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/**
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* Copyright (C) 2017 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.registration;
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import java.io.IOException;
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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.HashSet;
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import java.util.List;
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import java.util.Optional;
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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.hibernate.Hibernate;
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import org.joda.time.DateTime;
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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.beans.factory.annotation.Qualifier;
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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.application.CdmRepository;
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import eu.etaxonomy.cdm.api.service.dto.RegistrationDTO;
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import eu.etaxonomy.cdm.api.service.dto.RegistrationWorkingSet;
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import eu.etaxonomy.cdm.api.service.exception.RegistrationValidationException;
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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.utility.UserHelper;
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import eu.etaxonomy.cdm.database.PermissionDeniedException;
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import eu.etaxonomy.cdm.format.reference.ReferenceEllypsisFormatter;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.name.Registration;
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import eu.etaxonomy.cdm.model.name.RegistrationStatus;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.permission.CRUD;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceType;
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import eu.etaxonomy.cdm.persistence.dao.initializer.EntityInitStrategy;
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import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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import eu.etaxonomy.cdm.persistence.query.OrderHint.SortOrder;
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/**
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* Provides RegistrationDTOs and RegistrationWorkingsets for Registrations in the database.
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*
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*
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* @author a.kohlbecker
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* @since Mar 10, 2017
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*
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*/
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@Service("registrationWorkingSetService")
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@Transactional(readOnly=true)
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public class RegistrationWorkingSetService implements IRegistrationWorkingSetService {
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public static final EntityInitStrategy REGISTRATION_DTO_INIT_STRATEGY = new EntityInitStrategy(Arrays.asList(new String []{
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"blockedBy",
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// typeDesignation
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"typeDesignations.typeStatus",
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"typeDesignations.typifiedNames.typeDesignations", // important !!
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"typeDesignations.typeSpecimen",
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"typeDesignations.typeName.$",
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"typeDesignations.citation",
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"typeDesignations.annotations", // needed for AnnotatableEntity.clone() in DerivedUnitConverter.copyPropertiesTo
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"typeDesignations.markers", // needed for AnnotatableEntity.clone() in DerivedUnitConverter.copyPropertiesTo
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"typeDesignations.registrations", // DerivedUnitConverter.copyPropertiesTo(TARGET n)
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// name
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"name.$",
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"name.nomenclaturalSource.citation",
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"name.rank",
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"name.homotypicalGroup.typifiedNames",
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"name.status.type",
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"name.typeDesignations", // important !!"
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// institution
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"institution",
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}
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))
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.extend("typeDesignations.citation", ReferenceEllypsisFormatter.INIT_STRATEGY, false)
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.extend("name.nomenclaturalSource.citation", ReferenceEllypsisFormatter.INIT_STRATEGY, false);
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public EntityInitStrategy DERIVEDUNIT_INIT_STRATEGY = new EntityInitStrategy(Arrays.asList(new String[]{
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"*", // initialize all related entities to allow DerivedUnit conversion, see DerivedUnitConverter.copyPropertiesTo()
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"derivedFrom.$",
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"derivedFrom.type", // TODO remove?
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"derivedFrom.originals.derivationEvents", // important!!
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"specimenTypeDesignations.typifiedNames.typeDesignations", // important!!
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"mediaSpecimen.sources.citation",
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"collection.institute"// see CollectionCaptionGenerator
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})).extend("mediaSpecimen.sources.citation", ReferenceEllypsisFormatter.INIT_STRATEGY, false);
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public List<String> FIELDUNIT_INIT_STRATEGY = Arrays.asList(new String[]{
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"$",
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"annotations.*", // * is needed as log as we are using a table in FilterableAnnotationsField
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"gatheringEvent.$",
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"gatheringEvent.country",
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"gatheringEvent.collectingAreas",
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"gatheringEvent.actor",
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"gatheringEvent.exactLocation.$",
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"derivationEvents.derivatives", // important, otherwise the DerivedUnits are not included into the graph of initialized entities!!!
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});
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public static final List<String> BLOCKING_REGISTRATION_INIT_STRATEGY = Arrays.asList(new String []{
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"blockedBy.blockedBy",
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// typeDesignation
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"blockedBy.typeDesignations.typeStatus",
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// "typeDesignations.typifiedNames.typeDesignations", // important !?
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// "blockedBy.name.$",
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"blockedBy.name.nomenclaturalSource.citation.authorship",
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"blockedBy.name.nomenclaturalSource.citation.inReference",
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"blockedBy.name.rank",
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// institution
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"blockedBy.institution",
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}
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);
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/**
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*
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*/
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private static final int PAGE_SIZE = 50;
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private static final Logger logger = Logger.getLogger(RegistrationWorkingSetService.class);
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@Autowired
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@Qualifier("cdmRepository")
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private CdmRepository repo;
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@Autowired
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private UserHelper userHelper;
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@Autowired
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protected IBeanInitializer defaultBeanInitializer;
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public RegistrationWorkingSetService() {
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}
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/**
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* @param id the Registration entity id
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* @return
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*/
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@Override
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public RegistrationDTO loadDtoById(Integer id) {
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Registration reg = repo.getRegistrationService().load(id, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
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inititializeSpecimen(reg);
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return new RegistrationDTO(reg);
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}
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/**
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* @param id the Registration entity id
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* @return
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*/
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@Override
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public RegistrationDTO loadDtoByUuid(UUID uuid) {
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Registration reg = repo.getRegistrationService().load(uuid, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
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inititializeSpecimen(reg);
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return new RegistrationDTO(reg);
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}
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@Override
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public Pager<RegistrationDTO> pageDTOs(String identifier, Integer pageIndex, Integer pageSize) throws IOException {
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Pager<Registration> regPager = repo.getRegistrationService().pageByIdentifier(identifier, pageIndex, pageSize, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
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return convertToDTOPager(regPager);
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}
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/**
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* @param regPager
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* @return
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*/
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@Override
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public Pager<RegistrationDTO> convertToDTOPager(Pager<Registration> regPager) {
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return new DefaultPagerImpl<RegistrationDTO>(regPager.getCurrentIndex(), regPager.getCount(), regPager.getPageSize(), makeDTOs(regPager.getRecords()));
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}
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@Override
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public Pager<RegistrationDTO> pageDTOs(Integer pageSize, Integer pageIndex) {
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return pageDTOs((UUID)null, null, null, null, null, null, pageSize, pageIndex, null);
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}
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/**
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* @param submitterUuid
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* Filter by the uuid of the {@link User} associated with the Registration as <code>Registration.submitter</code>
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* @param includedStatus
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* Filter by one or more {@link RegistrationStatus}. Multiple status will be combined with OR. In case the current user
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* is not authenticated (i.e. the authentication is anonymous) the includedStatus will be set to {@link RegistrationStatus#PUBLISHED}
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* to protect all other Registrations from being undisclosed.
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* @param identifierFilterPattern
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* Filter by the {@link Registration#getIdentifier() Registration.identifier}.
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* The method matches Registrations which contain the the passed pattern in the identifier.
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* @param taxonNameFilterPattern
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* The method matches Registrations which contain the the passed pattern in the
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* {@link Registration#getName() Registration.name}
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* @param typeDesignationStatusUuids
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* Filter by one or more {@link eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus} or {@link eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus}.
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* Multiple status will be combined with OR.
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* @param pageSize
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* @param pageIndex
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* @param orderHints
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* @return
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*/
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@Override
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public Pager<RegistrationDTO> pageDTOs(UUID submitterUuid, Collection<RegistrationStatus> includedStatus, String identifierFilterPattern,
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String taxonNameFilterPattern, String referenceFilterPattern, Collection<UUID> typeDesignationStatusUuids,
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Integer pageSize, Integer pageIndex, List<OrderHint> orderHints){
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if(pageSize == null){
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pageSize = PAGE_SIZE;
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}
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if(orderHints == null){
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orderHints = Arrays.asList(new OrderHint("identifier", SortOrder.ASCENDING));
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}
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Pager<Registration> pager = repo.getRegistrationService().page(submitterUuid, includedStatus,
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identifierFilterPattern, taxonNameFilterPattern,
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referenceFilterPattern, typeDesignationStatusUuids, PAGE_SIZE , pageIndex, orderHints, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
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Pager<RegistrationDTO> dtoPager = convertToDTOPager(pager);
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if(logger.isDebugEnabled()){
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logger.debug(String.format("pageDTOs() pageIndex: $1%d, pageSize: $2%d, includedStatusUuids: $3%s, typeDesignationStatusUuids: $4%s, taxonNameFilterPattern: $5%s, submitterUuid: $6%s",
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pageIndex, pageSize, includedStatus, identifierFilterPattern, taxonNameFilterPattern, submitterUuid));
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logger.debug("pageDTOs() result: " + pager.toString());
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}
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return dtoPager;
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}
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@Override
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public Pager<RegistrationDTO> findInTaxonGraph(UUID submitterUuid, Collection<RegistrationStatus> includedStatus,
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String taxonNameFilterPattern, MatchMode matchMode,
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Integer pageSize, Integer pageIndex, List<OrderHint> orderHints) {
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Pager<Registration> regPager = repo.getRegistrationService().pageTaxomicInclusion(null, includedStatus,
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taxonNameFilterPattern, matchMode,
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pageSize, pageIndex, orderHints, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
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return convertToDTOPager(regPager);
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}
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/**
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* {@inheritDoc}
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* @throws RegistrationValidationException
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*/
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@Override
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public RegistrationWorkingSet loadWorkingSetByReferenceUuid(UUID referenceUuid, boolean resolveSections) throws RegistrationValidationException, PermissionDeniedException {
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Reference reference = repo.getReferenceService().load(referenceUuid); // needed to use load to avoid the problem described in #7331
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if(resolveSections){
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reference = resolveSection(reference);
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}
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checkPermissions(reference);
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Pager<Registration> pager = repo.getRegistrationService().page(Optional.of(reference), null, null, null, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
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/* for debugging https://dev.e-taxonomy.eu/redmine/issues/7331 */
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// debugIssue7331(pager);
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RegistrationWorkingSet registrationWorkingSet;
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if(pager.getCount() > 0) {
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registrationWorkingSet = new RegistrationWorkingSet(makeDTOs(pager.getRecords()));
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} else {
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registrationWorkingSet = new RegistrationWorkingSet(reference);
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}
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return registrationWorkingSet;
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}
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/**
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* @param reference
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*/
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private void checkPermissions(Reference reference) throws PermissionDeniedException {
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boolean permissionDenied = isPermissionDenied(reference);
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if(permissionDenied) {
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throw new PermissionDeniedException("Access to the workingset is denied for the current user.");
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}
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}
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/**
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* @param reference
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* @return
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*/
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public boolean isPermissionDenied(Reference reference) {
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boolean permissionDenied = false;
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if(!checkReferencePublished(reference)){
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permissionDenied = !userHelper.userHasPermission(reference, CRUD.UPDATE);
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}
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return permissionDenied;
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}
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/**
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* @param reference
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* @return
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*/
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public boolean checkReferencePublished(Reference reference) {
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if(reference.getDatePublished() == null){
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return false;
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}
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Partial pubPartial = null;
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if(reference.getDatePublished().getStart() != null){
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pubPartial = reference.getDatePublished().getStart();
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} else {
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pubPartial = reference.getDatePublished().getEnd();
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}
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if(pubPartial == null){
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return !reference.getDatePublished().getFreeText().isEmpty();
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}
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DateTime nowLocal = new DateTime();
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//LocalDateTime nowUTC = nowLocal.withZone(DateTimeZone.UTC).toLocalDateTime();
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DateTime pubDateTime = pubPartial.toDateTime(null);
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return nowLocal.isAfter(pubDateTime);
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}
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/**
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* @param reference
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* @return
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*/
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protected Reference resolveSection(Reference reference) {
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repo.getReferenceService().load(reference.getUuid(), Arrays.asList(new String[]{"inReference"})); // needed to avoid the problem described in #7331
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if(reference.isOfType(ReferenceType.Section) && reference.getInReference() != null) {
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reference = reference.getInReference();
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}
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return reference;
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}
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/**
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* {@inheritDoc}
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* @throws RegistrationValidationException
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*/
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@Override
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public RegistrationWorkingSet loadWorkingSetByReferenceID(Integer referenceID, boolean resolveSections) throws RegistrationValidationException, PermissionDeniedException {
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Reference reference = repo.getReferenceService().find(referenceID);
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if(resolveSections){
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reference = resolveSection(reference);
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}
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checkPermissions(reference);
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repo.getReferenceService().load(reference.getUuid()); // needed to avoid the problem described in #7331
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Pager<Registration> pager = repo.getRegistrationService().page(Optional.of(reference), null, null, null, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
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/* for debugging https://dev.e-taxonomy.eu/redmine/issues/7331 */
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// debugIssue7331(pager);
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return new RegistrationWorkingSet(makeDTOs(pager.getRecords()));
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}
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@Override
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public Pager<RegistrationDTO> pageWorkingSetsByNameUUID(Collection<UUID> taxonNameUuids, Integer pageIndex, Integer pageSize, List<OrderHint> orderHints) throws RegistrationValidationException, PermissionDeniedException {
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if(orderHints == null){
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orderHints = Arrays.asList(new OrderHint("identifier", SortOrder.ASCENDING));
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}
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Pager<Registration> pager = repo.getRegistrationService().page((UUID)null, null, taxonNameUuids, pageSize, pageIndex, orderHints, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
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return new DefaultPagerImpl<RegistrationDTO>(pager.getCurrentIndex(), pager.getCount(), pager.getPageSize(), makeDTOs(pager.getRecords()));
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}
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/**
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* @param pager
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*/
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@SuppressWarnings("unused")
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private void debugIssue7331(Pager<Registration> pager) {
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for(Registration reg : pager.getRecords()){
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if(reg.getName() != null && reg.getName().getNomenclaturalReference().getAuthorship() != null){
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Reference ref = reg.getName().getNomenclaturalReference();
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if(!Hibernate.isInitialized(ref.getAuthorship())){
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logger.error("UNINITIALIZED");
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}
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} else {
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logger.debug("NO AUTHORS");
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}
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}
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}
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@Override
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412
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public Set<RegistrationDTO> loadBlockingRegistrations(UUID blockedRegistrationUuid){
|
413
|
|
414
|
Registration registration = repo.getRegistrationService().load(blockedRegistrationUuid, BLOCKING_REGISTRATION_INIT_STRATEGY);
|
415
|
Set<Registration> registrations = registration.getBlockedBy();
|
416
|
|
417
|
Set<RegistrationDTO> blockingSet = new HashSet<>();
|
418
|
for(Registration reg : registrations){
|
419
|
blockingSet.add(new RegistrationDTO(reg));
|
420
|
}
|
421
|
return blockingSet;
|
422
|
}
|
423
|
|
424
|
/**
|
425
|
* @param regs
|
426
|
* @return
|
427
|
*/
|
428
|
@Override
|
429
|
public List<RegistrationDTO> makeDTOs(Collection<Registration> regs) {
|
430
|
initializeSpecimens(regs);
|
431
|
List<RegistrationDTO> dtos = new ArrayList<>(regs.size());
|
432
|
regs.forEach(reg -> {dtos.add(new RegistrationDTO(reg));});
|
433
|
return dtos;
|
434
|
}
|
435
|
|
436
|
|
437
|
/**
|
438
|
* @param regs
|
439
|
*/
|
440
|
public void initializeSpecimens(Collection<Registration> regs) {
|
441
|
for(Registration reg : regs){
|
442
|
inititializeSpecimen(reg);
|
443
|
}
|
444
|
|
445
|
}
|
446
|
|
447
|
|
448
|
/**
|
449
|
* @param reg
|
450
|
*/
|
451
|
public void inititializeSpecimen(Registration reg) {
|
452
|
|
453
|
for(TypeDesignationBase<?> td : reg.getTypeDesignations()){
|
454
|
if(td instanceof SpecimenTypeDesignation){
|
455
|
|
456
|
DerivedUnit derivedUnit = ((SpecimenTypeDesignation) td).getTypeSpecimen();
|
457
|
@SuppressWarnings("rawtypes")
|
458
|
Set<SpecimenOrObservationBase> sobs = new HashSet<>();
|
459
|
sobs.add(HibernateProxyHelper.deproxy(derivedUnit));
|
460
|
|
461
|
while(sobs != null && !sobs.isEmpty()){
|
462
|
@SuppressWarnings("rawtypes")
|
463
|
Set<SpecimenOrObservationBase> nextSobs = null;
|
464
|
for(@SuppressWarnings("rawtypes") SpecimenOrObservationBase sob : sobs){
|
465
|
sob = HibernateProxyHelper.deproxy(sob);
|
466
|
if(sob == null){
|
467
|
continue;
|
468
|
}
|
469
|
if(DerivedUnit.class.isAssignableFrom(sob.getClass())) {
|
470
|
defaultBeanInitializer.initialize(sob, DERIVEDUNIT_INIT_STRATEGY.getPropertyPaths());
|
471
|
nextSobs = ((DerivedUnit)sob).getOriginals();
|
472
|
}
|
473
|
if(sob instanceof FieldUnit){
|
474
|
defaultBeanInitializer.initialize(sob, FIELDUNIT_INIT_STRATEGY);
|
475
|
}
|
476
|
}
|
477
|
sobs = nextSobs;
|
478
|
}
|
479
|
}
|
480
|
}
|
481
|
}
|
482
|
|
483
|
|
484
|
|
485
|
|
486
|
|
487
|
|
488
|
}
|