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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.io.stream;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.api.service.IIdentifiableEntityService;
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import eu.etaxonomy.cdm.io.common.ImportStateBase;
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import eu.etaxonomy.cdm.io.dwca.TermUri;
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import eu.etaxonomy.cdm.io.dwca.in.IImportMapping;
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import eu.etaxonomy.cdm.io.dwca.in.IImportMapping.CdmKey;
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import eu.etaxonomy.cdm.io.dwca.in.InMemoryMapping;
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import eu.etaxonomy.cdm.io.dwca.in.MappedCdmBase;
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import eu.etaxonomy.cdm.io.dwca.in.MappingEntry;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.reference.Reference;
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/**
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* @author a.mueller
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* @created 23.11.2011
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*/
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public abstract class StreamImportStateBase<CONFIG extends StreamImportConfiguratorBase, IO extends StreamImportBase> extends ImportStateBase<CONFIG, IO>{
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private static final Logger logger = Logger.getLogger(StreamImportStateBase.class);
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private UUID uuid = UUID.randomUUID();
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boolean taxaCreated;
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private Map<String, Map<String, IdentifiableEntity>> partitionStore;
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private final IImportMapping mapping;
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public StreamImportStateBase(CONFIG config) {
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super(config);
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if (config.getStateUuid()!= null){
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uuid = config.getStateUuid();
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}else{
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String message = "State uuid: " + uuid.toString();
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logger.warn(message);
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System.out.println(message);
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}
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mapping = getConfig().getMappingType().getMappingInstance(uuid.toString(), getConfig().getDatabaseMappingFile());
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}
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/**
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* True, if taxa have been fully created.
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* @return
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*/
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public boolean isTaxaCreated() {
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return taxaCreated;
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}
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/**
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* @param taxaCreated the taxaCreated to set
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*/
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public void setTaxaCreated(boolean taxaCreated) {
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this.taxaCreated = taxaCreated;
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}
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public void finish(){
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this.mapping.finish();
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}
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//********************* MAPPING ACCESS *********************************
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//TODO this may move to an external class soon
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public void putMapping(MappedCdmBase mappedCdmBase) throws IllegalArgumentException{
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if (! mappedCdmBase.getCdmBase().isInstanceOf(IdentifiableEntity.class)){
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throw new IllegalArgumentException("Mapped cdmBase does not map an identifiable entity");
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}
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mapping.putMapping(mappedCdmBase.getNamespace(), mappedCdmBase.getSourceId(), CdmBase.deproxy(mappedCdmBase.getCdmBase(), IdentifiableEntity.class));
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}
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public void putMapping(String namespace, Integer sourceKey, IdentifiableEntity<?> destinationObject){
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mapping.putMapping(namespace, sourceKey, destinationObject);
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}
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public void putMapping(String namespace, String sourceKey, IdentifiableEntity<?> destinationObject){
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mapping.putMapping(namespace, sourceKey, destinationObject);
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}
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public List<IdentifiableEntity> get(String namespace, String sourceKey){
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return get(namespace, sourceKey, null);
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}
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public <CLASS extends IdentifiableEntity> List<CLASS> get(String namespace, String sourceKey,Class<CLASS> destinationClass){
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List<CLASS> result = new ArrayList<CLASS>();
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if (this.partitionStore != null){
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Map<String, IdentifiableEntity> namespaceMap = this.partitionStore.get(namespace);
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if (namespaceMap != null){
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IdentifiableEntity<?> cdmBase = namespaceMap.get(sourceKey);
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if (cdmBase == null){
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logger.info("CdmBase does not exist in mapping: " + sourceKey);
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}else if (cdmBase.isInstanceOf(destinationClass)){
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CLASS typedCdmBase = CdmBase.deproxy(cdmBase, destinationClass);
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result.add(typedCdmBase);
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}
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}
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}else{
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Set<CdmKey> keySet = mapping.get(namespace, sourceKey);
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for (CdmKey<CLASS> key: keySet){
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if (destinationClass == null || destinationClass.isAssignableFrom(key.getClazz())){
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IIdentifiableEntityService<CLASS> service = getCurrentIO().getServiceByClass(key.getClazz());
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CLASS entity = CdmBase.deproxy(service.find(key.getId()), key.getClazz());
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result.add(entity);
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}
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}
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return result;
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}
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return result;
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}
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public boolean exists(String namespace, String sourceKey,Class<?> destinationClass){
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return mapping.exists(namespace, sourceKey, destinationClass);
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}
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public void loadRelatedObjects (InMemoryMapping mapping){
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Map<String, Map<String, IdentifiableEntity>> result = new HashMap<>();
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List<MappingEntry<String, String, Class, Integer>> mappingEntryList = mapping.getEntryList();
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//order ids by destination classes
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Map<Class, Set<Integer>> destinationNamespaceMap = new HashMap<>();
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for (MappingEntry<String, String, Class, Integer> entry : mappingEntryList){
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Set<Integer> idSet = destinationNamespaceMap.get(entry.getDestinationNamespace());
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if (idSet == null){
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idSet = new HashSet<Integer>();
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destinationNamespaceMap.put(entry.getDestinationNamespace(), idSet);
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}
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idSet.add(entry.getDestinationId());
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}
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//retrieve cdm objects per class
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Map<Class, Map<Integer, IdentifiableEntity>> classMap = new HashMap<>();
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for (Class<?> cdmClass : destinationNamespaceMap.keySet()){
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IIdentifiableEntityService<?> classService = getCurrentIO().getServiceByClass(cdmClass);
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Set<Integer> idSet = destinationNamespaceMap.get(cdmClass);
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List<? extends IdentifiableEntity> relatedObjects = classService.findById(idSet);
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//put into id map
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Map<Integer, IdentifiableEntity> idMap = new HashMap<>();
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for (IdentifiableEntity<?> identEnt : relatedObjects){
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idMap.put(identEnt.getId(), identEnt);
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}
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//add to class map
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classMap.put(cdmClass, idMap);
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}
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//fill related object map
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for (MappingEntry<String, String, Class, Integer> entry : mappingEntryList){
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IdentifiableEntity cdmBase = getCdmObject(classMap, entry);
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Map<String, IdentifiableEntity> namespaceMap = getOrMakeNamespaceMap(result, entry.getNamespace());
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if (cdmBase != null){
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namespaceMap.put(entry.getSourceKey(), cdmBase);
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}else{
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logger.info("CdmBase not found for mapping entry.");
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}
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}
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//store
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this.partitionStore = result;
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}
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public void addRelatedObject(String sourceNamespace, String sourceKey, IdentifiableEntity<?> cdmEntity){
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Map<String, IdentifiableEntity> namespaceMap = getOrMakeNamespaceMap(this.partitionStore, sourceNamespace);
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if (cdmEntity != null){
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namespaceMap.put(sourceKey, cdmEntity);
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}else{
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logger.info("CdmBase is null and will not be added to related objects.");
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}
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}
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// public Map<String, Map<String, IdentifiableEntity>> getPartitionStore() {
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// return partitionStore;
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// }
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public void unloadPartitionStore(Map<String, Map<String, IdentifiableEntity>> partitionStore) {
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this.partitionStore = new HashMap<>();
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}
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public IImportMapping getMapping() {
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return this.mapping;
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}
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private Map<String, IdentifiableEntity> getOrMakeNamespaceMap(Map<String, Map<String, IdentifiableEntity>> relatedObjectMap2, String namespace) {
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Map<String, IdentifiableEntity> namespaceMap = relatedObjectMap2.get(namespace);
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if (namespaceMap == null){
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namespaceMap = new HashMap<>();
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relatedObjectMap2.put(namespace, namespaceMap);
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}
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return namespaceMap;
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}
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private IdentifiableEntity getCdmObject(Map<Class, Map<Integer, IdentifiableEntity>> classMap,
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MappingEntry<String, String, Class, Integer> entry) {
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Class<?> cdmClass = entry.getDestinationNamespace();
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Integer cdmKey = entry.getDestinationId();
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Map<Integer, IdentifiableEntity> idMap = classMap.get(cdmClass);
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if (idMap != null){
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return idMap.get(cdmKey);
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}else{
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return null;
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}
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}
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/**
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* Returns the source reference object that is attached to the current transaction.
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* @return
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*/
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public Reference getTransactionalSourceReference() {
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TermUri namespaceSourceReference = TermUri.CDM_SOURCE_REFERENCE;
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UUID sourceReferenceUuid = getConfig().getSourceRefUuid();
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List<Reference> references = this.get(namespaceSourceReference.toString(), sourceReferenceUuid.toString(), Reference.class);
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if (references.isEmpty()){
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//TODO better fire warning, but not yet available for state
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throw new RuntimeException("Source reference can not be found. This should not happen.");
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}else if (references.size() > 1){
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//TODO better fire warning, but not yet available for state
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throw new RuntimeException("More than 1 source reference found. This is not yet handled.");
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}else{
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return references.get(0);
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}
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}
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}
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