|
Andreas Müller
|
if (relatedObject.isInstanceOf(TaxonDescription.class)) {
|
| 1323 |
651c925a
|
Patrick Plitzner
|
TaxonDescription description = HibernateProxyHelper.deproxy(relatedObject, TaxonDescription.class);
|
| 1324 |
|
|
description.setDescribedSpecimenOrObservation(null);
|
| 1325 |
887126ca
|
Andreas Müller
|
}
|
| 1326 |
|
|
// check for specimen description
|
| 1327 |
|
|
if (relatedObject.isInstanceOf(SpecimenDescription.class)) {
|
| 1328 |
|
|
SpecimenDescription specimenDescription = HibernateProxyHelper.deproxy(relatedObject, SpecimenDescription.class);
|
| 1329 |
651c925a
|
Patrick Plitzner
|
specimenDescription.setDescribedSpecimenOrObservation(null);
|
| 1330 |
887126ca
|
Andreas Müller
|
// check if description is a description of the given specimen
|
| 1331 |
|
|
if (specimen.getDescriptions().contains(specimenDescription)) {
|
| 1332 |
|
|
specimen.removeDescription(specimenDescription);
|
| 1333 |
|
|
}
|
| 1334 |
645658b9
|
Katja Luther
|
DeleteResult descriptionDelete = descriptionService.isDeletable(specimenDescription.getUuid(), null);
|
| 1335 |
07c3eb13
|
Katja Luther
|
if (descriptionDelete.isOk()){
|
| 1336 |
815a9015
|
Katja Luther
|
deleteResult.includeResult(descriptionService.delete(specimenDescription));
|
| 1337 |
07c3eb13
|
Katja Luther
|
}
|
| 1338 |
887126ca
|
Andreas Müller
|
}
|
| 1339 |
|
|
// check for amplification
|
| 1340 |
|
|
if (relatedObject.isInstanceOf(AmplificationResult.class)) {
|
| 1341 |
|
|
AmplificationResult amplificationResult = HibernateProxyHelper.deproxy(relatedObject, AmplificationResult.class);
|
| 1342 |
|
|
amplificationResult.getDnaSample().removeAmplificationResult(amplificationResult);
|
| 1343 |
|
|
}
|
| 1344 |
|
|
// check for sequence
|
| 1345 |
|
|
if (relatedObject.isInstanceOf(Sequence.class)) {
|
| 1346 |
|
|
Sequence sequence = HibernateProxyHelper.deproxy(relatedObject, Sequence.class);
|
| 1347 |
|
|
sequence.getDnaSample().removeSequence(sequence);
|
| 1348 |
|
|
}
|
| 1349 |
|
|
// check for children and parents (derivation events)
|
| 1350 |
|
|
if (relatedObject.isInstanceOf(DerivationEvent.class)) {
|
| 1351 |
|
|
DerivationEvent derivationEvent = HibernateProxyHelper.deproxy(relatedObject, DerivationEvent.class);
|
| 1352 |
|
|
// parent derivation event (derivedFrom)
|
| 1353 |
|
|
if (derivationEvent.getDerivatives().contains(specimen) && specimen.isInstanceOf(DerivedUnit.class)) {
|
| 1354 |
|
|
derivationEvent.removeDerivative(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class));
|
| 1355 |
|
|
if (derivationEvent.getDerivatives().isEmpty()) {
|
| 1356 |
|
|
Set<SpecimenOrObservationBase> originals = derivationEvent.getOriginals();
|
| 1357 |
|
|
for (SpecimenOrObservationBase specimenOrObservationBase : originals) {
|
| 1358 |
|
|
specimenOrObservationBase.removeDerivationEvent(derivationEvent);
|
| 1359 |
|
|
deleteResult.addUpdatedObject(specimenOrObservationBase);
|
| 1360 |
|
|
}
|
| 1361 |
a9c2b3c3
|
Katja Luther
|
// if derivationEvent has no derivates anymore, delete it
|
| 1362 |
815a9015
|
Katja Luther
|
deleteResult.includeResult(eventService.delete(derivationEvent));
|
| 1363 |
887126ca
|
Andreas Müller
|
}
|
| 1364 |
|
|
}
|
| 1365 |
|
|
else{
|
| 1366 |
|
|
//child derivation events should not occur since we delete the hierarchy from bottom to top
|
| 1367 |
|
|
}
|
| 1368 |
|
|
}
|
| 1369 |
|
|
}
|
| 1370 |
07dbf1bc
|
Katja Luther
|
if (specimen instanceof FieldUnit){
|
| 1371 |
|
|
FieldUnit fieldUnit = HibernateProxyHelper.deproxy(specimen, FieldUnit.class);
|
| 1372 |
|
|
GatheringEvent event = fieldUnit.getGatheringEvent();
|
| 1373 |
|
|
fieldUnit.setGatheringEvent(null);
|
| 1374 |
8f5a9520
|
Katja Luther
|
if (event != null){
|
| 1375 |
|
|
DeleteResult result = eventService.isDeletable(event.getUuid(), null);
|
| 1376 |
|
|
if (result.isOk()){
|
| 1377 |
815a9015
|
Katja Luther
|
deleteResult.includeResult( eventService.delete(event));
|
| 1378 |
8f5a9520
|
Katja Luther
|
}
|
| 1379 |
|
|
}
|
| 1380 |
07dbf1bc
|
Katja Luther
|
|
| 1381 |
|
|
}
|
| 1382 |
887126ca
|
Andreas Müller
|
deleteResult.includeResult(delete(specimen));
|
| 1383 |
eb3c2286
|
Patrick Plitzner
|
|
| 1384 |
887126ca
|
Andreas Müller
|
return deleteResult;
|
| 1385 |
|
|
}
|
| 1386 |
|
|
|
| 1387 |
|
|
@Override
|
| 1388 |
|
|
public Collection<IndividualsAssociation> listIndividualsAssociations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 1389 |
42002c0a
|
Patrick Plitzner
|
return dao.listIndividualsAssociations(specimen, limit, start, orderHints, propertyPaths);
|
| 1390 |
887126ca
|
Andreas Müller
|
}
|
| 1391 |
|
|
|
| 1392 |
12b3d645
|
Andreas Müller
|
/**
|
| 1393 |
|
|
* {@inheritDoc}
|
| 1394 |
|
|
*/
|
| 1395 |
b6b6d586
|
Patrick Plitzner
|
@Override
|
| 1396 |
12b3d645
|
Andreas Müller
|
public Collection<TaxonBase<?>> listAssociatedTaxa(SpecimenOrObservationBase<?> specimen, Integer limit,
|
| 1397 |
|
|
Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 1398 |
|
|
return listAssociatedTaxa(specimen, INCLUDE_UNPUBLISHED, limit, start, orderHints, propertyPaths);
|
| 1399 |
|
|
}
|
| 1400 |
|
|
@Override
|
| 1401 |
|
|
public Collection<TaxonBase<?>> listAssociatedTaxa(SpecimenOrObservationBase<?> specimen, boolean includeUnpublished,
|
| 1402 |
|
|
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 1403 |
7e7e032e
|
Andreas Müller
|
Collection<TaxonBase<?>> associatedTaxa = new HashSet<>();
|
| 1404 |
550eeb6f
|
Patrick Plitzner
|
|
| 1405 |
|
|
//individuals associations
|
| 1406 |
12b3d645
|
Andreas Müller
|
associatedTaxa.addAll(listIndividualsAssociationTaxa(specimen, includeUnpublished, limit, start, orderHints, propertyPaths));
|
| 1407 |
40b943c7
|
Patrick Plitzner
|
//type designation
|
| 1408 |
95964a96
|
Patrick Plitzner
|
if(specimen.isInstanceOf(DerivedUnit.class)){
|
| 1409 |
12b3d645
|
Andreas Müller
|
associatedTaxa.addAll(listTypeDesignationTaxa(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class),
|
| 1410 |
|
|
includeUnpublished, limit, start, orderHints, propertyPaths));
|
| 1411 |
95964a96
|
Patrick Plitzner
|
}
|
| 1412 |
40b943c7
|
Patrick Plitzner
|
//determinations
|
| 1413 |
12b3d645
|
Andreas Müller
|
associatedTaxa.addAll(listDeterminedTaxa(specimen, includeUnpublished, limit, start, orderHints, propertyPaths));
|
| 1414 |
40b943c7
|
Patrick Plitzner
|
|
| 1415 |
|
|
return associatedTaxa;
|
| 1416 |
|
|
}
|
| 1417 |
|
|
|
| 1418 |
|
|
|
| 1419 |
12b3d645
|
Andreas Müller
|
|
| 1420 |
|
|
/**
|
| 1421 |
|
|
* {@inheritDoc}
|
| 1422 |
|
|
*/
|
| 1423 |
40b943c7
|
Patrick Plitzner
|
@Override
|
| 1424 |
12b3d645
|
Andreas Müller
|
public Collection<TaxonBase<?>> listDeterminedTaxa(SpecimenOrObservationBase<?> specimen, Integer limit,
|
| 1425 |
|
|
Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 1426 |
|
|
return listDeterminedTaxa(specimen, INCLUDE_UNPUBLISHED, limit, start, orderHints, propertyPaths);
|
| 1427 |
|
|
}
|
| 1428 |
|
|
@Override
|
| 1429 |
|
|
public Collection<TaxonBase<?>> listDeterminedTaxa(SpecimenOrObservationBase<?> specimen, boolean includeUnpublished, Integer limit, Integer start,
|
| 1430 |
40b943c7
|
Patrick Plitzner
|
List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 1431 |
7e7e032e
|
Andreas Müller
|
Collection<TaxonBase<?>> associatedTaxa = new HashSet<>();
|
| 1432 |
40b943c7
|
Patrick Plitzner
|
for (DeterminationEvent determinationEvent : listDeterminationEvents(specimen, limit, start, orderHints, propertyPaths)) {
|
| 1433 |
|
|
if(determinationEvent.getIdentifiedUnit().equals(specimen)){
|
| 1434 |
|
|
if(determinationEvent.getTaxon()!=null){
|
| 1435 |
12b3d645
|
Andreas Müller
|
associatedTaxa.add(taxonService.load(determinationEvent.getTaxon().getUuid(), includeUnpublished, propertyPaths));
|
| 1436 |
40b943c7
|
Patrick Plitzner
|
}
|
| 1437 |
|
|
if(determinationEvent.getTaxonName()!=null){
|
| 1438 |
42002c0a
|
Patrick Plitzner
|
Collection<TaxonBase> taxonBases = determinationEvent.getTaxonName().getTaxonBases();
|
| 1439 |
|
|
for (TaxonBase taxonBase : taxonBases) {
|
| 1440 |
12b3d645
|
Andreas Müller
|
associatedTaxa.add(taxonService.load(taxonBase.getUuid(), includeUnpublished, propertyPaths));
|
| 1441 |
42002c0a
|
Patrick Plitzner
|
}
|
| 1442 |
550eeb6f
|
Patrick Plitzner
|
}
|
| 1443 |
b6b6d586
|
Patrick Plitzner
|
}
|
| 1444 |
|
|
}
|
| 1445 |
40b943c7
|
Patrick Plitzner
|
return associatedTaxa;
|
| 1446 |
|
|
}
|
| 1447 |
|
|
|
| 1448 |
12b3d645
|
Andreas Müller
|
/**
|
| 1449 |
|
|
* {@inheritDoc}
|
| 1450 |
|
|
*/
|
| 1451 |
40b943c7
|
Patrick Plitzner
|
@Override
|
| 1452 |
95964a96
|
Patrick Plitzner
|
public Collection<TaxonBase<?>> listTypeDesignationTaxa(DerivedUnit specimen, Integer limit, Integer start,
|
| 1453 |
40b943c7
|
Patrick Plitzner
|
List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 1454 |
12b3d645
|
Andreas Müller
|
return listTypeDesignationTaxa(specimen, INCLUDE_UNPUBLISHED, limit, start, orderHints, propertyPaths);
|
| 1455 |
|
|
}
|
| 1456 |
|
|
@Override
|
| 1457 |
|
|
public Collection<TaxonBase<?>> listTypeDesignationTaxa(DerivedUnit specimen, boolean includeUnpublished,
|
| 1458 |
|
|
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 1459 |
7e7e032e
|
Andreas Müller
|
Collection<TaxonBase<?>> associatedTaxa = new HashSet<>();
|
| 1460 |
eeef091f
|
Patrick Plitzner
|
for (SpecimenTypeDesignation typeDesignation : listTypeDesignations(specimen, limit, start, orderHints, propertyPaths)) {
|
| 1461 |
|
|
if(typeDesignation.getTypeSpecimen().equals(specimen)){
|
| 1462 |
9dc896c9
|
Andreas Müller
|
Set<TaxonName> typifiedNames = typeDesignation.getTypifiedNames();
|
| 1463 |
|
|
for (TaxonName taxonName : typifiedNames) {
|
| 1464 |
42002c0a
|
Patrick Plitzner
|
Set<Taxon> taxa = taxonName.getTaxa();
|
| 1465 |
|
|
for (Taxon taxon : taxa) {
|
| 1466 |
12b3d645
|
Andreas Müller
|
associatedTaxa.add(taxonService.load(taxon.getUuid(), includeUnpublished, propertyPaths));
|
| 1467 |
42002c0a
|
Patrick Plitzner
|
}
|
| 1468 |
eeef091f
|
Patrick Plitzner
|
}
|
| 1469 |
|
|
}
|
| 1470 |
|
|
}
|
| 1471 |
40b943c7
|
Patrick Plitzner
|
return associatedTaxa;
|
| 1472 |
|
|
}
|
| 1473 |
|
|
|
| 1474 |
12b3d645
|
Andreas Müller
|
/**
|
| 1475 |
|
|
* {@inheritDoc}
|
| 1476 |
|
|
*/
|
| 1477 |
|
|
@Override
|
| 1478 |
|
|
public Collection<TaxonBase<?>> listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen, Integer limit,
|
| 1479 |
|
|
Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 1480 |
|
|
return listIndividualsAssociationTaxa(specimen, INCLUDE_UNPUBLISHED, limit, start, orderHints, propertyPaths);
|
| 1481 |
|
|
}
|
| 1482 |
|
|
|
| 1483 |
40b943c7
|
Patrick Plitzner
|
@Override
|
| 1484 |
12b3d645
|
Andreas Müller
|
public Collection<TaxonBase<?>> listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen, boolean includeUnpublished,
|
| 1485 |
|
|
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 1486 |
7e7e032e
|
Andreas Müller
|
Collection<TaxonBase<?>> associatedTaxa = new HashSet<>();
|
| 1487 |
42002c0a
|
Patrick Plitzner
|
for (IndividualsAssociation individualsAssociation : listIndividualsAssociations(specimen, null, null, null, null)) {
|
| 1488 |
40b943c7
|
Patrick Plitzner
|
if(individualsAssociation.getInDescription().isInstanceOf(TaxonDescription.class)){
|
| 1489 |
|
|
TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(individualsAssociation.getInDescription(), TaxonDescription.class);
|
| 1490 |
|
|
if(taxonDescription.getTaxon()!=null){
|
| 1491 |
12b3d645
|
Andreas Müller
|
associatedTaxa.add(taxonService.load(taxonDescription.getTaxon().getUuid(), includeUnpublished, propertyPaths));
|
| 1492 |
550eeb6f
|
Patrick Plitzner
|
}
|
| 1493 |
|
|
}
|
| 1494 |
|
|
}
|
| 1495 |
b6b6d586
|
Patrick Plitzner
|
return associatedTaxa;
|
| 1496 |
|
|
}
|
| 1497 |
|
|
|
| 1498 |
550eeb6f
|
Patrick Plitzner
|
@Override
|
| 1499 |
|
|
public Collection<DeterminationEvent> listDeterminationEvents(SpecimenOrObservationBase<?> specimen,
|
| 1500 |
|
|
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 1501 |
|
|
return dao.listDeterminationEvents(specimen, limit, start, orderHints, propertyPaths);
|
| 1502 |
|
|
}
|
| 1503 |
|
|
|
| 1504 |
887126ca
|
Andreas Müller
|
@Override
|
| 1505 |
95964a96
|
Patrick Plitzner
|
public Map<DerivedUnit, Collection<SpecimenTypeDesignation>> listTypeDesignations(
|
| 1506 |
|
|
Collection<DerivedUnit> specimens, Integer limit, Integer start,
|
| 1507 |
|
|
List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 1508 |
7e7e032e
|
Andreas Müller
|
Map<DerivedUnit, Collection<SpecimenTypeDesignation>> typeDesignationMap = new HashMap<>();
|
| 1509 |
95964a96
|
Patrick Plitzner
|
for (DerivedUnit specimen : specimens) {
|
| 1510 |
|
|
Collection<SpecimenTypeDesignation> typeDesignations = listTypeDesignations(specimen, limit, start, orderHints, propertyPaths);
|
| 1511 |
|
|
typeDesignationMap.put(specimen, typeDesignations);
|
| 1512 |
|
|
}
|
| 1513 |
|
|
return typeDesignationMap;
|
| 1514 |
|
|
}
|
| 1515 |
|
|
|
| 1516 |
|
|
@Override
|
| 1517 |
|
|
public Collection<SpecimenTypeDesignation> listTypeDesignations(DerivedUnit specimen,
|
| 1518 |
887126ca
|
Andreas Müller
|
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 1519 |
|
|
return dao.listTypeDesignations(specimen, limit, start, orderHints, propertyPaths);
|
| 1520 |
|
|
}
|
| 1521 |
|
|
|
| 1522 |
|
|
@Override
|
| 1523 |
|
|
public Collection<DescriptionBase<?>> listDescriptionsWithDescriptionSpecimen(
|
| 1524 |
|
|
SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints,
|
| 1525 |
|
|
List<String> propertyPaths) {
|
| 1526 |
|
|
return dao.listDescriptionsWithDescriptionSpecimen(specimen, limit, start, orderHints, propertyPaths);
|
| 1527 |
|
|
}
|
| 1528 |
|
|
|
| 1529 |
|
|
@Override
|
| 1530 |
45546a91
|
Andreas Müller
|
@Deprecated //this is not a service layer task so it may be removed in future versions
|
| 1531 |
887126ca
|
Andreas Müller
|
public Collection<DescriptionElementBase> getCharacterDataForSpecimen(SpecimenOrObservationBase<?> specimen) {
|
| 1532 |
|
|
if (specimen != null) {
|
| 1533 |
|
|
return specimen.characterData();
|
| 1534 |
|
|
}else{
|
| 1535 |
7e7e032e
|
Andreas Müller
|
return new ArrayList<>();
|
| 1536 |
887126ca
|
Andreas Müller
|
}
|
| 1537 |
|
|
}
|
| 1538 |
|
|
|
| 1539 |
|
|
@Override
|
| 1540 |
|
|
public Collection<DescriptionElementBase> getCharacterDataForSpecimen(UUID specimenUuid) {
|
| 1541 |
|
|
SpecimenOrObservationBase<?> specimen = load(specimenUuid);
|
| 1542 |
|
|
if (specimen != null) {
|
| 1543 |
|
|
return getCharacterDataForSpecimen(specimen);
|
| 1544 |
|
|
}
|
| 1545 |
|
|
else{
|
| 1546 |
|
|
throw new DataRetrievalFailureException("Specimen with the given uuid not found in the data base");
|
| 1547 |
|
|
}
|
| 1548 |
|
|
}
|
| 1549 |
|
|
|
| 1550 |
|
|
|
| 1551 |
1c1517f9
|
Patrick Plitzner
|
@Override
|
| 1552 |
9a21de1f
|
Andreas Müller
|
public long countByTitle(IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config){
|
| 1553 |
1c1517f9
|
Patrick Plitzner
|
if (config instanceof FindOccurrencesConfigurator) {
|
| 1554 |
|
|
FindOccurrencesConfigurator occurrenceConfig = (FindOccurrencesConfigurator) config;
|
| 1555 |
|
|
Taxon taxon = null;
|
| 1556 |
|
|
if(occurrenceConfig.getAssociatedTaxonUuid()!=null){
|
| 1557 |
9a21de1f
|
Andreas Müller
|
TaxonBase<?> taxonBase = taxonService.load(occurrenceConfig.getAssociatedTaxonUuid());
|
| 1558 |
1c1517f9
|
Patrick Plitzner
|
if(taxonBase.isInstanceOf(Taxon.class)){
|
| 1559 |
|
|
taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
|
| 1560 |
|
|
}
|
| 1561 |
|
|
}
|
| 1562 |
9dc896c9
|
Andreas Müller
|
TaxonName taxonName = null;
|
| 1563 |
1c1517f9
|
Patrick Plitzner
|
if(occurrenceConfig.getAssociatedTaxonNameUuid()!=null){
|
| 1564 |
|
|
taxonName = nameService.load(occurrenceConfig.getAssociatedTaxonNameUuid());
|
| 1565 |
|
|
}
|
| 1566 |
7dab8082
|
Patrick Plitzner
|
/*TODO: #6484 Neither isRetrieveIndirectlyAssociatedSpecimens() nor the AssignmentStatus
|
| 1567 |
|
|
* is currently reflected in the HQL query. So using these in the count method will
|
| 1568 |
|
|
* significantly slow down this method as we have to retreive the entities instead of
|
| 1569 |
|
|
* the just the amount.
|
| 1570 |
|
|
*/
|
| 1571 |
|
|
if(occurrenceConfig.isRetrieveIndirectlyAssociatedSpecimens() || !occurrenceConfig.getAssignmentStatus().equals(AssignmentStatus.ALL_SPECIMENS)){
|
| 1572 |
|
|
List<SpecimenOrObservationBase> occurrences = new ArrayList<>();
|
| 1573 |
|
|
occurrences.addAll(dao.findOccurrences(occurrenceConfig.getClazz(),
|
| 1574 |
1e037cd6
|
Patrick Plitzner
|
occurrenceConfig.getTitleSearchStringSqlized(), occurrenceConfig.getSignificantIdentifier(),
|
| 1575 |
7dab8082
|
Patrick Plitzner
|
occurrenceConfig.getSpecimenType(), taxon, taxonName, occurrenceConfig.getMatchMode(), null, null,
|
| 1576 |
|
|
occurrenceConfig.getOrderHints(), occurrenceConfig.getPropertyPaths()));
|
| 1577 |
|
|
occurrences = filterOccurencesByAssignmentAndHierarchy(occurrenceConfig, occurrences, taxon, taxonName);
|
| 1578 |
|
|
return occurrences.size();
|
| 1579 |
|
|
}
|
| 1580 |
|
|
|
| 1581 |
1c1517f9
|
Patrick Plitzner
|
return dao.countOccurrences(occurrenceConfig.getClazz(),
|
| 1582 |
1e037cd6
|
Patrick Plitzner
|
occurrenceConfig.getTitleSearchStringSqlized(), occurrenceConfig.getSignificantIdentifier(),
|
| 1583 |
1c1517f9
|
Patrick Plitzner
|
occurrenceConfig.getSpecimenType(), taxon, taxonName, occurrenceConfig.getMatchMode(), null, null,
|
| 1584 |
|
|
occurrenceConfig.getOrderHints(), occurrenceConfig.getPropertyPaths());
|
| 1585 |
|
|
}
|
| 1586 |
|
|
else{
|
| 1587 |
1e037cd6
|
Patrick Plitzner
|
return super.countByTitle(config);
|
| 1588 |
1c1517f9
|
Patrick Plitzner
|
}
|
| 1589 |
|
|
}
|
| 1590 |
|
|
|
| 1591 |
79c29018
|
Patrick Plitzner
|
@Override
|
| 1592 |
|
|
public Pager<UuidAndTitleCache<SpecimenOrObservationBase>> findByTitleUuidAndTitleCache(
|
| 1593 |
|
|
FindOccurrencesConfigurator config){
|
| 1594 |
|
|
List<UuidAndTitleCache<SpecimenOrObservationBase>> occurrences = new ArrayList<>();
|
| 1595 |
|
|
Taxon taxon = null;
|
| 1596 |
|
|
if(config.getAssociatedTaxonUuid()!=null){
|
| 1597 |
9a21de1f
|
Andreas Müller
|
TaxonBase<?> taxonBase = taxonService.load(config.getAssociatedTaxonUuid());
|
| 1598 |
79c29018
|
Patrick Plitzner
|
if(taxonBase.isInstanceOf(Taxon.class)){
|
| 1599 |
f6df4cfb
|
Andreas Müller
|
taxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
| 1600 |
79c29018
|
Patrick Plitzner
|
}
|
| 1601 |
|
|
}
|
| 1602 |
|
|
TaxonName taxonName = null;
|
| 1603 |
|
|
if(config.getAssociatedTaxonNameUuid()!=null){
|
| 1604 |
|
|
taxonName = nameService.load(config.getAssociatedTaxonNameUuid());
|
| 1605 |
|
|
}
|
| 1606 |
|
|
occurrences.addAll(dao.findOccurrencesUuidAndTitleCache(config.getClazz(),
|
| 1607 |
|
|
config.getTitleSearchString(), config.getSignificantIdentifier(),
|
| 1608 |
|
|
config.getSpecimenType(), taxon, taxonName, config.getMatchMode(), null, null,
|
| 1609 |
|
|
config.getOrderHints()));
|
| 1610 |
|
|
|
| 1611 |
f6df4cfb
|
Andreas Müller
|
return new DefaultPagerImpl<>(config.getPageNumber(), occurrences.size(), config.getPageSize(), occurrences);
|
| 1612 |
79c29018
|
Patrick Plitzner
|
}
|
| 1613 |
|
|
|
| 1614 |
887126ca
|
Andreas Müller
|
@Override
|
| 1615 |
98ce4a92
|
Andreas Müller
|
public <S extends SpecimenOrObservationBase> Pager<S> findByTitle(
|
| 1616 |
|
|
IIdentifiableEntityServiceConfigurator<S> config) {
|
| 1617 |
887126ca
|
Andreas Müller
|
if (config instanceof FindOccurrencesConfigurator) {
|
| 1618 |
|
|
FindOccurrencesConfigurator occurrenceConfig = (FindOccurrencesConfigurator) config;
|
| 1619 |
7e7e032e
|
Andreas Müller
|
List<SpecimenOrObservationBase> occurrences = new ArrayList<>();
|
| 1620 |
887126ca
|
Andreas Müller
|
Taxon taxon = null;
|
| 1621 |
|
|
if(occurrenceConfig.getAssociatedTaxonUuid()!=null){
|
| 1622 |
f6df4cfb
|
Andreas Müller
|
TaxonBase<?> taxonBase = taxonService.load(occurrenceConfig.getAssociatedTaxonUuid());
|
| 1623 |
887126ca
|
Andreas Müller
|
if(taxonBase.isInstanceOf(Taxon.class)){
|
| 1624 |
|
|
taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
|
| 1625 |
|
|
}
|
| 1626 |
|
|
}
|
| 1627 |
9dc896c9
|
Andreas Müller
|
TaxonName taxonName = null;
|
| 1628 |
e6e5ebdc
|
Patrick Plitzner
|
if(occurrenceConfig.getAssociatedTaxonNameUuid()!=null){
|
| 1629 |
604df0ab
|
Patrick Plitzner
|
taxonName = nameService.load(occurrenceConfig.getAssociatedTaxonNameUuid());
|
| 1630 |
e6e5ebdc
|
Patrick Plitzner
|
}
|
| 1631 |
98ce4a92
|
Andreas Müller
|
List<? extends SpecimenOrObservationBase> foundOccurrences = dao.findOccurrences(occurrenceConfig.getClazz(),
|
| 1632 |
887126ca
|
Andreas Müller
|
occurrenceConfig.getTitleSearchString(), occurrenceConfig.getSignificantIdentifier(),
|
| 1633 |
e6e5ebdc
|
Patrick Plitzner
|
occurrenceConfig.getSpecimenType(), taxon, taxonName, occurrenceConfig.getMatchMode(), null, null,
|
| 1634 |
98ce4a92
|
Andreas Müller
|
occurrenceConfig.getOrderHints(), occurrenceConfig.getPropertyPaths());
|
| 1635 |
|
|
occurrences.addAll(foundOccurrences);
|
| 1636 |
7dab8082
|
Patrick Plitzner
|
occurrences = filterOccurencesByAssignmentAndHierarchy(occurrenceConfig, occurrences, taxon, taxonName);
|
| 1637 |
|
|
|
| 1638 |
98ce4a92
|
Andreas Müller
|
return new DefaultPagerImpl<>(config.getPageNumber(), occurrences.size(), config.getPageSize(), (List<S>)occurrences);
|
| 1639 |
7dab8082
|
Patrick Plitzner
|
}
|
| 1640 |
|
|
return super.findByTitle(config);
|
| 1641 |
|
|
}
|
| 1642 |
|
|
|
| 1643 |
|
|
private List<SpecimenOrObservationBase> filterOccurencesByAssignmentAndHierarchy(
|
| 1644 |
|
|
FindOccurrencesConfigurator occurrenceConfig, List<SpecimenOrObservationBase> occurrences, Taxon taxon,
|
| 1645 |
|
|
TaxonName taxonName) {
|
| 1646 |
|
|
//filter out (un-)assigned specimens
|
| 1647 |
|
|
if(taxon==null && taxonName==null){
|
| 1648 |
|
|
AssignmentStatus assignmentStatus = occurrenceConfig.getAssignmentStatus();
|
| 1649 |
98ce4a92
|
Andreas Müller
|
List<SpecimenOrObservationBase> specimenWithAssociations = new ArrayList<>();
|
| 1650 |
7dab8082
|
Patrick Plitzner
|
if(!assignmentStatus.equals(AssignmentStatus.ALL_SPECIMENS)){
|
| 1651 |
98ce4a92
|
Andreas Müller
|
for (SpecimenOrObservationBase specimenOrObservationBase : occurrences) {
|
| 1652 |
12b3d645
|
Andreas Müller
|
boolean includeUnpublished = true; //TODO not sure if this is correct, maybe we have to propagate publish flag to higher methods.
|
| 1653 |
|
|
Collection<TaxonBase<?>> associatedTaxa = listAssociatedTaxa(specimenOrObservationBase,
|
| 1654 |
|
|
includeUnpublished, null, null, null, null);
|
| 1655 |
7dab8082
|
Patrick Plitzner
|
if(!associatedTaxa.isEmpty()){
|
| 1656 |
|
|
specimenWithAssociations.add(specimenOrObservationBase);
|
| 1657 |
02942c8c
|
Patrick Plitzner
|
}
|
| 1658 |
|
|
}
|
| 1659 |
|
|
}
|
| 1660 |
7dab8082
|
Patrick Plitzner
|
if(assignmentStatus.equals(AssignmentStatus.UNASSIGNED_SPECIMENS)){
|
| 1661 |
|
|
occurrences.removeAll(specimenWithAssociations);
|
| 1662 |
|
|
}
|
| 1663 |
|
|
if(assignmentStatus.equals(AssignmentStatus.ASSIGNED_SPECIMENS)){
|
| 1664 |
|
|
occurrences = new ArrayList<>(specimenWithAssociations);
|
| 1665 |
|
|
}
|
| 1666 |
|
|
}
|
| 1667 |
|
|
// indirectly associated specimens
|
| 1668 |
|
|
if(occurrenceConfig.isRetrieveIndirectlyAssociatedSpecimens()){
|
| 1669 |
|
|
List<SpecimenOrObservationBase> indirectlyAssociatedOccurrences = new ArrayList<>(occurrences);
|
| 1670 |
f6df4cfb
|
Andreas Müller
|
for (SpecimenOrObservationBase<?> specimen : occurrences) {
|
| 1671 |
7dab8082
|
Patrick Plitzner
|
List<SpecimenOrObservationBase<?>> allHierarchyDerivates = getAllHierarchyDerivatives(specimen);
|
| 1672 |
|
|
for (SpecimenOrObservationBase<?> specimenOrObservationBase : allHierarchyDerivates) {
|
| 1673 |
|
|
if(!occurrences.contains(specimenOrObservationBase)){
|
| 1674 |
|
|
indirectlyAssociatedOccurrences.add(specimenOrObservationBase);
|
| 1675 |
887126ca
|
Andreas Müller
|
}
|
| 1676 |
|
|
}
|
| 1677 |
|
|
}
|
| 1678 |
7dab8082
|
Patrick Plitzner
|
occurrences = indirectlyAssociatedOccurrences;
|
| 1679 |
887126ca
|
Andreas Müller
|
}
|
| 1680 |
7dab8082
|
Patrick Plitzner
|
return occurrences;
|
| 1681 |
887126ca
|
Andreas Müller
|
}
|
| 1682 |
|
|
|
| 1683 |
|
|
@Override
|
| 1684 |
|
|
public List<SpecimenOrObservationBase<?>> getAllHierarchyDerivatives(SpecimenOrObservationBase<?> specimen){
|
| 1685 |
7e7e032e
|
Andreas Müller
|
List<SpecimenOrObservationBase<?>> allHierarchyDerivatives = new ArrayList<>();
|
| 1686 |
6b53ead8
|
Katja Luther
|
Collection<FieldUnit> fieldUnits = findFieldUnits(specimen.getUuid(), null);
|
| 1687 |
887126ca
|
Andreas Müller
|
if(fieldUnits.isEmpty()){
|
| 1688 |
|
|
allHierarchyDerivatives.add(specimen);
|
| 1689 |
|
|
allHierarchyDerivatives.addAll(getAllChildDerivatives(specimen));
|
| 1690 |
|
|
}
|
| 1691 |
|
|
else{
|
| 1692 |
|
|
for (FieldUnit fieldUnit : fieldUnits) {
|
| 1693 |
|
|
allHierarchyDerivatives.add(fieldUnit);
|
| 1694 |
|
|
allHierarchyDerivatives.addAll(getAllChildDerivatives(fieldUnit));
|
| 1695 |
|
|
}
|
| 1696 |
|
|
}
|
| 1697 |
|
|
return allHierarchyDerivatives;
|
| 1698 |
|
|
}
|
| 1699 |
|
|
|
| 1700 |
d496803d
|
Patrick Plitzner
|
@Override
|
| 1701 |
|
|
public List<DerivedUnit> getAllChildDerivatives(UUID specimenUuid){
|
| 1702 |
|
|
return getAllChildDerivatives(load(specimenUuid));
|
| 1703 |
|
|
}
|
| 1704 |
|
|
|
| 1705 |
887126ca
|
Andreas Müller
|
@Override
|
| 1706 |
|
|
public List<DerivedUnit> getAllChildDerivatives(SpecimenOrObservationBase<?> specimen){
|
| 1707 |
09a260bb
|
Katja Luther
|
if (specimen == null){
|
| 1708 |
|
|
return null;
|
| 1709 |
|
|
}
|
| 1710 |
7e7e032e
|
Andreas Müller
|
List<DerivedUnit> childDerivate = new ArrayList<>();
|
| 1711 |
887126ca
|
Andreas Müller
|
Set<DerivationEvent> derivationEvents = specimen.getDerivationEvents();
|
| 1712 |
|
|
for (DerivationEvent derivationEvent : derivationEvents) {
|
| 1713 |
|
|
Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
|
| 1714 |
|
|
for (DerivedUnit derivedUnit : derivatives) {
|
| 1715 |
|
|
childDerivate.add(derivedUnit);
|
| 1716 |
d496803d
|
Patrick Plitzner
|
childDerivate.addAll(getAllChildDerivatives(derivedUnit.getUuid()));
|
| 1717 |
887126ca
|
Andreas Müller
|
}
|
| 1718 |
|
|
}
|
| 1719 |
|
|
return childDerivate;
|
| 1720 |
|
|
}
|
| 1721 |
|
|
|
| 1722 |
|
|
@Override
|
| 1723 |
9a21de1f
|
Andreas Müller
|
public long countOccurrences(IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config){
|
| 1724 |
1c1517f9
|
Patrick Plitzner
|
return countByTitle(config);
|
| 1725 |
887126ca
|
Andreas Müller
|
}
|
| 1726 |
|
|
|
| 1727 |
3835ed3e
|
Patrick Plitzner
|
/**
|
| 1728 |
|
|
* {@inheritDoc}
|
| 1729 |
|
|
*/
|
| 1730 |
|
|
@Override
|
| 1731 |
6b53ead8
|
Katja Luther
|
public List<FieldUnit> findFieldUnitsForGatheringEvent(UUID gatheringEventUuid) {
|
| 1732 |
|
|
return dao.findFieldUnitsForGatheringEvent(gatheringEventUuid, null, null, null, null);
|
| 1733 |
|
|
}
|
| 1734 |
|
|
|
| 1735 |
|
|
|
| 1736 |
|
|
/**
|
| 1737 |
|
|
* {@inheritDoc}
|
| 1738 |
|
|
*/
|
| 1739 |
|
|
@Override
|
| 1740 |
|
|
public List<Point> findPointsForFieldUnitList(List<UUID> fieldUnitUuids) {
|
| 1741 |
|
|
|
| 1742 |
|
|
return dao.findPointsForFieldUnitList(fieldUnitUuids);
|
| 1743 |
3835ed3e
|
Patrick Plitzner
|
}
|
| 1744 |
887126ca
|
Andreas Müller
|
}
|