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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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import java.util.Iterator;
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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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import org.apache.lucene.queryparser.classic.ParseException;
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import org.apache.lucene.search.BooleanClause.Occur;
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import org.apache.lucene.search.BooleanQuery.Builder;
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import org.apache.lucene.search.SortField;
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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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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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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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import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO.Link;
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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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import eu.etaxonomy.cdm.api.service.search.LuceneParseException;
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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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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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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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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.ICdmBase;
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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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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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import eu.etaxonomy.cdm.model.name.TaxonName;
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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.molecular.ISingleReadDao;
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import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.persistence.query.AssignmentStatus;
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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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import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;
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/**
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* @author a.babadshanjan
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* @created 01.09.2008
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*/
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@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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@Autowired
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private INameService nameService;
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@Autowired
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private IEventBaseService eventService;
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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 ISingleReadDao singleReadDao;
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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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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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List<? extends DefinedTermBase> terms = this.definedTermDao.findByTitle(Country.class, name, null, null, null, null, null, null);
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List<Country> countries = new ArrayList<>();
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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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Integer numberOfResults = dao.countDerivationEvents(occurence);
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List<DerivationEvent> results = new ArrayList<>();
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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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return new DefaultPagerImpl<DerivationEvent>(pageNumber, numberOfResults, pageSize, results);
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}
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@Override
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public int countDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonbase) {
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return dao.countDeterminations(occurence, taxonbase);
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}
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@Override
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public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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Integer numberOfResults = dao.countDeterminations(occurrence, taxonBase);
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List<DeterminationEvent> results = new ArrayList<>();
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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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return new DefaultPagerImpl<DeterminationEvent>(pageNumber, numberOfResults, pageSize, results);
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}
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@Override
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public Pager<Media> getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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Integer numberOfResults = dao.countMedia(occurence);
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List<Media> results = new ArrayList<>();
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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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return new DefaultPagerImpl<Media>(pageNumber, numberOfResults, pageSize, results);
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}
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@Override
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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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List<Media> media = new ArrayList<>();
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//media specimens
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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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// pherograms & gelPhotos
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if (rootOccurence.isInstanceOf(DnaSample.class)) {
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DnaSample dnaSample = CdmBase.deproxy(rootOccurence, DnaSample.class);
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Set<Sequence> sequences = dnaSample.getSequences();
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//we do show only those gelPhotos which lead to a consensus sequence
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for (Sequence sequence : sequences) {
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Set<Media> dnaRelatedMedia = new HashSet<>();
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for (SingleRead singleRead : sequence.getSingleReads()){
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AmplificationResult amplification = singleRead.getAmplificationResult();
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dnaRelatedMedia.add(amplification.getGelPhoto());
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dnaRelatedMedia.add(singleRead.getPherogram());
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dnaRelatedMedia.remove(null);
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}
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media.addAll(dnaRelatedMedia);
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}
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}
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if(rootOccurence.isInstanceOf(DerivedUnit.class)){
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DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(rootOccurence, DerivedUnit.class);
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for (DerivationEvent derivationEvent : derivedUnit.getDerivationEvents()) {
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for (DerivedUnit childDerivative : derivationEvent.getDerivatives()) {
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media.addAll(getMediainHierarchy(childDerivative, pageSize, pageNumber, propertyPaths).getRecords());
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}
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}
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}
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return new DefaultPagerImpl<Media>(pageNumber, media.size(), pageSize, media);
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}
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@Override
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public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonName determinedAs, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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Integer numberOfResults = dao.count(type, determinedAs);
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List<SpecimenOrObservationBase> results = new ArrayList<>();
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pageNumber = pageNumber == null ? 0 : pageNumber;
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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Integer start = pageSize == null ? 0 : pageSize * pageNumber;
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results = dao.list(type, determinedAs, pageSize, start, orderHints, propertyPaths);
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}
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return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, numberOfResults, pageSize, results);
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}
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@Override
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public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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Integer numberOfResults = dao.count(type, determinedAs);
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List<SpecimenOrObservationBase> results = new ArrayList<>();
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pageNumber = pageNumber == null ? 0 : pageNumber;
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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Integer start = pageSize == null ? 0 : pageSize * pageNumber;
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results = dao.list(type, determinedAs, pageSize, start, orderHints, propertyPaths);
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}
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return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, numberOfResults, pageSize, results);
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}
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@Override
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public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache(Integer limit, String pattern) {
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return dao.getDerivedUnitUuidAndTitleCache(limit, pattern);
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}
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@Override
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public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {
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313
|
return dao.getFieldUnitUuidAndTitleCache();
|
|
314
|
}
|
|
315
|
|
|
316
|
@Override
|
|
317
|
public DerivedUnitFacade getDerivedUnitFacade(DerivedUnit derivedUnit, List<String> propertyPaths) throws DerivedUnitFacadeNotSupportedException {
|
|
318
|
derivedUnit = (DerivedUnit) dao.load(derivedUnit.getUuid(), null);
|
|
319
|
DerivedUnitFacadeConfigurator config = DerivedUnitFacadeConfigurator.NewInstance();
|
|
320
|
config.setThrowExceptionForNonSpecimenPreservationMethodRequest(false);
|
|
321
|
DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit, config);
|
|
322
|
beanInitializer.initialize(derivedUnitFacade, propertyPaths);
|
|
323
|
return derivedUnitFacade;
|
|
324
|
}
|
|
325
|
|
|
326
|
@Override
|
|
327
|
public List<DerivedUnitFacade> listDerivedUnitFacades(
|
|
328
|
DescriptionBase description, List<String> propertyPaths) {
|
|
329
|
|
|
330
|
List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<>();
|
|
331
|
IndividualsAssociation tempIndividualsAssociation;
|
|
332
|
SpecimenOrObservationBase tempSpecimenOrObservationBase;
|
|
333
|
List<IndividualsAssociation> elements = descriptionService.listDescriptionElements(description, null, IndividualsAssociation.class, null, 0, Arrays.asList(new String []{"associatedSpecimenOrObservation"}));
|
|
334
|
for (IndividualsAssociation element : elements) {
|
|
335
|
tempIndividualsAssociation = HibernateProxyHelper.deproxy(element, IndividualsAssociation.class);
|
|
336
|
if (tempIndividualsAssociation.getAssociatedSpecimenOrObservation() != null) {
|
|
337
|
tempSpecimenOrObservationBase = HibernateProxyHelper.deproxy(tempIndividualsAssociation.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase.class);
|
|
338
|
if (tempSpecimenOrObservationBase.isInstanceOf(DerivedUnit.class)) {
|
|
339
|
try {
|
|
340
|
derivedUnitFacadeList.add(DerivedUnitFacade.NewInstance(HibernateProxyHelper.deproxy(tempSpecimenOrObservationBase, DerivedUnit.class)));
|
|
341
|
} catch (DerivedUnitFacadeNotSupportedException e) {
|
|
342
|
logger.warn(tempIndividualsAssociation.getAssociatedSpecimenOrObservation().getTitleCache() + " : " + e.getMessage());
|
|
343
|
}
|
|
344
|
}
|
|
345
|
}
|
|
346
|
}
|
|
347
|
|
|
348
|
beanInitializer.initializeAll(derivedUnitFacadeList, propertyPaths);
|
|
349
|
|
|
350
|
return derivedUnitFacadeList;
|
|
351
|
}
|
|
352
|
|
|
353
|
|
|
354
|
@Override
|
|
355
|
public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
|
|
356
|
Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
357
|
|
|
358
|
return pageByAssociatedTaxon(type, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
|
|
359
|
}
|
|
360
|
|
|
361
|
@Override
|
|
362
|
public Collection<SpecimenOrObservationBase> listFieldUnitsByAssociatedTaxon(Taxon associatedTaxon, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
363
|
return pageFieldUnitsByAssociatedTaxon(null, associatedTaxon, null, null, null, null, propertyPaths).getRecords();
|
|
364
|
}
|
|
365
|
|
|
366
|
@Override
|
|
367
|
public Pager<SpecimenOrObservationBase> pageFieldUnitsByAssociatedTaxon(Set<TaxonRelationshipEdge> includeRelationships,
|
|
368
|
Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
|
|
369
|
List<String> propertyPaths) {
|
|
370
|
|
|
371
|
if (!getSession().contains(associatedTaxon)) {
|
|
372
|
associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
|
|
373
|
}
|
|
374
|
|
|
375
|
// gather the IDs of all relevant field units
|
|
376
|
Set<UUID> fieldUnitUuids = new HashSet<>();
|
|
377
|
List<SpecimenOrObservationBase> records = listByAssociatedTaxon(null, includeRelationships, associatedTaxon, maxDepth, null, null, orderHints, propertyPaths);
|
|
378
|
for (SpecimenOrObservationBase<?> specimen : records) {
|
|
379
|
for (FieldUnit fieldUnit : getFieldUnits(specimen.getUuid(), null)) {
|
|
380
|
fieldUnitUuids.add(fieldUnit.getUuid());
|
|
381
|
}
|
|
382
|
}
|
|
383
|
//dao.list() does the paging of the field units. Passing the field units directly to the Pager would not work
|
|
384
|
List<SpecimenOrObservationBase> fieldUnits = dao.list(fieldUnitUuids, pageSize, pageNumber, orderHints, propertyPaths);
|
|
385
|
return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, fieldUnitUuids.size(), pageSize, fieldUnits);
|
|
386
|
}
|
|
387
|
|
|
388
|
@Override
|
|
389
|
public FieldUnitDTO assembleFieldUnitDTO(FieldUnit fieldUnit, UUID associatedTaxonUuid) {
|
|
390
|
|
|
391
|
if (!getSession().contains(fieldUnit)) {
|
|
392
|
fieldUnit = (FieldUnit) load(fieldUnit.getUuid());
|
|
393
|
}
|
|
394
|
TaxonBase associatedTaxon = taxonService.load(associatedTaxonUuid);
|
|
395
|
|
|
396
|
FieldUnitDTO fieldUnitDTO = new FieldUnitDTO();
|
|
397
|
|
|
398
|
if (fieldUnit.getGatheringEvent() != null) {
|
|
399
|
GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
|
|
400
|
// Country
|
|
401
|
NamedArea country = gatheringEvent.getCountry();
|
|
402
|
fieldUnitDTO.setCountry(country != null ? country.getLabel() : null);
|
|
403
|
// Collection
|
|
404
|
AgentBase collector = gatheringEvent.getCollector();
|
|
405
|
String fieldNumber = fieldUnit.getFieldNumber();
|
|
406
|
String collectionString = "";
|
|
407
|
if (collector != null || fieldNumber != null) {
|
|
408
|
collectionString += collector != null ? collector : "";
|
|
409
|
if (!collectionString.isEmpty()) {
|
|
410
|
collectionString += " ";
|
|
411
|
}
|
|
412
|
collectionString += (fieldNumber != null ? fieldNumber : "");
|
|
413
|
collectionString.trim();
|
|
414
|
}
|
|
415
|
fieldUnitDTO.setCollection(collectionString);
|
|
416
|
// Date
|
|
417
|
Partial gatheringDate = gatheringEvent.getGatheringDate();
|
|
418
|
String dateString = null;
|
|
419
|
if (gatheringDate != null) {
|
|
420
|
dateString = gatheringDate.toString();
|
|
421
|
}
|
|
422
|
else if(gatheringEvent.getTimeperiod()!=null && gatheringEvent.getTimeperiod().getFreeText()!=null){
|
|
423
|
dateString = gatheringEvent.getTimeperiod().getFreeText();
|
|
424
|
}
|
|
425
|
fieldUnitDTO.setDate(dateString);
|
|
426
|
}
|
|
427
|
|
|
428
|
// Taxon Name
|
|
429
|
fieldUnitDTO.setTaxonName(associatedTaxon.getName().getTitleCache());
|
|
430
|
|
|
431
|
// Herbaria map
|
|
432
|
Map<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> collectionToCountMap = new HashMap<>();
|
|
433
|
// List of accession numbers for citation
|
|
434
|
List<String> preservedSpecimenAccessionNumbers = new ArrayList<>();
|
|
435
|
|
|
436
|
// assemble preserved specimen DTOs
|
|
437
|
Set<DerivationEvent> derivationEvents = fieldUnit.getDerivationEvents();
|
|
438
|
for (DerivationEvent derivationEvent : derivationEvents) {
|
|
439
|
Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
|
|
440
|
for (DerivedUnit derivedUnit : derivatives) {
|
|
441
|
if(!derivedUnit.isPublish()){
|
|
442
|
continue;
|
|
443
|
}
|
|
444
|
// collect accession numbers for citation
|
|
445
|
String mostSignificantIdentifier = getMostSignificantIdentifier(derivedUnit);
|
|
446
|
if (mostSignificantIdentifier != null) {
|
|
447
|
preservedSpecimenAccessionNumbers.add(mostSignificantIdentifier);
|
|
448
|
}
|
|
449
|
// collect collections for herbaria column
|
|
450
|
if (derivedUnit.getCollection() != null) {
|
|
451
|
Integer herbariumCount = collectionToCountMap.get(derivedUnit.getCollection());
|
|
452
|
if (herbariumCount == null) {
|
|
453
|
herbariumCount = 0;
|
|
454
|
}
|
|
455
|
collectionToCountMap.put(derivedUnit.getCollection(), herbariumCount + 1);
|
|
456
|
}
|
|
457
|
if (derivedUnit.getRecordBasis().equals(SpecimenOrObservationType.PreservedSpecimen)) {
|
|
458
|
PreservedSpecimenDTO preservedSpecimenDTO = assemblePreservedSpecimenDTO(derivedUnit, fieldUnitDTO);
|
|
459
|
fieldUnitDTO.addPreservedSpecimenDTO(preservedSpecimenDTO);
|
|
460
|
fieldUnitDTO.setHasCharacterData(fieldUnitDTO.isHasCharacterData() || preservedSpecimenDTO.isHasCharacterData());
|
|
461
|
fieldUnitDTO.setHasDetailImage(fieldUnitDTO.isHasDetailImage() || preservedSpecimenDTO.isHasDetailImage());
|
|
462
|
fieldUnitDTO.setHasDna(fieldUnitDTO.isHasDna() || preservedSpecimenDTO.isHasDna());
|
|
463
|
fieldUnitDTO.setHasSpecimenScan(fieldUnitDTO.isHasSpecimenScan() || preservedSpecimenDTO.isHasSpecimenScan());
|
|
464
|
}
|
|
465
|
}
|
|
466
|
}
|
|
467
|
// assemble derivate data DTO
|
|
468
|
assembleDerivateDataDTO(fieldUnitDTO, fieldUnit);
|
|
469
|
|
|
470
|
// assemble citation
|
|
471
|
String citation = fieldUnit.getTitleCache();
|
|
472
|
if((CdmUtils.isBlank(citation) || citation.equals(IdentifiableEntityDefaultCacheStrategy.TITLE_CACHE_GENERATION_NOT_IMPLEMENTED))
|
|
473
|
&& !fieldUnit.isProtectedTitleCache()){
|
|
474
|
fieldUnit.setTitleCache(null);
|
|
475
|
citation = fieldUnit.getTitleCache();
|
|
476
|
}
|
|
477
|
if (!preservedSpecimenAccessionNumbers.isEmpty()) {
|
|
478
|
citation += " (";
|
|
479
|
for (String accessionNumber : preservedSpecimenAccessionNumbers) {
|
|
480
|
if (!accessionNumber.isEmpty()) {
|
|
481
|
citation += accessionNumber + SEPARATOR_STRING;
|
|
482
|
}
|
|
483
|
}
|
|
484
|
citation = removeTail(citation, SEPARATOR_STRING);
|
|
485
|
citation += ")";
|
|
486
|
}
|
|
487
|
fieldUnitDTO.setCitation(citation);
|
|
488
|
|
|
489
|
// assemble herbaria string
|
|
490
|
String herbariaString = "";
|
|
491
|
for (Entry<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> e : collectionToCountMap.entrySet()) {
|
|
492
|
eu.etaxonomy.cdm.model.occurrence.Collection collection = e.getKey();
|
|
493
|
if (collection.getCode() != null) {
|
|
494
|
herbariaString += collection.getCode();
|
|
495
|
}
|
|
496
|
if (e.getValue() > 1) {
|
|
497
|
herbariaString += "(" + e.getValue() + ")";
|
|
498
|
}
|
|
499
|
herbariaString += SEPARATOR_STRING;
|
|
500
|
}
|
|
501
|
herbariaString = removeTail(herbariaString, SEPARATOR_STRING);
|
|
502
|
fieldUnitDTO.setHerbarium(herbariaString);
|
|
503
|
|
|
504
|
return fieldUnitDTO;
|
|
505
|
}
|
|
506
|
|
|
507
|
@Override
|
|
508
|
public PreservedSpecimenDTO assemblePreservedSpecimenDTO(DerivedUnit derivedUnit) {
|
|
509
|
return assemblePreservedSpecimenDTO(derivedUnit, null);
|
|
510
|
}
|
|
511
|
|
|
512
|
@Override
|
|
513
|
public String getMostSignificantIdentifier(DerivedUnit derivedUnit) {
|
|
514
|
if (derivedUnit.getAccessionNumber() != null && !derivedUnit.getAccessionNumber().isEmpty()) {
|
|
515
|
return derivedUnit.getAccessionNumber();
|
|
516
|
}
|
|
517
|
else if(derivedUnit.getBarcode()!=null && !derivedUnit.getBarcode().isEmpty()){
|
|
518
|
return derivedUnit.getBarcode();
|
|
519
|
}
|
|
520
|
else if(derivedUnit.getCatalogNumber()!=null && !derivedUnit.getCatalogNumber().isEmpty()){
|
|
521
|
return derivedUnit.getCatalogNumber();
|
|
522
|
}
|
|
523
|
return null;
|
|
524
|
}
|
|
525
|
|
|
526
|
public PreservedSpecimenDTO assemblePreservedSpecimenDTO(DerivedUnit derivedUnit, FieldUnitDTO fieldUnitDTO) {
|
|
527
|
if (!getSession().contains(derivedUnit)) {
|
|
528
|
derivedUnit = (DerivedUnit) load(derivedUnit.getUuid());
|
|
529
|
}
|
|
530
|
PreservedSpecimenDTO preservedSpecimenDTO = new PreservedSpecimenDTO();
|
|
531
|
|
|
532
|
//specimen identifier
|
|
533
|
FormatKey collectionKey = FormatKey.COLLECTION_CODE;
|
|
534
|
String specimenIdentifier = CdmFormatterFactory.format(derivedUnit, collectionKey);
|
|
535
|
if (CdmUtils.isBlank(specimenIdentifier)) {
|
|
536
|
collectionKey = FormatKey.COLLECTION_NAME;
|
|
537
|
}
|
|
538
|
specimenIdentifier = CdmFormatterFactory.format(derivedUnit, new FormatKey[] {
|
|
539
|
collectionKey, FormatKey.SPACE,
|
|
540
|
FormatKey.MOST_SIGNIFICANT_IDENTIFIER, FormatKey.SPACE });
|
|
541
|
if(CdmUtils.isBlank(specimenIdentifier)){
|
|
542
|
specimenIdentifier = derivedUnit.getUuid().toString();
|
|
543
|
}
|
|
544
|
preservedSpecimenDTO.setAccessionNumber(specimenIdentifier);
|
|
545
|
preservedSpecimenDTO.setUuid(derivedUnit.getUuid().toString());
|
|
546
|
|
|
547
|
//preferred stable URI
|
|
548
|
preservedSpecimenDTO.setPreferredStableUri(derivedUnit.getPreferredStableUri());
|
|
549
|
|
|
550
|
// citation
|
|
551
|
Collection<FieldUnit> fieldUnits = getFieldUnits(derivedUnit, null);
|
|
552
|
if (fieldUnits.size() == 1) {
|
|
553
|
preservedSpecimenDTO.setCitation(fieldUnits.iterator().next().getTitleCache());
|
|
554
|
}
|
|
555
|
else{
|
|
556
|
preservedSpecimenDTO.setCitation("No Citation available. This specimen either has no or multiple field units.");
|
|
557
|
}
|
|
558
|
|
|
559
|
// character state data
|
|
560
|
Collection<DescriptionElementBase> characterDataForSpecimen = getCharacterDataForSpecimen(derivedUnit);
|
|
561
|
if (!characterDataForSpecimen.isEmpty()) {
|
|
562
|
if (fieldUnitDTO != null) {
|
|
563
|
fieldUnitDTO.setHasCharacterData(true);
|
|
564
|
}
|
|
565
|
}
|
|
566
|
for (DescriptionElementBase descriptionElementBase : characterDataForSpecimen) {
|
|
567
|
String character = descriptionElementBase.getFeature().getLabel();
|
|
568
|
ArrayList<Language> languages = new ArrayList<>(Collections.singleton(Language.DEFAULT()));
|
|
569
|
if (descriptionElementBase instanceof QuantitativeData) {
|
|
570
|
QuantitativeData quantitativeData = (QuantitativeData) descriptionElementBase;
|
|
571
|
DefaultQuantitativeDescriptionBuilder builder = new DefaultQuantitativeDescriptionBuilder();
|
|
572
|
String state = builder.build(quantitativeData, languages).getText(Language.DEFAULT());
|
|
573
|
preservedSpecimenDTO.addCharacterData(character, state);
|
|
574
|
}
|
|
575
|
else if(descriptionElementBase instanceof CategoricalData){
|
|
576
|
CategoricalData categoricalData = (CategoricalData) descriptionElementBase;
|
|
577
|
DefaultCategoricalDescriptionBuilder builder = new DefaultCategoricalDescriptionBuilder();
|
|
578
|
String state = builder.build(categoricalData, languages).getText(Language.DEFAULT());
|
|
579
|
preservedSpecimenDTO.addCharacterData(character, state);
|
|
580
|
}
|
|
581
|
}
|
|
582
|
// check type designations
|
|
583
|
Collection<SpecimenTypeDesignation> specimenTypeDesignations = listTypeDesignations(derivedUnit, null, null, null, null);
|
|
584
|
for (SpecimenTypeDesignation specimenTypeDesignation : specimenTypeDesignations) {
|
|
585
|
if (fieldUnitDTO != null) {
|
|
586
|
fieldUnitDTO.setHasType(true);
|
|
587
|
}
|
|
588
|
TypeDesignationStatusBase<?> typeStatus = specimenTypeDesignation.getTypeStatus();
|
|
589
|
if (typeStatus != null) {
|
|
590
|
List<String> typedTaxaNames = new ArrayList<>();
|
|
591
|
String label = typeStatus.getLabel();
|
|
592
|
Set<TaxonName> typifiedNames = specimenTypeDesignation.getTypifiedNames();
|
|
593
|
for (TaxonName taxonName : typifiedNames) {
|
|
594
|
typedTaxaNames.add(taxonName.getFullTitleCache());
|
|
595
|
}
|
|
596
|
preservedSpecimenDTO.addTypes(label, typedTaxaNames);
|
|
597
|
}
|
|
598
|
}
|
|
599
|
|
|
600
|
// individuals associations
|
|
601
|
Collection<IndividualsAssociation> individualsAssociations = listIndividualsAssociations(derivedUnit, null, null, null, null);
|
|
602
|
for (IndividualsAssociation individualsAssociation : individualsAssociations) {
|
|
603
|
if (individualsAssociation.getInDescription() != null) {
|
|
604
|
if (individualsAssociation.getInDescription().isInstanceOf(TaxonDescription.class)) {
|
|
605
|
TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(individualsAssociation.getInDescription(), TaxonDescription.class);
|
|
606
|
Taxon taxon = taxonDescription.getTaxon();
|
|
607
|
if (taxon != null) {
|
|
608
|
preservedSpecimenDTO.addAssociatedTaxon(taxon);
|
|
609
|
}
|
|
610
|
}
|
|
611
|
}
|
|
612
|
}
|
|
613
|
// assemble sub derivates
|
|
614
|
preservedSpecimenDTO.setDerivateDataDTO(assembleDerivateDataDTO(preservedSpecimenDTO, derivedUnit));
|
|
615
|
return preservedSpecimenDTO;
|
|
616
|
}
|
|
617
|
|
|
618
|
private DerivateDataDTO assembleDerivateDataDTO(DerivateDTO derivateDTO, SpecimenOrObservationBase<?> specimenOrObservation) {
|
|
619
|
DerivateDataDTO derivateDataDTO = new DerivateDataDTO();
|
|
620
|
Collection<DerivedUnit> childDerivates = getDerivedUnitsFor(specimenOrObservation);
|
|
621
|
for (DerivedUnit childDerivate : childDerivates) {
|
|
622
|
// assemble molecular data
|
|
623
|
//pattern: DNAMarker [contig1, primer1_1, primer1_2, ...][contig2, primer2_1, ...]...
|
|
624
|
if (childDerivate.isInstanceOf(DnaSample.class)) {
|
|
625
|
if (childDerivate.getRecordBasis() == SpecimenOrObservationType.TissueSample) {
|
|
626
|
// TODO implement TissueSample assembly for web service
|
|
627
|
}
|
|
628
|
if (childDerivate.getRecordBasis() == SpecimenOrObservationType.DnaSample) {
|
|
629
|
|
|
630
|
DnaSample dna = HibernateProxyHelper.deproxy(childDerivate, DnaSample.class);
|
|
631
|
if (!dna.getSequences().isEmpty()) {
|
|
632
|
derivateDTO.setHasDna(true);
|
|
633
|
}
|
|
634
|
for (Sequence sequence : dna.getSequences()) {
|
|
635
|
URI boldUri = null;
|
|
636
|
try {
|
|
637
|
boldUri = sequence.getBoldUri();
|
|
638
|
} catch (URISyntaxException e1) {
|
|
639
|
logger.error("Could not create BOLD URI", e1);
|
|
640
|
}
|
|
641
|
final DefinedTerm dnaMarker = sequence.getDnaMarker();
|
|
642
|
Link providerLink = null;
|
|
643
|
if(boldUri!=null && dnaMarker!=null){
|
|
644
|
providerLink = new DerivateDataDTO.Link(boldUri, dnaMarker.getLabel());
|
|
645
|
}
|
|
646
|
MolecularData molecularData = derivateDataDTO.addProviderLink(providerLink);
|
|
647
|
|
|
648
|
//contig file
|
|
649
|
ContigFile contigFile = null;
|
|
650
|
if (sequence.getContigFile() != null) {
|
|
651
|
MediaRepresentationPart contigMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile());
|
|
652
|
if (contigMediaRepresentationPart != null) {
|
|
653
|
contigFile = molecularData.addContigFile(new Link(contigMediaRepresentationPart.getUri(), "contig"));
|
|
654
|
}
|
|
655
|
}
|
|
656
|
else{
|
|
657
|
contigFile = molecularData.addContigFile(null);
|
|
658
|
}
|
|
659
|
// primer files
|
|
660
|
if (sequence.getSingleReads() != null) {
|
|
661
|
int readCount = 1;
|
|
662
|
for (SingleRead singleRead : sequence.getSingleReads()) {
|
|
663
|
MediaRepresentationPart pherogramMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram());
|
|
664
|
if (pherogramMediaRepresentationPart != null) {
|
|
665
|
contigFile.addPrimerLink(pherogramMediaRepresentationPart.getUri(), "read"+readCount++);
|
|
666
|
}
|
|
667
|
}
|
|
668
|
}
|
|
669
|
}
|
|
670
|
}
|
|
671
|
}
|
|
672
|
// assemble media data
|
|
673
|
else if (childDerivate.isInstanceOf(MediaSpecimen.class)) {
|
|
674
|
MediaSpecimen media = HibernateProxyHelper.deproxy(childDerivate, MediaSpecimen.class);
|
|
675
|
|
|
676
|
URI mediaUri = getMediaUri(media);
|
|
677
|
if (media.getKindOfUnit() != null) {
|
|
678
|
// specimen scan
|
|
679
|
if (media.getKindOfUnit().getUuid().equals(DefinedTerm.uuidSpecimenScan)) {
|
|
680
|
derivateDataDTO.addSpecimenScanUuid(media.getMediaSpecimen().getUuid());
|
|
681
|
derivateDTO.setHasSpecimenScan(true);
|
|
682
|
String imageLinkText = "scan";
|
|
683
|
if (derivateDTO instanceof PreservedSpecimenDTO && ((PreservedSpecimenDTO) derivateDTO).getAccessionNumber() != null) {
|
|
684
|
imageLinkText = ((PreservedSpecimenDTO) derivateDTO).getAccessionNumber();
|
|
685
|
}
|
|
686
|
derivateDataDTO.addSpecimenScan(mediaUri, imageLinkText);
|
|
687
|
}
|
|
688
|
// detail image
|
|
689
|
else if (media.getKindOfUnit().getUuid().equals(DefinedTerm.uuidDetailImage)) {
|
|
690
|
derivateDataDTO.addDetailImageUuid(media.getMediaSpecimen().getUuid());
|
|
691
|
derivateDTO.setHasDetailImage(true);
|
|
692
|
String motif = "detail image";
|
|
693
|
if (media.getMediaSpecimen()!=null){
|
|
694
|
if(CdmUtils.isNotBlank(media.getMediaSpecimen().getTitleCache())) {
|
|
695
|
motif = media.getMediaSpecimen().getTitleCache();
|
|
696
|
}
|
|
697
|
}
|
|
698
|
derivateDataDTO.addDetailImage(mediaUri, motif);
|
|
699
|
}
|
|
700
|
}
|
|
701
|
}
|
|
702
|
}
|
|
703
|
return derivateDataDTO;
|
|
704
|
}
|
|
705
|
|
|
706
|
private String removeTail(String string, final String tail) {
|
|
707
|
if (string.endsWith(tail)) {
|
|
708
|
string = string.substring(0, string.length() - tail.length());
|
|
709
|
}
|
|
710
|
return string;
|
|
711
|
}
|
|
712
|
|
|
713
|
private URI getMediaUri(MediaSpecimen mediaSpecimen) {
|
|
714
|
URI mediaUri = null;
|
|
715
|
Collection<MediaRepresentation> mediaRepresentations = mediaSpecimen.getMediaSpecimen().getRepresentations();
|
|
716
|
if (mediaRepresentations != null && !mediaRepresentations.isEmpty()) {
|
|
717
|
Collection<MediaRepresentationPart> mediaRepresentationParts = mediaRepresentations.iterator().next().getParts();
|
|
718
|
if (mediaRepresentationParts != null && !mediaRepresentationParts.isEmpty()) {
|
|
719
|
MediaRepresentationPart part = mediaRepresentationParts.iterator().next();
|
|
720
|
if (part.getUri() != null) {
|
|
721
|
mediaUri = part.getUri();
|
|
722
|
}
|
|
723
|
}
|
|
724
|
}
|
|
725
|
return mediaUri;
|
|
726
|
}
|
|
727
|
|
|
728
|
private Collection<DerivedUnit> getDerivedUnitsFor(SpecimenOrObservationBase<?> specimen) {
|
|
729
|
Collection<DerivedUnit> derivedUnits = new ArrayList<>();
|
|
730
|
for (DerivationEvent derivationEvent : specimen.getDerivationEvents()) {
|
|
731
|
for (DerivedUnit derivative : derivationEvent.getDerivatives()) {
|
|
732
|
derivedUnits.add(derivative);
|
|
733
|
derivedUnits.addAll(getDerivedUnitsFor(derivative));
|
|
734
|
}
|
|
735
|
}
|
|
736
|
return derivedUnits;
|
|
737
|
}
|
|
738
|
|
|
739
|
|
|
740
|
@SuppressWarnings("unchecked")
|
|
741
|
@Override
|
|
742
|
public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
|
|
743
|
Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
744
|
|
|
745
|
Set<Taxon> taxa = new HashSet<>();
|
|
746
|
Set<Integer> occurrenceIds = new HashSet<>();
|
|
747
|
List<T> occurrences = new ArrayList<>();
|
|
748
|
|
|
749
|
// Integer limit = PagerUtils.limitFor(pageSize);
|
|
750
|
// Integer start = PagerUtils.startFor(pageSize, pageNumber);
|
|
751
|
|
|
752
|
if (!getSession().contains(associatedTaxon)) {
|
|
753
|
associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
|
|
754
|
}
|
|
755
|
|
|
756
|
if (includeRelationships != null) {
|
|
757
|
taxa = taxonService.listRelatedTaxa(associatedTaxon, includeRelationships, maxDepth, null, null, propertyPaths);
|
|
758
|
}
|
|
759
|
|
|
760
|
taxa.add(associatedTaxon);
|
|
761
|
|
|
762
|
for (Taxon taxon : taxa) {
|
|
763
|
List<T> perTaxonOccurrences = dao.listByAssociatedTaxon(type, taxon, null, null, orderHints, propertyPaths);
|
|
764
|
for (SpecimenOrObservationBase o : perTaxonOccurrences) {
|
|
765
|
occurrenceIds.add(o.getId());
|
|
766
|
}
|
|
767
|
}
|
|
768
|
occurrences = (List<T>) dao.loadList(occurrenceIds, propertyPaths);
|
|
769
|
|
|
770
|
return new DefaultPagerImpl<T>(pageNumber, occurrenceIds.size(), pageSize, occurrences);
|
|
771
|
|
|
772
|
}
|
|
773
|
|
|
774
|
@Override
|
|
775
|
public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
|
|
776
|
String taxonUUID, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
777
|
|
|
778
|
UUID uuid = UUID.fromString(taxonUUID);
|
|
779
|
Taxon tax = (Taxon) taxonService.load(uuid);
|
|
780
|
// TODO REMOVE NULL STATEMENT
|
|
781
|
type = null;
|
|
782
|
return pageByAssociatedTaxon(type, includeRelationships, tax, maxDepth, pageSize, pageNumber, orderHints, propertyPaths);
|
|
783
|
|
|
784
|
}
|
|
785
|
|
|
786
|
@Override
|
|
787
|
public Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(
|
|
788
|
Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle boundingBox, List<Language> languages,
|
|
789
|
boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
|
|
790
|
List<String> propertyPaths) throws IOException, LuceneParseException {
|
|
791
|
|
|
792
|
LuceneSearch luceneSearch = prepareByFullTextSearch(clazz, queryString, boundingBox, languages, highlightFragments);
|
|
793
|
|
|
794
|
// --- execute search
|
|
795
|
TopGroups<BytesRef> topDocsResultSet;
|
|
796
|
try {
|
|
797
|
topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);
|
|
798
|
} catch (ParseException e) {
|
|
799
|
LuceneParseException parseException = new LuceneParseException(e.getMessage());
|
|
800
|
parseException.setStackTrace(e.getStackTrace());
|
|
801
|
throw parseException;
|
|
802
|
}
|
|
803
|
|
|
804
|
Map<CdmBaseType, String> idFieldMap = new HashMap<>();
|
|
805
|
idFieldMap.put(CdmBaseType.SPECIMEN_OR_OBSERVATIONBASE, "id");
|
|
806
|
|
|
807
|
// --- initialize taxa, highlight matches ....
|
|
808
|
ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
|
|
809
|
@SuppressWarnings("rawtypes")
|
|
810
|
List<SearchResult<SpecimenOrObservationBase>> searchResults = searchResultBuilder.createResultSet(
|
|
811
|
topDocsResultSet, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);
|
|
812
|
|
|
813
|
int totalHits = topDocsResultSet != null ? topDocsResultSet.totalGroupCount : 0;
|
|
814
|
|
|
815
|
return new DefaultPagerImpl<SearchResult<SpecimenOrObservationBase>>(pageNumber, totalHits, pageSize,
|
|
816
|
searchResults);
|
|
817
|
|
|
818
|
}
|
|
819
|
|
|
820
|
private LuceneSearch prepareByFullTextSearch(Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle bbox,
|
|
821
|
List<Language> languages, boolean highlightFragments) {
|
|
822
|
|
|
823
|
Builder finalQueryBuilder = new Builder();
|
|
824
|
Builder textQueryBuilder = new Builder();
|
|
825
|
|
|
826
|
LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, FieldUnit.class);
|
|
827
|
QueryFactory queryFactory = luceneIndexToolProvider.newQueryFactoryFor(FieldUnit.class);
|
|
828
|
|
|
829
|
// --- criteria
|
|
830
|
luceneSearch.setCdmTypRestriction(clazz);
|
|
831
|
if (queryString != null) {
|
|
832
|
textQueryBuilder.add(queryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);
|
|
833
|
finalQueryBuilder.add(textQueryBuilder.build(), Occur.MUST);
|
|
834
|
}
|
|
835
|
|
|
836
|
// --- spacial query
|
|
837
|
if (bbox != null) {
|
|
838
|
finalQueryBuilder.add(QueryFactory.buildSpatialQueryByRange(bbox, "gatheringEvent.exactLocation.point"), Occur.MUST);
|
|
839
|
}
|
|
840
|
|
|
841
|
luceneSearch.setQuery(finalQueryBuilder.build());
|
|
842
|
|
|
843
|
// --- sorting
|
|
844
|
SortField[] sortFields = new SortField[] { SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.Type.STRING, false) };
|
|
845
|
luceneSearch.setSortFields(sortFields);
|
|
846
|
|
|
847
|
if (highlightFragments) {
|
|
848
|
luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());
|
|
849
|
}
|
|
850
|
return luceneSearch;
|
|
851
|
}
|
|
852
|
|
|
853
|
|
|
854
|
@Override
|
|
855
|
public Collection<FieldUnit> getFieldUnits(UUID derivedUnitUuid, List<String> propertyPaths) {
|
|
856
|
//It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})
|
|
857
|
//from which this DerivedUnit was derived until all FieldUnits are found.
|
|
858
|
|
|
859
|
// FIXME: use HQL queries to increase performance
|
|
860
|
SpecimenOrObservationBase<?> specimen = load(derivedUnitUuid, propertyPaths);
|
|
861
|
// specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
|
|
862
|
Collection<FieldUnit> fieldUnits = new ArrayList<>();
|
|
863
|
|
|
864
|
if (specimen.isInstanceOf(FieldUnit.class)) {
|
|
865
|
fieldUnits.add(HibernateProxyHelper.deproxy(specimen, FieldUnit.class));
|
|
866
|
}
|
|
867
|
else if(specimen.isInstanceOf(DerivedUnit.class)){
|
|
868
|
fieldUnits.addAll(getFieldUnits(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class), propertyPaths));
|
|
869
|
}
|
|
870
|
return fieldUnits;
|
|
871
|
}
|
|
872
|
|
|
873
|
private Collection<FieldUnit> getFieldUnits(DerivedUnit derivedUnit, List<String> propertyPaths) {
|
|
874
|
Collection<FieldUnit> fieldUnits = new HashSet<>();
|
|
875
|
Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
|
|
876
|
if (originals != null && !originals.isEmpty()) {
|
|
877
|
for (SpecimenOrObservationBase<?> original : originals) {
|
|
878
|
if (original.isInstanceOf(FieldUnit.class)) {
|
|
879
|
fieldUnits.add((FieldUnit) load(original.getUuid(), propertyPaths));
|
|
880
|
}
|
|
881
|
else if(original.isInstanceOf(DerivedUnit.class)){
|
|
882
|
fieldUnits.addAll(getFieldUnits(HibernateProxyHelper.deproxy(original, DerivedUnit.class), propertyPaths));
|
|
883
|
}
|
|
884
|
}
|
|
885
|
}
|
|
886
|
return fieldUnits;
|
|
887
|
}
|
|
888
|
|
|
889
|
@Override
|
|
890
|
@Transactional(readOnly = false)
|
|
891
|
public UpdateResult moveSequence(DnaSample from, DnaSample to, Sequence sequence) {
|
|
892
|
return moveSequence(from.getUuid(), to.getUuid(), sequence.getUuid());
|
|
893
|
}
|
|
894
|
|
|
895
|
@Override
|
|
896
|
@Transactional(readOnly = false)
|
|
897
|
public UpdateResult moveSequence(UUID fromUuid, UUID toUuid, UUID sequenceUuid) {
|
|
898
|
// reload specimens to avoid session conflicts
|
|
899
|
DnaSample from = (DnaSample) load(fromUuid);
|
|
900
|
DnaSample to = (DnaSample) load(toUuid);
|
|
901
|
Sequence sequence = sequenceService.load(sequenceUuid);
|
|
902
|
|
|
903
|
if (from == null || to == null || sequence == null) {
|
|
904
|
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" +
|
|
905
|
"Operation was move "+sequence+ " from "+from+" to "+to);
|
|
906
|
}
|
|
907
|
UpdateResult result = new UpdateResult();
|
|
908
|
from.removeSequence(sequence);
|
|
909
|
saveOrUpdate(from);
|
|
910
|
to.addSequence(sequence);
|
|
911
|
saveOrUpdate(to);
|
|
912
|
result.setStatus(Status.OK);
|
|
913
|
result.addUpdatedObject(from);
|
|
914
|
result.addUpdatedObject(to);
|
|
915
|
return result;
|
|
916
|
}
|
|
917
|
|
|
918
|
@Override
|
|
919
|
@Transactional(readOnly = false)
|
|
920
|
public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate) {
|
|
921
|
return moveDerivate(from!=null?from.getUuid():null, to.getUuid(), derivate.getUuid()).isOk();
|
|
922
|
}
|
|
923
|
|
|
924
|
@Override
|
|
925
|
@Transactional(readOnly = false)
|
|
926
|
public UpdateResult moveDerivate(UUID specimenFromUuid, UUID specimenToUuid, UUID derivateUuid) {
|
|
927
|
// reload specimens to avoid session conflicts
|
|
928
|
SpecimenOrObservationBase<?> from = null;
|
|
929
|
if(specimenFromUuid!=null){
|
|
930
|
from = load(specimenFromUuid);
|
|
931
|
}
|
|
932
|
SpecimenOrObservationBase<?> to = load(specimenToUuid);
|
|
933
|
DerivedUnit derivate = (DerivedUnit) load(derivateUuid);
|
|
934
|
|
|
935
|
if ((specimenFromUuid!=null && from == null) || to == null || derivate == null) {
|
|
936
|
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" +
|
|
937
|
"Operation was move "+derivate+ " from "+from+" to "+to);
|
|
938
|
}
|
|
939
|
UpdateResult result = new UpdateResult();
|
|
940
|
SpecimenOrObservationType derivateType = derivate.getRecordBasis();
|
|
941
|
SpecimenOrObservationType toType = to.getRecordBasis();
|
|
942
|
// check if type is a sub derivate type
|
|
943
|
if(toType==SpecimenOrObservationType.FieldUnit //moving to FieldUnit always works
|
|
944
|
|| derivateType==SpecimenOrObservationType.Media //moving media always works
|
|
945
|
|| (derivateType.isKindOf(toType) && toType!=derivateType)){ //moving only to parent derivate type
|
|
946
|
if(from!=null){
|
|
947
|
// remove derivation event from parent specimen of dragged object
|
|
948
|
DerivationEvent eventToRemove = null;
|
|
949
|
for (DerivationEvent event : from.getDerivationEvents()) {
|
|
950
|
if (event.getDerivatives().contains(derivate)) {
|
|
951
|
eventToRemove = event;
|
|
952
|
break;
|
|
953
|
}
|
|
954
|
}
|
|
955
|
from.removeDerivationEvent(eventToRemove);
|
|
956
|
if(eventToRemove!=null){
|
|
957
|
// add new derivation event to target and copy the event parameters of the old one
|
|
958
|
DerivationEvent derivedFromNewOriginalEvent = DerivationEvent.NewSimpleInstance(to, derivate, null);
|
|
959
|
derivedFromNewOriginalEvent.setActor(eventToRemove.getActor());
|
|
960
|
derivedFromNewOriginalEvent.setDescription(eventToRemove.getDescription());
|
|
961
|
derivedFromNewOriginalEvent.setInstitution(eventToRemove.getInstitution());
|
|
962
|
derivedFromNewOriginalEvent.setTimeperiod(eventToRemove.getTimeperiod());
|
|
963
|
derivedFromNewOriginalEvent.setType(eventToRemove.getType());
|
|
964
|
to.addDerivationEvent(derivedFromNewOriginalEvent);
|
|
965
|
derivate.setDerivedFrom(derivedFromNewOriginalEvent);
|
|
966
|
}
|
|
967
|
}
|
|
968
|
else{
|
|
969
|
//derivative had no parent before so we use empty derivation event
|
|
970
|
DerivationEvent derivedFromNewOriginalEvent = DerivationEvent.NewSimpleInstance(to, derivate, null);
|
|
971
|
to.addDerivationEvent(derivedFromNewOriginalEvent);
|
|
972
|
derivate.setDerivedFrom(derivedFromNewOriginalEvent);
|
|
973
|
}
|
|
974
|
|
|
975
|
if(from!=null){
|
|
976
|
saveOrUpdate(from);
|
|
977
|
}
|
|
978
|
saveOrUpdate(to);
|
|
979
|
result.setStatus(Status.OK);
|
|
980
|
result.addUpdatedObject(from);
|
|
981
|
result.addUpdatedObject(to);
|
|
982
|
} else {
|
|
983
|
result.setStatus(Status.ERROR);
|
|
984
|
}
|
|
985
|
return result;
|
|
986
|
}
|
|
987
|
|
|
988
|
private Collection<ICdmBase> getFieldUnitNonCascadedAssociatedElements(FieldUnit fieldUnit) {
|
|
989
|
// get non cascaded element on SpecimenOrObservationBase level
|
|
990
|
Collection<ICdmBase> nonCascadedCdmEntities = getSpecimenOrObservationNonCascadedAssociatedElements(fieldUnit);
|
|
991
|
|
|
992
|
// get FieldUnit specific elements
|
|
993
|
GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
|
|
994
|
if (gatheringEvent != null) {
|
|
995
|
// country
|
|
996
|
if (gatheringEvent.getCountry() != null) {
|
|
997
|
nonCascadedCdmEntities.add(gatheringEvent.getCountry());
|
|
998
|
}
|
|
999
|
// collecting areas
|
|
1000
|
for (NamedArea namedArea : gatheringEvent.getCollectingAreas()) {
|
|
1001
|
nonCascadedCdmEntities.add(namedArea);
|
|
1002
|
}
|
|
1003
|
}
|
|
1004
|
for (DerivationEvent derivationEvent : fieldUnit.getDerivationEvents()) {
|
|
1005
|
for (DerivedUnit derivedUnit : derivationEvent.getDerivatives()) {
|
|
1006
|
nonCascadedCdmEntities.addAll(getDerivedUnitNonCascadedAssociatedElements(derivedUnit));
|
|
1007
|
}
|
|
1008
|
}
|
|
1009
|
return nonCascadedCdmEntities;
|
|
1010
|
}
|
|
1011
|
|
|
1012
|
private Collection<ICdmBase> getDerivedUnitNonCascadedAssociatedElements(DerivedUnit derivedUnit) {
|
|
1013
|
// get non cascaded element on SpecimenOrObservationBase level
|
|
1014
|
Collection<ICdmBase> nonCascadedCdmEntities = getSpecimenOrObservationNonCascadedAssociatedElements(derivedUnit);
|
|
1015
|
|
|
1016
|
// get DerivedUnit specific elements
|
|
1017
|
if (derivedUnit.getCollection() != null && derivedUnit.getCollection().getInstitute() != null) {
|
|
1018
|
for (DefinedTerm type : derivedUnit.getCollection().getInstitute().getTypes()) {
|
|
1019
|
nonCascadedCdmEntities.add(type);
|
|
1020
|
}
|
|
1021
|
}
|
|
1022
|
if (derivedUnit.getPreservation() != null && derivedUnit.getPreservation().getMedium() != null) {
|
|
1023
|
nonCascadedCdmEntities.add(derivedUnit.getPreservation().getMedium());
|
|
1024
|
}
|
|
1025
|
if (derivedUnit.getStoredUnder() != null) {
|
|
1026
|
nonCascadedCdmEntities.add(derivedUnit.getStoredUnder());
|
|
1027
|
}
|
|
1028
|
return nonCascadedCdmEntities;
|
|
1029
|
}
|
|
1030
|
|
|
1031
|
private Collection<ICdmBase> getSpecimenOrObservationNonCascadedAssociatedElements(
|
|
1032
|
SpecimenOrObservationBase<?> specimen) {
|
|
1033
|
Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<>();
|
|
1034
|
// scan SpecimenOrObservationBase
|
|
1035
|
for (DeterminationEvent determinationEvent : specimen.getDeterminations()) {
|
|
1036
|
// modifier
|
|
1037
|
if (determinationEvent.getModifier() != null) {
|
|
1038
|
nonCascadedCdmEntities.add(determinationEvent.getModifier());
|
|
1039
|
}
|
|
1040
|
}
|
|
1041
|
// kindOfUnit
|
|
1042
|
if (specimen.getKindOfUnit() != null) {
|
|
1043
|
nonCascadedCdmEntities.add(specimen.getKindOfUnit());
|
|
1044
|
}
|
|
1045
|
// lifeStage
|
|
1046
|
if (specimen.getLifeStage() != null) {
|
|
1047
|
nonCascadedCdmEntities.add(specimen.getLifeStage());
|
|
1048
|
}
|
|
1049
|
// sex
|
|
1050
|
if (specimen.getSex() != null) {
|
|
1051
|
nonCascadedCdmEntities.add(specimen.getSex());
|
|
1052
|
}
|
|
1053
|
return nonCascadedCdmEntities;
|
|
1054
|
}
|
|
1055
|
|
|
1056
|
@Override
|
|
1057
|
public DeleteResult isDeletable(UUID specimenUuid, DeleteConfiguratorBase config) {
|
|
1058
|
DeleteResult deleteResult = new DeleteResult();
|
|
1059
|
SpecimenOrObservationBase specimen = this.load(specimenUuid);
|
|
1060
|
SpecimenDeleteConfigurator specimenDeleteConfigurator = (SpecimenDeleteConfigurator) config;
|
|
1061
|
|
|
1062
|
// check elements found by super method
|
|
1063
|
Set<CdmBase> relatedObjects = super.isDeletable(specimenUuid, config).getRelatedObjects();
|
|
1064
|
for (CdmBase cdmBase : relatedObjects) {
|
|
1065
|
// check for type designation
|
|
1066
|
if (cdmBase.isInstanceOf(SpecimenTypeDesignation.class) && !specimenDeleteConfigurator.isDeleteFromTypeDesignation()) {
|
|
1067
|
deleteResult.setAbort();
|
|
1068
|
deleteResult.addException(new ReferencedObjectUndeletableException("Specimen or obeservation is a type specimen."));
|
|
1069
|
deleteResult.addRelatedObject(cdmBase);
|
|
1070
|
break;
|
|
1071
|
}
|
|
1072
|
// check for IndividualsAssociations
|
|
1073
|
else if (cdmBase.isInstanceOf(IndividualsAssociation.class) && !specimenDeleteConfigurator.isDeleteFromIndividualsAssociation()) {
|
|
1074
|
deleteResult.setAbort();
|
|
1075
|
deleteResult.addException(new ReferencedObjectUndeletableException("Specimen or obeservation is still associated via IndividualsAssociations"));
|
|
1076
|
deleteResult.addRelatedObject(cdmBase);
|
|
1077
|
break;
|
|
1078
|
}
|
|
1079
|
// check for taxon description
|
|
1080
|
else if(cdmBase.isInstanceOf(TaxonDescription.class)
|
|
1081
|
&& HibernateProxyHelper.deproxy(cdmBase, TaxonDescription.class).getDescribedSpecimenOrObservation().equals(specimen)
|
|
1082
|
&& !specimenDeleteConfigurator.isDeleteFromDescription()){
|
|
1083
|
deleteResult.setAbort();
|
|
1084
|
deleteResult.addException(new ReferencedObjectUndeletableException("Specimen or obeservation is still used as \"Described Specimen\" in a taxon description."));
|
|
1085
|
deleteResult.addRelatedObject(cdmBase);
|
|
1086
|
break;
|
|
1087
|
}
|
|
1088
|
// check for children and parents (derivation events)
|
|
1089
|
else if (cdmBase.isInstanceOf(DerivationEvent.class)) {
|
|
1090
|
DerivationEvent derivationEvent = HibernateProxyHelper.deproxy(cdmBase, DerivationEvent.class);
|
|
1091
|
// check if derivation event is empty
|
|
1092
|
if (!derivationEvent.getDerivatives().isEmpty() && derivationEvent.getOriginals().contains(specimen)) {
|
|
1093
|
// if derivationEvent is the childEvent and contains derivations
|
|
1094
|
// if (derivationEvent.getDerivatives().contains(specimen)) {
|
|
1095
|
// //if it is the parent event the specimen is still deletable
|
|
1096
|
// continue;
|
|
1097
|
// }
|
|
1098
|
if(!specimenDeleteConfigurator.isDeleteChildren()){
|
|
1099
|
//if children should not be deleted then it is undeletable
|
|
1100
|
deleteResult.setAbort();
|
|
1101
|
deleteResult.addException(new ReferencedObjectUndeletableException("Specimen or obeservation still has child derivatives."));
|
|
1102
|
deleteResult.addRelatedObject(cdmBase);
|
|
1103
|
break;
|
|
1104
|
}
|
|
1105
|
else{
|
|
1106
|
// check all children if they can be deleted
|
|
1107
|
Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
|
|
1108
|
DeleteResult childResult = new DeleteResult();
|
|
1109
|
for (DerivedUnit derivedUnit : derivatives) {
|
|
1110
|
childResult.includeResult(isDeletable(derivedUnit.getUuid(), specimenDeleteConfigurator));
|
|
1111
|
}
|
|
1112
|
if (!childResult.isOk()) {
|
|
1113
|
deleteResult.setAbort();
|
|
1114
|
deleteResult.includeResult(childResult);
|
|
1115
|
deleteResult.addRelatedObject(cdmBase);
|
|
1116
|
break;
|
|
1117
|
}
|
|
1118
|
}
|
|
1119
|
}
|
|
1120
|
}
|
|
1121
|
// check for amplification
|
|
1122
|
else if (cdmBase.isInstanceOf(AmplificationResult.class)
|
|
1123
|
&& !specimenDeleteConfigurator.isDeleteMolecularData()
|
|
1124
|
&& !specimenDeleteConfigurator.isDeleteChildren()) {
|
|
1125
|
deleteResult.setAbort();
|
|
1126
|
deleteResult.addException(new ReferencedObjectUndeletableException("DnaSample is used in amplification results."));
|
|
1127
|
deleteResult.addRelatedObject(cdmBase);
|
|
1128
|
break;
|
|
1129
|
}
|
|
1130
|
// check for sequence
|
|
1131
|
else if (cdmBase.isInstanceOf(Sequence.class)
|
|
1132
|
&& !specimenDeleteConfigurator.isDeleteMolecularData()
|
|
1133
|
&& !specimenDeleteConfigurator.isDeleteChildren()) {
|
|
1134
|
deleteResult.setAbort();
|
|
1135
|
deleteResult.addException(new ReferencedObjectUndeletableException("DnaSample is used in sequences."));
|
|
1136
|
deleteResult.addRelatedObject(cdmBase);
|
|
1137
|
break;
|
|
1138
|
}
|
|
1139
|
}
|
|
1140
|
if (deleteResult.isOk()) {
|
|
1141
|
//add all related object if deletion is OK so they can be handled by the delete() method
|
|
1142
|
deleteResult.addRelatedObjects(relatedObjects);
|
|
1143
|
}
|
|
1144
|
return deleteResult;
|
|
1145
|
}
|
|
1146
|
|
|
1147
|
/**
|
|
1148
|
* {@inheritDoc}
|
|
1149
|
*/
|
|
1150
|
@Transactional(readOnly = false)
|
|
1151
|
@Override
|
|
1152
|
public DeleteResult delete(UUID specimenUuid, SpecimenDeleteConfigurator config) {
|
|
1153
|
return delete(load(specimenUuid), config);
|
|
1154
|
}
|
|
1155
|
|
|
1156
|
|
|
1157
|
@Transactional(readOnly = false)
|
|
1158
|
@Override
|
|
1159
|
public DeleteResult delete(SpecimenOrObservationBase<?> specimen, SpecimenDeleteConfigurator config) {
|
|
1160
|
specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
|
|
1161
|
|
|
1162
|
DeleteResult deleteResult = isDeletable(specimen.getUuid(), config);
|
|
1163
|
if (!deleteResult.isOk()) {
|
|
1164
|
return deleteResult;
|
|
1165
|
}
|
|
1166
|
|
|
1167
|
if (config.isDeleteChildren()) {
|
|
1168
|
Set<DerivationEvent> derivationEvents = specimen.getDerivationEvents();
|
|
1169
|
//clone to avoid concurrent modification
|
|
1170
|
//can happen if the child is deleted and deleted its own derivedFrom event
|
|
1171
|
Set<DerivationEvent> derivationEventsClone = new HashSet<>(derivationEvents);
|
|
1172
|
for (DerivationEvent derivationEvent : derivationEventsClone) {
|
|
1173
|
Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
|
|
1174
|
Iterator<DerivedUnit> it = derivatives.iterator();
|
|
1175
|
Set<DerivedUnit> derivativesToDelete = new HashSet<>();
|
|
1176
|
while (it.hasNext()) {
|
|
1177
|
DerivedUnit unit = it.next();
|
|
1178
|
derivativesToDelete.add(unit);
|
|
1179
|
}
|
|
1180
|
for (DerivedUnit unit:derivativesToDelete){
|
|
1181
|
deleteResult.includeResult(delete(unit, config));
|
|
1182
|
}
|
|
1183
|
}
|
|
1184
|
}
|
|
1185
|
|
|
1186
|
|
|
1187
|
|
|
1188
|
|
|
1189
|
// check related objects
|
|
1190
|
Set<CdmBase> relatedObjects = deleteResult.getRelatedObjects();
|
|
1191
|
|
|
1192
|
for (CdmBase relatedObject : relatedObjects) {
|
|
1193
|
// check for TypeDesignations
|
|
1194
|
if (relatedObject.isInstanceOf(SpecimenTypeDesignation.class)) {
|
|
1195
|
SpecimenTypeDesignation designation = HibernateProxyHelper.deproxy(relatedObject, SpecimenTypeDesignation.class);
|
|
1196
|
designation.setTypeSpecimen(null);
|
|
1197
|
List<TaxonName> typifiedNames = new ArrayList<>();
|
|
1198
|
typifiedNames.addAll(designation.getTypifiedNames());
|
|
1199
|
for (TaxonName taxonName : typifiedNames) {
|
|
1200
|
taxonName.removeTypeDesignation(designation);
|
|
1201
|
}
|
|
1202
|
}
|
|
1203
|
// delete IndividualsAssociation
|
|
1204
|
if (relatedObject.isInstanceOf(IndividualsAssociation.class)) {
|
|
1205
|
IndividualsAssociation association = HibernateProxyHelper.deproxy(relatedObject, IndividualsAssociation.class);
|
|
1206
|
association.setAssociatedSpecimenOrObservation(null);
|
|
1207
|
association.getInDescription().removeElement(association);
|
|
1208
|
}
|
|
1209
|
// check for "described specimen" (deprecated)
|
|
1210
|
if (relatedObject.isInstanceOf(TaxonDescription.class)) {
|
|
1211
|
TaxonDescription description = HibernateProxyHelper.deproxy(relatedObject, TaxonDescription.class);
|
|
1212
|
description.setDescribedSpecimenOrObservation(null);
|
|
1213
|
}
|
|
1214
|
// check for specimen description
|
|
1215
|
if (relatedObject.isInstanceOf(SpecimenDescription.class)) {
|
|
1216
|
SpecimenDescription specimenDescription = HibernateProxyHelper.deproxy(relatedObject, SpecimenDescription.class);
|
|
1217
|
specimenDescription.setDescribedSpecimenOrObservation(null);
|
|
1218
|
// check if description is a description of the given specimen
|
|
1219
|
if (specimen.getDescriptions().contains(specimenDescription)) {
|
|
1220
|
specimen.removeDescription(specimenDescription);
|
|
1221
|
}
|
|
1222
|
DeleteResult descriptionDelete = descriptionService.isDeletable(specimenDescription.getUuid(), null);
|
|
1223
|
if (descriptionDelete.isOk()){
|
|
1224
|
deleteResult.includeResult(descriptionService.delete(specimenDescription));
|
|
1225
|
}
|
|
1226
|
}
|
|
1227
|
// check for amplification
|
|
1228
|
if (relatedObject.isInstanceOf(AmplificationResult.class)) {
|
|
1229
|
AmplificationResult amplificationResult = HibernateProxyHelper.deproxy(relatedObject, AmplificationResult.class);
|
|
1230
|
amplificationResult.getDnaSample().removeAmplificationResult(amplificationResult);
|
|
1231
|
}
|
|
1232
|
// check for sequence
|
|
1233
|
if (relatedObject.isInstanceOf(Sequence.class)) {
|
|
1234
|
Sequence sequence = HibernateProxyHelper.deproxy(relatedObject, Sequence.class);
|
|
1235
|
sequence.getDnaSample().removeSequence(sequence);
|
|
1236
|
}
|
|
1237
|
// check for children and parents (derivation events)
|
|
1238
|
if (relatedObject.isInstanceOf(DerivationEvent.class)) {
|
|
1239
|
DerivationEvent derivationEvent = HibernateProxyHelper.deproxy(relatedObject, DerivationEvent.class);
|
|
1240
|
// parent derivation event (derivedFrom)
|
|
1241
|
if (derivationEvent.getDerivatives().contains(specimen) && specimen.isInstanceOf(DerivedUnit.class)) {
|
|
1242
|
derivationEvent.removeDerivative(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class));
|
|
1243
|
if (derivationEvent.getDerivatives().isEmpty()) {
|
|
1244
|
Set<SpecimenOrObservationBase> originals = derivationEvent.getOriginals();
|
|
1245
|
for (SpecimenOrObservationBase specimenOrObservationBase : originals) {
|
|
1246
|
specimenOrObservationBase.removeDerivationEvent(derivationEvent);
|
|
1247
|
deleteResult.addUpdatedObject(specimenOrObservationBase);
|
|
1248
|
}
|
|
1249
|
// if derivationEvent has no derivates anymore, delete it
|
|
1250
|
deleteResult.includeResult(eventService.delete(derivationEvent));
|
|
1251
|
}
|
|
1252
|
}
|
|
1253
|
else{
|
|
1254
|
//child derivation events should not occur since we delete the hierarchy from bottom to top
|
|
1255
|
}
|
|
1256
|
}
|
|
1257
|
}
|
|
1258
|
if (specimen instanceof FieldUnit){
|
|
1259
|
FieldUnit fieldUnit = HibernateProxyHelper.deproxy(specimen, FieldUnit.class);
|
|
1260
|
GatheringEvent event = fieldUnit.getGatheringEvent();
|
|
1261
|
fieldUnit.setGatheringEvent(null);
|
|
1262
|
if (event != null){
|
|
1263
|
DeleteResult result = eventService.isDeletable(event.getUuid(), null);
|
|
1264
|
if (result.isOk()){
|
|
1265
|
deleteResult.includeResult( eventService.delete(event));
|
|
1266
|
}
|
|
1267
|
}
|
|
1268
|
|
|
1269
|
}
|
|
1270
|
deleteResult.includeResult(delete(specimen));
|
|
1271
|
|
|
1272
|
return deleteResult;
|
|
1273
|
}
|
|
1274
|
|
|
1275
|
@Override
|
|
1276
|
public Collection<IndividualsAssociation> listIndividualsAssociations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1277
|
return dao.listIndividualsAssociations(specimen, limit, start, orderHints, propertyPaths);
|
|
1278
|
}
|
|
1279
|
|
|
1280
|
@Override
|
|
1281
|
public Collection<TaxonBase<?>> listAssociatedTaxa(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start,
|
|
1282
|
List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1283
|
Collection<TaxonBase<?>> associatedTaxa = new HashSet<>();
|
|
1284
|
|
|
1285
|
//individuals associations
|
|
1286
|
associatedTaxa.addAll(listIndividualsAssociationTaxa(specimen, limit, start, orderHints, propertyPaths));
|
|
1287
|
//type designation
|
|
1288
|
if(specimen.isInstanceOf(DerivedUnit.class)){
|
|
1289
|
associatedTaxa.addAll(listTypeDesignationTaxa(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class), limit, start, orderHints, propertyPaths));
|
|
1290
|
}
|
|
1291
|
//determinations
|
|
1292
|
associatedTaxa.addAll(listDeterminedTaxa(specimen, limit, start, orderHints, propertyPaths));
|
|
1293
|
|
|
1294
|
return associatedTaxa;
|
|
1295
|
}
|
|
1296
|
|
|
1297
|
|
|
1298
|
@Override
|
|
1299
|
public Collection<TaxonBase<?>> listDeterminedTaxa(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start,
|
|
1300
|
List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1301
|
Collection<TaxonBase<?>> associatedTaxa = new HashSet<>();
|
|
1302
|
for (DeterminationEvent determinationEvent : listDeterminationEvents(specimen, limit, start, orderHints, propertyPaths)) {
|
|
1303
|
if(determinationEvent.getIdentifiedUnit().equals(specimen)){
|
|
1304
|
if(determinationEvent.getTaxon()!=null){
|
|
1305
|
associatedTaxa.add(taxonService.load(determinationEvent.getTaxon().getUuid(), propertyPaths));
|
|
1306
|
}
|
|
1307
|
if(determinationEvent.getTaxonName()!=null){
|
|
1308
|
Collection<TaxonBase> taxonBases = determinationEvent.getTaxonName().getTaxonBases();
|
|
1309
|
for (TaxonBase taxonBase : taxonBases) {
|
|
1310
|
associatedTaxa.add(taxonService.load(taxonBase.getUuid(), propertyPaths));
|
|
1311
|
}
|
|
1312
|
}
|
|
1313
|
}
|
|
1314
|
}
|
|
1315
|
return associatedTaxa;
|
|
1316
|
}
|
|
1317
|
|
|
1318
|
@Override
|
|
1319
|
public Collection<TaxonBase<?>> listTypeDesignationTaxa(DerivedUnit specimen, Integer limit, Integer start,
|
|
1320
|
List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1321
|
Collection<TaxonBase<?>> associatedTaxa = new HashSet<>();
|
|
1322
|
for (SpecimenTypeDesignation typeDesignation : listTypeDesignations(specimen, limit, start, orderHints, propertyPaths)) {
|
|
1323
|
if(typeDesignation.getTypeSpecimen().equals(specimen)){
|
|
1324
|
Set<TaxonName> typifiedNames = typeDesignation.getTypifiedNames();
|
|
1325
|
for (TaxonName taxonName : typifiedNames) {
|
|
1326
|
Set<Taxon> taxa = taxonName.getTaxa();
|
|
1327
|
for (Taxon taxon : taxa) {
|
|
1328
|
associatedTaxa.add(taxonService.load(taxon.getUuid(), propertyPaths));
|
|
1329
|
}
|
|
1330
|
}
|
|
1331
|
}
|
|
1332
|
}
|
|
1333
|
return associatedTaxa;
|
|
1334
|
}
|
|
1335
|
|
|
1336
|
@Override
|
|
1337
|
public Collection<TaxonBase<?>> listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start,
|
|
1338
|
List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1339
|
Collection<TaxonBase<?>> associatedTaxa = new HashSet<>();
|
|
1340
|
for (IndividualsAssociation individualsAssociation : listIndividualsAssociations(specimen, null, null, null, null)) {
|
|
1341
|
if(individualsAssociation.getInDescription().isInstanceOf(TaxonDescription.class)){
|
|
1342
|
TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(individualsAssociation.getInDescription(), TaxonDescription.class);
|
|
1343
|
if(taxonDescription.getTaxon()!=null){
|
|
1344
|
associatedTaxa.add(taxonService.load(taxonDescription.getTaxon().getUuid(), propertyPaths));
|
|
1345
|
}
|
|
1346
|
}
|
|
1347
|
}
|
|
1348
|
return associatedTaxa;
|
|
1349
|
}
|
|
1350
|
|
|
1351
|
@Override
|
|
1352
|
public Collection<DeterminationEvent> listDeterminationEvents(SpecimenOrObservationBase<?> specimen,
|
|
1353
|
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1354
|
return dao.listDeterminationEvents(specimen, limit, start, orderHints, propertyPaths);
|
|
1355
|
}
|
|
1356
|
|
|
1357
|
@Override
|
|
1358
|
public Map<DerivedUnit, Collection<SpecimenTypeDesignation>> listTypeDesignations(
|
|
1359
|
Collection<DerivedUnit> specimens, Integer limit, Integer start,
|
|
1360
|
List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1361
|
Map<DerivedUnit, Collection<SpecimenTypeDesignation>> typeDesignationMap = new HashMap<>();
|
|
1362
|
for (DerivedUnit specimen : specimens) {
|
|
1363
|
Collection<SpecimenTypeDesignation> typeDesignations = listTypeDesignations(specimen, limit, start, orderHints, propertyPaths);
|
|
1364
|
typeDesignationMap.put(specimen, typeDesignations);
|
|
1365
|
}
|
|
1366
|
return typeDesignationMap;
|
|
1367
|
}
|
|
1368
|
|
|
1369
|
@Override
|
|
1370
|
public Collection<SpecimenTypeDesignation> listTypeDesignations(DerivedUnit specimen,
|
|
1371
|
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1372
|
return dao.listTypeDesignations(specimen, limit, start, orderHints, propertyPaths);
|
|
1373
|
}
|
|
1374
|
|
|
1375
|
@Override
|
|
1376
|
public Collection<DescriptionBase<?>> listDescriptionsWithDescriptionSpecimen(
|
|
1377
|
SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints,
|
|
1378
|
List<String> propertyPaths) {
|
|
1379
|
return dao.listDescriptionsWithDescriptionSpecimen(specimen, limit, start, orderHints, propertyPaths);
|
|
1380
|
}
|
|
1381
|
|
|
1382
|
@Override
|
|
1383
|
@Deprecated //this is not a service layer task so it may be removed in future versions
|
|
1384
|
public Collection<DescriptionElementBase> getCharacterDataForSpecimen(SpecimenOrObservationBase<?> specimen) {
|
|
1385
|
if (specimen != null) {
|
|
1386
|
return specimen.characterData();
|
|
1387
|
}else{
|
|
1388
|
return new ArrayList<>();
|
|
1389
|
}
|
|
1390
|
}
|
|
1391
|
|
|
1392
|
@Override
|
|
1393
|
public Collection<DescriptionElementBase> getCharacterDataForSpecimen(UUID specimenUuid) {
|
|
1394
|
SpecimenOrObservationBase<?> specimen = load(specimenUuid);
|
|
1395
|
if (specimen != null) {
|
|
1396
|
return getCharacterDataForSpecimen(specimen);
|
|
1397
|
}
|
|
1398
|
else{
|
|
1399
|
throw new DataRetrievalFailureException("Specimen with the given uuid not found in the data base");
|
|
1400
|
}
|
|
1401
|
}
|
|
1402
|
|
|
1403
|
|
|
1404
|
@Override
|
|
1405
|
public Integer countByTitle(IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config){
|
|
1406
|
if (config instanceof FindOccurrencesConfigurator) {
|
|
1407
|
FindOccurrencesConfigurator occurrenceConfig = (FindOccurrencesConfigurator) config;
|
|
1408
|
Taxon taxon = null;
|
|
1409
|
if(occurrenceConfig.getAssociatedTaxonUuid()!=null){
|
|
1410
|
TaxonBase taxonBase = taxonService.load(occurrenceConfig.getAssociatedTaxonUuid());
|
|
1411
|
if(taxonBase.isInstanceOf(Taxon.class)){
|
|
1412
|
taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
|
|
1413
|
}
|
|
1414
|
}
|
|
1415
|
TaxonName taxonName = null;
|
|
1416
|
if(occurrenceConfig.getAssociatedTaxonNameUuid()!=null){
|
|
1417
|
taxonName = nameService.load(occurrenceConfig.getAssociatedTaxonNameUuid());
|
|
1418
|
}
|
|
1419
|
/*TODO: #6484 Neither isRetrieveIndirectlyAssociatedSpecimens() nor the AssignmentStatus
|
|
1420
|
* is currently reflected in the HQL query. So using these in the count method will
|
|
1421
|
* significantly slow down this method as we have to retreive the entities instead of
|
|
1422
|
* the just the amount.
|
|
1423
|
*/
|
|
1424
|
if(occurrenceConfig.isRetrieveIndirectlyAssociatedSpecimens() || !occurrenceConfig.getAssignmentStatus().equals(AssignmentStatus.ALL_SPECIMENS)){
|
|
1425
|
List<SpecimenOrObservationBase> occurrences = new ArrayList<>();
|
|
1426
|
occurrences.addAll(dao.findOccurrences(occurrenceConfig.getClazz(),
|
|
1427
|
occurrenceConfig.getTitleSearchString(), occurrenceConfig.getSignificantIdentifier(),
|
|
1428
|
occurrenceConfig.getSpecimenType(), taxon, taxonName, occurrenceConfig.getMatchMode(), null, null,
|
|
1429
|
occurrenceConfig.getOrderHints(), occurrenceConfig.getPropertyPaths()));
|
|
1430
|
occurrences = filterOccurencesByAssignmentAndHierarchy(occurrenceConfig, occurrences, taxon, taxonName);
|
|
1431
|
return occurrences.size();
|
|
1432
|
}
|
|
1433
|
|
|
1434
|
return dao.countOccurrences(occurrenceConfig.getClazz(),
|
|
1435
|
occurrenceConfig.getTitleSearchString(), occurrenceConfig.getSignificantIdentifier(),
|
|
1436
|
occurrenceConfig.getSpecimenType(), taxon, taxonName, occurrenceConfig.getMatchMode(), null, null,
|
|
1437
|
occurrenceConfig.getOrderHints(), occurrenceConfig.getPropertyPaths());
|
|
1438
|
}
|
|
1439
|
else{
|
|
1440
|
return dao.countByTitle(config.getTitleSearchString());
|
|
1441
|
}
|
|
1442
|
}
|
|
1443
|
|
|
1444
|
@Override
|
|
1445
|
public Pager<SpecimenOrObservationBase> findByTitle(
|
|
1446
|
IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config) {
|
|
1447
|
if (config instanceof FindOccurrencesConfigurator) {
|
|
1448
|
FindOccurrencesConfigurator occurrenceConfig = (FindOccurrencesConfigurator) config;
|
|
1449
|
List<SpecimenOrObservationBase> occurrences = new ArrayList<>();
|
|
1450
|
Taxon taxon = null;
|
|
1451
|
if(occurrenceConfig.getAssociatedTaxonUuid()!=null){
|
|
1452
|
TaxonBase taxonBase = taxonService.load(occurrenceConfig.getAssociatedTaxonUuid());
|
|
1453
|
if(taxonBase.isInstanceOf(Taxon.class)){
|
|
1454
|
taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
|
|
1455
|
}
|
|
1456
|
}
|
|
1457
|
TaxonName taxonName = null;
|
|
1458
|
if(occurrenceConfig.getAssociatedTaxonNameUuid()!=null){
|
|
1459
|
taxonName = nameService.load(occurrenceConfig.getAssociatedTaxonNameUuid());
|
|
1460
|
}
|
|
1461
|
occurrences.addAll(dao.findOccurrences(occurrenceConfig.getClazz(),
|
|
1462
|
occurrenceConfig.getTitleSearchString(), occurrenceConfig.getSignificantIdentifier(),
|
|
1463
|
occurrenceConfig.getSpecimenType(), taxon, taxonName, occurrenceConfig.getMatchMode(), null, null,
|
|
1464
|
occurrenceConfig.getOrderHints(), occurrenceConfig.getPropertyPaths()));
|
|
1465
|
occurrences = filterOccurencesByAssignmentAndHierarchy(occurrenceConfig, occurrences, taxon, taxonName);
|
|
1466
|
|
|
1467
|
return new DefaultPagerImpl<SpecimenOrObservationBase>(config.getPageNumber(), occurrences.size(), config.getPageSize(), occurrences);
|
|
1468
|
}
|
|
1469
|
return super.findByTitle(config);
|
|
1470
|
}
|
|
1471
|
|
|
1472
|
private List<SpecimenOrObservationBase> filterOccurencesByAssignmentAndHierarchy(
|
|
1473
|
FindOccurrencesConfigurator occurrenceConfig, List<SpecimenOrObservationBase> occurrences, Taxon taxon,
|
|
1474
|
TaxonName taxonName) {
|
|
1475
|
//filter out (un-)assigned specimens
|
|
1476
|
if(taxon==null && taxonName==null){
|
|
1477
|
AssignmentStatus assignmentStatus = occurrenceConfig.getAssignmentStatus();
|
|
1478
|
List<SpecimenOrObservationBase<?>> specimenWithAssociations = new ArrayList<>();
|
|
1479
|
if(!assignmentStatus.equals(AssignmentStatus.ALL_SPECIMENS)){
|
|
1480
|
for (SpecimenOrObservationBase specimenOrObservationBase : occurrences) {
|
|
1481
|
Collection<TaxonBase<?>> associatedTaxa = listAssociatedTaxa(specimenOrObservationBase, null, null, null, null);
|
|
1482
|
if(!associatedTaxa.isEmpty()){
|
|
1483
|
specimenWithAssociations.add(specimenOrObservationBase);
|
|
1484
|
}
|
|
1485
|
}
|
|
1486
|
}
|
|
1487
|
if(assignmentStatus.equals(AssignmentStatus.UNASSIGNED_SPECIMENS)){
|
|
1488
|
occurrences.removeAll(specimenWithAssociations);
|
|
1489
|
}
|
|
1490
|
if(assignmentStatus.equals(AssignmentStatus.ASSIGNED_SPECIMENS)){
|
|
1491
|
occurrences = new ArrayList<>(specimenWithAssociations);
|
|
1492
|
}
|
|
1493
|
}
|
|
1494
|
// indirectly associated specimens
|
|
1495
|
if(occurrenceConfig.isRetrieveIndirectlyAssociatedSpecimens()){
|
|
1496
|
List<SpecimenOrObservationBase> indirectlyAssociatedOccurrences = new ArrayList<>(occurrences);
|
|
1497
|
for (SpecimenOrObservationBase specimen : occurrences) {
|
|
1498
|
List<SpecimenOrObservationBase<?>> allHierarchyDerivates = getAllHierarchyDerivatives(specimen);
|
|
1499
|
for (SpecimenOrObservationBase<?> specimenOrObservationBase : allHierarchyDerivates) {
|
|
1500
|
if(!occurrences.contains(specimenOrObservationBase)){
|
|
1501
|
indirectlyAssociatedOccurrences.add(specimenOrObservationBase);
|
|
1502
|
}
|
|
1503
|
}
|
|
1504
|
}
|
|
1505
|
occurrences = indirectlyAssociatedOccurrences;
|
|
1506
|
}
|
|
1507
|
return occurrences;
|
|
1508
|
}
|
|
1509
|
|
|
1510
|
@Override
|
|
1511
|
public List<SpecimenOrObservationBase<?>> getAllHierarchyDerivatives(SpecimenOrObservationBase<?> specimen){
|
|
1512
|
List<SpecimenOrObservationBase<?>> allHierarchyDerivatives = new ArrayList<>();
|
|
1513
|
Collection<FieldUnit> fieldUnits = getFieldUnits(specimen.getUuid(), null);
|
|
1514
|
if(fieldUnits.isEmpty()){
|
|
1515
|
allHierarchyDerivatives.add(specimen);
|
|
1516
|
allHierarchyDerivatives.addAll(getAllChildDerivatives(specimen));
|
|
1517
|
}
|
|
1518
|
else{
|
|
1519
|
for (FieldUnit fieldUnit : fieldUnits) {
|
|
1520
|
allHierarchyDerivatives.add(fieldUnit);
|
|
1521
|
allHierarchyDerivatives.addAll(getAllChildDerivatives(fieldUnit));
|
|
1522
|
}
|
|
1523
|
}
|
|
1524
|
return allHierarchyDerivatives;
|
|
1525
|
}
|
|
1526
|
|
|
1527
|
@Override
|
|
1528
|
public List<DerivedUnit> getAllChildDerivatives(UUID specimenUuid){
|
|
1529
|
return getAllChildDerivatives(load(specimenUuid));
|
|
1530
|
}
|
|
1531
|
|
|
1532
|
@Override
|
|
1533
|
public List<DerivedUnit> getAllChildDerivatives(SpecimenOrObservationBase<?> specimen){
|
|
1534
|
if (specimen == null){
|
|
1535
|
return null;
|
|
1536
|
}
|
|
1537
|
List<DerivedUnit> childDerivate = new ArrayList<>();
|
|
1538
|
Set<DerivationEvent> derivationEvents = specimen.getDerivationEvents();
|
|
1539
|
for (DerivationEvent derivationEvent : derivationEvents) {
|
|
1540
|
Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
|
|
1541
|
for (DerivedUnit derivedUnit : derivatives) {
|
|
1542
|
childDerivate.add(derivedUnit);
|
|
1543
|
childDerivate.addAll(getAllChildDerivatives(derivedUnit.getUuid()));
|
|
1544
|
}
|
|
1545
|
}
|
|
1546
|
return childDerivate;
|
|
1547
|
}
|
|
1548
|
|
|
1549
|
@Override
|
|
1550
|
public int countOccurrences(IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config){
|
|
1551
|
return countByTitle(config);
|
|
1552
|
}
|
|
1553
|
|
|
1554
|
/**
|
|
1555
|
* {@inheritDoc}
|
|
1556
|
*/
|
|
1557
|
@Override
|
|
1558
|
public List<FieldUnit> getFieldUnitsForGatheringEvent(UUID gatheringEventUuid) {
|
|
1559
|
return dao.getFieldUnitsForGatheringEvent(gatheringEventUuid, null, null, null, null);
|
|
1560
|
}
|
|
1561
|
|
|
1562
|
}
|