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Revision ff5db610

Added by Katja Luther over 4 years ago

ref #1445: merging fauna europaea and erms

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/app/common/tasks/CacheUpdater.java
14 14 

  		




  15
  15
  
    
import org.apache.log4j.Logger;


  		




  16
  16
  
    

  		




  
  17
  
    
import eu.etaxonomy.cdm.api.service.config.CacheUpdaterConfigurator;


  		




  17
  18
  
    
import eu.etaxonomy.cdm.app.common.CdmDestinations;


  		




  18
  19
  
    
import eu.etaxonomy.cdm.database.ICdmDataSource;


  		




  19
  20
  
    
import eu.etaxonomy.cdm.io.common.CdmDefaultImport;


  		




  20
  21
  
    
import eu.etaxonomy.cdm.io.common.ImportResult;


  		




  21
  
  
    
import eu.etaxonomy.cdm.io.operation.config.CacheUpdaterConfigurator;


  		




  
  22
  
    

  		




  22
  23
  
    
import eu.etaxonomy.cdm.model.name.TaxonName;


  		




  23
  24
  
    
import eu.etaxonomy.cdm.model.reference.Reference;


  		




  24
  25
  
    
import eu.etaxonomy.cdm.model.taxon.TaxonBase;


  		




  ......




  63
  64
  
    

  		




  64
  65
  
    
		CacheUpdaterConfigurator config;


  		




  65
  66
  
    
		try {


  		




  66
  
  
    
			config = CacheUpdaterConfigurator.NewExludedInstance(destination, classListStrings);


  		




  
  67
  
    
			config = CacheUpdaterConfigurator.NewInstance(destination, classListStrings);


  		




  67
  68
  
    

  		




  68
  69
  
    
			// invoke import


  		




  69
  70
  
    
			CdmDefaultImport<CacheUpdaterConfigurator> myImport = new CdmDefaultImport<>();


  		












  

    
      cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java
    
  





  34
  34
  
    
	public static ICdmDataSource cdm_test_local_faunaEu_mysql(){


  		




  35
  35
  
    
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;


  		




  36
  36
  
    
		String cdmServer = "127.0.0.1";


  		




  37
  
  
    
		String cdmDB = "cdm_faunaeu_2017_03";


  		




  
  37
  
    
		String cdmDB = "cdm_fauna_europaea";


  		




  38
  38
  
    
		String cdmUserName = "root";


  		




  39
  39
  
    
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);


  		




  40
  40
  
    
	}


  		












  

    
      cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/FaunaEuErmsFindIdenticalNamesActivator.java
    
  





  3
  3
  
    
import java.io.FileWriter;


  		




  4
  4
  
    
import java.io.IOException;


  		




  5
  5
  
    
import java.util.ArrayList;


  		




  
  6
  
    
import java.util.HashSet;


  		




  6
  7
  
    
import java.util.Iterator;


  		




  7
  8
  
    
import java.util.List;


  		




  8
  9
  
    
import java.util.Set;


  		




  
  10
  
    
import java.util.UUID;


  		




  9
  11
  
    

  		




  10
  12
  
    
import eu.etaxonomy.cdm.api.application.CdmApplicationController;


  		




  11
  13
  
    
import eu.etaxonomy.cdm.app.common.CdmDestinations;


  		




  
  14
  
    
import eu.etaxonomy.cdm.app.util.TestDatabase;


  		




  12
  15
  
    
import eu.etaxonomy.cdm.database.DbSchemaValidation;


  		




  13
  16
  
    
import eu.etaxonomy.cdm.database.ICdmDataSource;


  		




  14
  17
  
    
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;


  		




  ......




  18
  21
  
    
import eu.etaxonomy.cdm.model.name.IZoologicalName;


  		




  19
  22
  
    
import eu.etaxonomy.cdm.model.name.Rank;


  		




  20
  23
  
    
import eu.etaxonomy.cdm.model.name.TaxonName;


  		




  
  24
  
    
import eu.etaxonomy.cdm.model.taxon.Classification;


  		




  21
  25
  
    
import eu.etaxonomy.cdm.model.taxon.Taxon;


  		




  22
  26
  
    
import eu.etaxonomy.cdm.model.taxon.TaxonNode;


  		




  
  27
  
    
import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;


  		




  23
  28
  
    

  		




  24
  29
  
    
public class FaunaEuErmsFindIdenticalNamesActivator {


  		




  25
  30
  
    

  		




  26
  
  
    
	static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.localH2();


  		




  27
  
  
    
	//static final ICdmDataSource ermsSource = CdmDestinations.cdm_test_andreasM();


  		




  
  31
  
    
	//static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.localH2();


  		




  
  32
  
    
	static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.cdm_test_local_faunaEu_mysql();


  		




  28
  33
  
    

  		




  29
  34
  
    
	//TODO hole aus beiden DB alle TaxonNameBases


  		




  30
  35
  
    

  		




  ......




  59
  64
  
    
		propertyPaths.add("taxonBases.taxonNodes.parent.*");


  		




  60
  65
  
    
		propertyPaths.add("taxonBases.taxonNodes.parent.taxon.name.*");


  		




  61
  66
  
    
		System.err.println("Start getIdenticalNames...");


  		




  62
  
  
    
		List<TaxonName> namesOfIdenticalTaxa = appCtrFaunaEu.getTaxonService().findIdenticalTaxonNameIds(propertyPaths);


  		




  
  67
  
    
		List<UUID> namesOfIdenticalTaxa = appCtrFaunaEu.getTaxonService().findIdenticalTaxonNameIds(propertyPaths);


  		




  63
  68
  
    
		//List<UUID> namesOfIdenticalTaxa = appCtrFaunaEu.getTaxonService().findIdenticalTaxonNameIds(propertyPaths);


  		




  64
  69
  
    

  		




  65
  70
  
    
		System.err.println("first name: " + namesOfIdenticalTaxa.get(0) + " " + namesOfIdenticalTaxa.size());


  		




  66
  
  
    
		TaxonName zooName = namesOfIdenticalTaxa.get(0);


  		




  67
  
  
    
		System.err.println(zooName + " nr of taxa " + namesOfIdenticalTaxa.size());


  		




  
  71
  
    
		//TaxonName zooName = namesOfIdenticalTaxa.get(0);


  		




  
  72
  
    
		//System.err.println(zooName + " nr of taxa " + namesOfIdenticalTaxa.size());


  		




  68
  73
  
    
		//TaxonNameComparator taxComp = new TaxonNameComparator();


  		




  69
  74
  
    

  		




  70
  75
  
    
		//Collections.sort(namesOfIdenticalTaxa,taxComp);


  		




  ......




  275
  280
  
    
			writer.append("synonym");


  		




  276
  281
  
    
		}


  		




  277
  282
  
    
		writer.append(';');


  		




  278
  
  
    
		writer.append(merging.getPhylumInFaunaEu());


  		




  
  283
  
    
		writer.append(merging.getPhylumInFaunaEu().getTaxonTitleCache());


  		




  279
  284
  
    
		writer.append(';');


  		




  280
  285
  
    
		writer.append(merging.getParentStringInFaunaEu());


  		




  281
  286
  
    
		writer.append(';');


  		




  ......




  299
  304
  
    
		}


  		




  300
  305
  
    

  		




  301
  306
  
    
		writer.append(';');


  		




  302
  
  
    
		writer.append(merging.getPhylumInErms());


  		




  
  307
  
    
		writer.append(merging.getPhylumInErms().getTaxonTitleCache());


  		




  303
  308
  
    
		writer.append(';');


  		




  304
  309
  
    
		writer.append(merging.getParentStringInErms());


  		




  305
  310
  
    
		writer.append(';');


  		




  ......




  308
  313
  
    
	}


  		




  309
  314
  
    

  		




  310
  315
  
    

  		




  311
  
  
    
	private List<FaunaEuErmsMerging> createMergeObjects(List<TaxonName> names, CdmApplicationController appCtr){


  		




  
  316
  
    
	private List<FaunaEuErmsMerging> createMergeObjects(List<UUID> uuids, CdmApplicationController appCtr){


  		




  312
  317
  
    

  		




  313
  318
  
    
		List<FaunaEuErmsMerging> merge = new ArrayList<>();


  		




  314
  319
  
    
		TaxonName zooName, zooName2;


  		




  315
  320
  
    
		FaunaEuErmsMerging mergeObject;


  		




  316
  321
  
    
		String idInSource1;


  		




  317
  
  
    
		for (int i = 0; i<names.size()-1; i=i+2){


  		




  318
  
  
    
			zooName = names.get(i);


  		




  319
  
  
    
			zooName2 = names.get(i+1);


  		




  320
  
  
    
			mergeObject = new FaunaEuErmsMerging();


  		




  321
  
  
    
			//TODO:überprüfen, ob die beiden Namen identisch sind und aus unterschiedlichen DB kommen


  		




  322
  
  
    

  		




  323
  
  
    
			//getPhylum


  		




  324
  
  
    
			String phylum1 = null;


  		




  325
  
  
    
			if (!zooName.getRank().isHigher(Rank.PHYLUM())){


  		




  326
  
  
    
				phylum1 =appCtr.getTaxonService().getPhylumName(zooName);


  		




  327
  
  
    
			}


  		




  328
  
  
    

  		




  329
  
  
    
			String phylum2 = null;


  		




  330
  
  
    
			if (!zooName2.getRank().isHigher(Rank.PHYLUM())){


  		




  331
  
  
    
				phylum2 = appCtr.getTaxonService().getPhylumName(zooName2);


  		




  332
  
  
    
			}


  		




  333
  
  
    
			mergeObject.setPhylumInErms(phylum1);


  		




  334
  
  
    
			mergeObject.setPhylumInFaunaEu(phylum2);


  		




  335
  
  
    

  		




  336
  
  
    
			//getUuids


  		




  337
  
  
    
			mergeObject.setUuidErms(zooName.getUuid().toString());


  		




  338
  
  
    
			mergeObject.setUuidFaunaEu(zooName.getUuid().toString());


  		




  339
  
  
    

  		




  340
  
  
    
			Iterator<IdentifiableSource> sources = zooName.getSources().iterator();


  		




  341
  
  
    
			if (sources.hasNext()){


  		




  342
  
  
    
				IdentifiableSource source = sources.next();


  		




  343
  
  
    
				idInSource1 = source.getIdInSource();


  		




  344
  
  
    
				mergeObject.setIdInErms(idInSource1);


  		




  345
  
  
    
			}


  		




  346
  
  
    
			sources = zooName2.getSources().iterator();


  		




  347
  
  
    
			if (sources.hasNext()){


  		




  348
  
  
    
				IdentifiableSource source = sources.next();


  		




  349
  
  
    
				idInSource1 = source.getIdInSource();


  		




  350
  
  
    
				mergeObject.setIdInFaunaEu(idInSource1);


  		




  351
  
  
    
			}


  		




  352
  
  
    

  		




  353
  
  
    
			mergeObject.setNameCacheInErms(zooName.getNameCache());


  		




  354
  
  
    
			mergeObject.setNameCacheInFaunaEu(zooName2.getNameCache());


  		




  355
  
  
    

  		




  356
  
  
    
			mergeObject.setAuthorInErms(zooName.getAuthorshipCache());


  		




  357
  
  
    
			mergeObject.setAuthorInFaunaEu(zooName2.getAuthorshipCache());


  		




  358
  
  
    
			Set<Taxon> taxa = zooName.getTaxa();


  		




  359
  
  
    
			if (!taxa.isEmpty()){


  		




  360
  
  
    
				mergeObject.setStatInErms(true);


  		




  361
  
  
    
				Iterator<Taxon> taxaIterator = taxa.iterator();


  		




  362
  
  
    
				Taxon taxon = null;


  		




  363
  
  
    
				while (taxaIterator.hasNext()){


  		




  364
  
  
    
					taxon = taxaIterator.next();


  		




  365
  
  
    
					if (!taxon.isMisapplication()){


  		




  366
  
  
    
						break;


  		




  367
  
  
    
					}


  		




  
  322
  
    
		for(int j = 0; j<uuids.size()-1; j = j + 500) {


  		




  
  323
  
    
			Set<UUID> subset = new HashSet( uuids.subList(j, j+499));


  		




  
  324
  
    
			List<TaxonName> names = appCtr.getNameService().find(subset);


  		




  
  325
  
    
			for (int i = 0; i<names.size()-1; i=i+2){


  		




  
  326
  
    
				zooName = names.get(i);


  		




  
  327
  
    
				zooName2 = names.get(i+1);


  		




  
  328
  
    
				mergeObject = new FaunaEuErmsMerging();


  		




  
  329
  
    
				//TODO:überprüfen, ob die beiden Namen identisch sind und aus unterschiedlichen DB kommen


  		




  
  330
  
    
				Classification faunaEuClassification = appCtr.getClassificationService().load(UUID.fromString("44d8605e-a7ce-41e1-bee9-99edfec01e7c"));


  		




  
  331
  
    
				Classification ermsClassification = appCtr.getClassificationService().load(UUID.fromString("6fa988a9-10b7-48b0-a370-2586fbc066eb"));


  		




  
  332
  
    
				//getPhylum


  		




  
  333
  
    
				TaxonNodeDto phylum1 = null;


  		




  
  334
  
    
				if (!zooName.getRank().isHigher(Rank.PHYLUM())){


  		




  
  335
  
    
						phylum1 =appCtr.getTaxonNodeService().taxonNodeDtoParentRank(faunaEuClassification, Rank.PHYLUM(), zooName);


  		




  368
  336
  
    
				}


  		




  369
  
  
    
				Set<TaxonNode> nodes = taxon.getTaxonNodes();


  		




  370
  
  
    
				Iterator<TaxonNode> taxonNodeIterator = nodes.iterator();


  		




  371
  
  
    
				TaxonNode node, parentNode = null;


  		




  372
  
  
    
				while (taxonNodeIterator.hasNext()){


  		




  373
  
  
    
					node = taxonNodeIterator.next();


  		




  374
  
  
    
					if (!node.isTopmostNode()){


  		




  375
  
  
    
						parentNode = node.getParent();


  		




  376
  
  
    
					}


  		




  
  337
  
    
	


  		




  
  338
  
    
				TaxonNodeDto phylum2 = null;


  		




  
  339
  
    
				if (!zooName2.getRank().isHigher(Rank.PHYLUM())){


  		




  
  340
  
    
					phylum2 = appCtr.getTaxonNodeService().taxonNodeDtoParentRank(ermsClassification, Rank.PHYLUM(), zooName2);


  		




  377
  341
  
    
				}


  		




  378
  
  
    
				//TODO: ändern mit erweitertem Initializer..


  		




  379
  
  
    
				if (parentNode != null){


  		




  380
  
  
    
				    TaxonName parentName = HibernateProxyHelper.deproxy(parentNode.getTaxon().getName());


  		




  381
  
  
    
					String parentNameCache = parentName.getNameCache();


  		




  382
  
  
    
					mergeObject.setParentStringInErms(parentNameCache);


  		




  383
  
  
    
					mergeObject.setParentRankStringInErms(parentName.getRank().getLabel());


  		




  384
  
  
    
					//System.err.println("parentName: " + parentNameCache);


  		




  
  342
  
    
				mergeObject.setPhylumInErms(phylum1);


  		




  
  343
  
    
				mergeObject.setPhylumInFaunaEu(phylum2);


  		




  
  344
  
    
	


  		




  
  345
  
    
				//getUuids


  		




  
  346
  
    
				mergeObject.setUuidErms(zooName.getUuid().toString());


  		




  
  347
  
    
				mergeObject.setUuidFaunaEu(zooName.getUuid().toString());


  		




  
  348
  
    
	


  		




  
  349
  
    
				Iterator<IdentifiableSource> sources = zooName.getSources().iterator();


  		




  
  350
  
    
				if (sources.hasNext()){


  		




  
  351
  
    
					IdentifiableSource source = sources.next();


  		




  
  352
  
    
					idInSource1 = source.getIdInSource();


  		




  
  353
  
    
					mergeObject.setIdInErms(idInSource1);


  		




  385
  354
  
    
				}


  		




  386
  
  
    
			}else{


  		




  387
  
  
    
				mergeObject.setStatInErms(false);


  		




  388
  
  
    
			}


  		




  389
  
  
    
			taxa = zooName2.getTaxa();


  		




  390
  
  
    
			if (!taxa.isEmpty()){


  		




  391
  
  
    
				mergeObject.setStatInFaunaEu(true);


  		




  392
  
  
    
				Iterator<Taxon> taxaIterator = taxa.iterator();


  		




  393
  
  
    
				Taxon taxon = null;


  		




  394
  
  
    
				while (taxaIterator.hasNext()){


  		




  395
  
  
    
					taxon = taxaIterator.next();


  		




  396
  
  
    
					if (!taxon.isMisapplication()){


  		




  397
  
  
    
						break;


  		




  398
  
  
    
					}


  		




  
  355
  
    
				sources = zooName2.getSources().iterator();


  		




  
  356
  
    
				if (sources.hasNext()){


  		




  
  357
  
    
					IdentifiableSource source = sources.next();


  		




  
  358
  
    
					idInSource1 = source.getIdInSource();


  		




  
  359
  
    
					mergeObject.setIdInFaunaEu(idInSource1);


  		




  399
  360
  
    
				}


  		




  400
  
  
    
				Set<TaxonNode> nodes = taxon.getTaxonNodes();


  		




  401
  
  
    
				Iterator<TaxonNode> taxonNodeIterator = nodes.iterator();


  		




  402
  
  
    
				TaxonNode node, parentNode = null;


  		




  403
  
  
    
				while (taxonNodeIterator.hasNext()){


  		




  404
  
  
    
					node = taxonNodeIterator.next();


  		




  405
  
  
    
					if (!node.isTopmostNode()){


  		




  406
  
  
    
						parentNode = node.getParent();


  		




  
  361
  
    
	


  		




  
  362
  
    
				mergeObject.setNameCacheInErms(zooName.getNameCache());


  		




  
  363
  
    
				mergeObject.setNameCacheInFaunaEu(zooName2.getNameCache());


  		




  
  364
  
    
	


  		




  
  365
  
    
				mergeObject.setAuthorInErms(zooName.getAuthorshipCache());


  		




  
  366
  
    
				mergeObject.setAuthorInFaunaEu(zooName2.getAuthorshipCache());


  		




  
  367
  
    
				Set<Taxon> taxa = zooName.getTaxa();


  		




  
  368
  
    
				if (!taxa.isEmpty()){


  		




  
  369
  
    
					mergeObject.setStatInErms(true);


  		




  
  370
  
    
					Iterator<Taxon> taxaIterator = taxa.iterator();


  		




  
  371
  
    
					Taxon taxon = null;


  		




  
  372
  
    
					while (taxaIterator.hasNext()){


  		




  
  373
  
    
						taxon = taxaIterator.next();


  		




  
  374
  
    
						if (!taxon.isMisapplication()){


  		




  
  375
  
    
							break;


  		




  
  376
  
    
						}


  		




  407
  377
  
    
					}


  		




  
  378
  
    
					Set<TaxonNode> nodes = taxon.getTaxonNodes();


  		




  
  379
  
    
					Iterator<TaxonNode> taxonNodeIterator = nodes.iterator();


  		




  
  380
  
    
					TaxonNode node, parentNode = null;


  		




  
  381
  
    
					while (taxonNodeIterator.hasNext()){


  		




  
  382
  
    
						node = taxonNodeIterator.next();


  		




  
  383
  
    
						if (!node.isTopmostNode()){


  		




  
  384
  
    
							parentNode = node.getParent();


  		




  
  385
  
    
						}


  		




  
  386
  
    
					}


  		




  
  387
  
    
					//TODO: ändern mit erweitertem Initializer..


  		




  
  388
  
    
					if (parentNode != null){


  		




  
  389
  
    
					    TaxonName parentName = HibernateProxyHelper.deproxy(parentNode.getTaxon().getName());


  		




  
  390
  
    
						String parentNameCache = parentName.getNameCache();


  		




  
  391
  
    
						mergeObject.setParentStringInErms(parentNameCache);


  		




  
  392
  
    
						mergeObject.setParentRankStringInErms(parentName.getRank().getLabel());


  		




  
  393
  
    
						//System.err.println("parentName: " + parentNameCache);


  		




  
  394
  
    
					}


  		




  
  395
  
    
				}else{


  		




  
  396
  
    
					mergeObject.setStatInErms(false);


  		




  408
  397
  
    
				}


  		




  409
  
  
    
				//TODO: ändern mit erweitertem Initializer..


  		




  410
  
  
    
				if (parentNode != null){


  		




  411
  
  
    
					if (parentNode.getTaxon().getName().isZoological()){


  		




  412
  
  
    

  		




  413
  
  
    
    					IZoologicalName parentName = CdmBase.deproxy(parentNode.getTaxon().getName());


  		




  414
  
  
    
    					String parentNameCache = parentName.getNameCache();


  		




  415
  
  
    
    					mergeObject.setParentStringInFaunaEu(parentNameCache);


  		




  416
  
  
    
    					mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel());


  		




  417
  
  
    
    					System.err.println("parentName: " + parentNameCache);


  		




  418
  
  
    
					}else{


  		




  419
  
  
    
						System.err.println("no zoologicalName: " + parentNode.getTaxon().getName().getTitleCache() +" . "+parentNode.getTaxon().getName().getUuid());


  		




  
  398
  
    
				taxa = zooName2.getTaxa();


  		




  
  399
  
    
				if (!taxa.isEmpty()){


  		




  
  400
  
    
					mergeObject.setStatInFaunaEu(true);


  		




  
  401
  
    
					Iterator<Taxon> taxaIterator = taxa.iterator();


  		




  
  402
  
    
					Taxon taxon = null;


  		




  
  403
  
    
					while (taxaIterator.hasNext()){


  		




  
  404
  
    
						taxon = taxaIterator.next();


  		




  
  405
  
    
						if (!taxon.isMisapplication()){


  		




  
  406
  
    
							break;


  		




  
  407
  
    
						}


  		




  420
  408
  
    
					}


  		




  421
  
  
    

  		




  
  409
  
    
					Set<TaxonNode> nodes = taxon.getTaxonNodes();


  		




  
  410
  
    
					Iterator<TaxonNode> taxonNodeIterator = nodes.iterator();


  		




  
  411
  
    
					TaxonNode node, parentNode = null;


  		




  
  412
  
    
					while (taxonNodeIterator.hasNext()){


  		




  
  413
  
    
						node = taxonNodeIterator.next();


  		




  
  414
  
    
						if (!node.isTopmostNode()){


  		




  
  415
  
    
							parentNode = node.getParent();


  		




  
  416
  
    
						}


  		




  
  417
  
    
					}


  		




  
  418
  
    
					//TODO: ändern mit erweitertem Initializer..


  		




  
  419
  
    
					if (parentNode != null){


  		




  
  420
  
    
						if (parentNode.getTaxon().getName().isZoological()){


  		




  
  421
  
    
	


  		




  
  422
  
    
	    					IZoologicalName parentName = CdmBase.deproxy(parentNode.getTaxon().getName());


  		




  
  423
  
    
	    					String parentNameCache = parentName.getNameCache();


  		




  
  424
  
    
	    					mergeObject.setParentStringInFaunaEu(parentNameCache);


  		




  
  425
  
    
	    					mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel());


  		




  
  426
  
    
	    					System.err.println("parentName: " + parentNameCache);


  		




  
  427
  
    
						}else{


  		




  
  428
  
    
							System.err.println("no zoologicalName: " + parentNode.getTaxon().getName().getTitleCache() +" . "+parentNode.getTaxon().getName().getUuid());


  		




  
  429
  
    
						}


  		




  
  430
  
    
	


  		




  
  431
  
    
					}


  		




  
  432
  
    
				}else{


  		




  
  433
  
    
					mergeObject.setStatInErms(false);


  		




  422
  434
  
    
				}


  		




  423
  
  
    
			}else{


  		




  424
  
  
    
				mergeObject.setStatInErms(false);


  		




  425
  
  
    
			}


  		




  426
  
  
    
			taxa = zooName2.getTaxa();


  		




  427
  
  
    
			if (!taxa.isEmpty()){


  		




  428
  
  
    
				mergeObject.setStatInFaunaEu(true);


  		




  429
  
  
    
			}else{


  		




  430
  
  
    
				mergeObject.setStatInFaunaEu(false);


  		




  431
  
  
    

  		




  432
  
  
    
			}


  		




  433
  
  
    

  		




  434
  
  
    
			mergeObject.setRankInErms(zooName.getRank().getLabel());


  		




  435
  
  
    
			mergeObject.setRankInFaunaEu(zooName2.getRank().getLabel());


  		




  436
  
  
    

  		




  437
  
  
    
			//set parent informations


  		




  438
  
  
    

  		




  439
  
  
    

  		




  440
  
  
    
			/*


  		




  441
  
  
    
			Set<HybridRelationship> parentRelations = zooName.getParentRelationships();


  		




  442
  
  
    
			Iterator parentIterator = parentRelations.iterator();


  		




  443
  
  
    
			HybridRelationship parentRel;


  		




  444
  
  
    
			ZoologicalName parentName;


  		




  445
  
  
    
			while (parentIterator.hasNext()){


  		




  446
  
  
    
				parentRel = (HybridRelationship)parentIterator.next();


  		




  447
  
  
    
				parentName = (ZoologicalName)parentRel.getParentName();


  		




  448
  
  
    
				mergeObject.setParentRankStringInErms(parentName.getRank().getLabel());


  		




  449
  
  
    
				mergeObject.setParentStringInErms(parentName.getNameCache());


  		




  
  435
  
    
				taxa = zooName2.getTaxa();


  		




  
  436
  
    
				if (!taxa.isEmpty()){


  		




  
  437
  
    
					mergeObject.setStatInFaunaEu(true);


  		




  
  438
  
    
				}else{


  		




  
  439
  
    
					mergeObject.setStatInFaunaEu(false);


  		




  
  440
  
    
	


  		




  
  441
  
    
				}


  		




  
  442
  
    
	


  		




  
  443
  
    
				mergeObject.setRankInErms(zooName.getRank().getLabel());


  		




  
  444
  
    
				mergeObject.setRankInFaunaEu(zooName2.getRank().getLabel());


  		




  
  445
  
    
	


  		




  
  446
  
    
				//set parent informations


  		




  
  447
  
    
	


  		




  
  448
  
    
	


  		




  
  449
  
    
				/*


  		




  
  450
  
    
				Set<HybridRelationship> parentRelations = zooName.getParentRelationships();


  		




  
  451
  
    
				Iterator parentIterator = parentRelations.iterator();


  		




  
  452
  
    
				HybridRelationship parentRel;


  		




  
  453
  
    
				ZoologicalName parentName;


  		




  
  454
  
    
				while (parentIterator.hasNext()){


  		




  
  455
  
    
					parentRel = (HybridRelationship)parentIterator.next();


  		




  
  456
  
    
					parentName = (ZoologicalName)parentRel.getParentName();


  		




  
  457
  
    
					mergeObject.setParentRankStringInErms(parentName.getRank().getLabel());


  		




  
  458
  
    
					mergeObject.setParentStringInErms(parentName.getNameCache());


  		




  
  459
  
    
				}


  		




  
  460
  
    
	


  		




  
  461
  
    
				parentRelations = zooName2.getParentRelationships();


  		




  
  462
  
    
				parentIterator = parentRelations.iterator();


  		




  
  463
  
    
	


  		




  
  464
  
    
				while (parentIterator.hasNext()){


  		




  
  465
  
    
					parentRel = (HybridRelationship)parentIterator.next();


  		




  
  466
  
    
					parentName = (ZoologicalName)parentRel.getParentName();


  		




  
  467
  
    
					mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel());


  		




  
  468
  
    
					mergeObject.setParentStringInFaunaEu(parentName.getNameCache());


  		




  
  469
  
    
				}*/


  		




  
  470
  
    
				merge.add(mergeObject);


  		




  450
  471
  
    
			}


  		




  451
  
  
    

  		




  452
  
  
    
			parentRelations = zooName2.getParentRelationships();


  		




  453
  
  
    
			parentIterator = parentRelations.iterator();


  		




  454
  
  
    

  		




  455
  
  
    
			while (parentIterator.hasNext()){


  		




  456
  
  
    
				parentRel = (HybridRelationship)parentIterator.next();


  		




  457
  
  
    
				parentName = (ZoologicalName)parentRel.getParentName();


  		




  458
  
  
    
				mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel());


  		




  459
  
  
    
				mergeObject.setParentStringInFaunaEu(parentName.getNameCache());


  		




  460
  
  
    
			}*/


  		




  461
  
  
    
			merge.add(mergeObject);


  		




  462
  472
  
    
		}


  		




  463
  473
  
    

  		




  464
  474
  
    
		return merge;


  		












  

    
      cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/FaunaEuErmsMergeActivator.java
    
  





  19
  19
  
    
import eu.etaxonomy.cdm.api.service.exception.ReferencedObjectUndeletableException;


  		




  20
  20
  
    
import eu.etaxonomy.cdm.api.service.pager.Pager;


  		




  21
  21
  
    
import eu.etaxonomy.cdm.app.common.CdmDestinations;


  		




  
  22
  
    
import eu.etaxonomy.cdm.app.util.TestDatabase;


  		




  22
  23
  
    
import eu.etaxonomy.cdm.database.DbSchemaValidation;


  		




  23
  24
  
    
import eu.etaxonomy.cdm.database.ICdmDataSource;


  		




  24
  25
  
    
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;


  		




  ......




  139
  140
  
    
			UUID uuidFaunaEu = UUID.fromString(row.get(faunaEuUuid));


  		




  140
  141
  
    
			UUID uuidErms = UUID.fromString(row.get(ermsUuid));


  		




  141
  142
  
    
			taxonFaunaEu = appCtrInit.getTaxonService().find(uuidFaunaEu);


  		




  142
  
  
    
			taxonErms = appCtrInit.getTaxonService().find(uuidFaunaEu);


  		




  
  143
  
    
			taxonErms = appCtrInit.getTaxonService().find(uuidErms);


  		




  143
  144
  
    

  		




  144
  145
  
    
			if (Integer.parseInt(row.get(18)) == 1){


  		




  145
  146
  
    
				//isFaunaEu = 1 -> copy the author of Fauna Europaea to Erms


  		












  

    
      cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/merging/FaunaEuErmsMerging.java
    
  





  1
  1
  
    
package eu.etaxonomy.cdm.io.pesi.merging;


  		




  2
  2
  
    

  		




  
  3
  
    
import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;


  		




  
  4
  
    

  		




  3
  5
  
    
public class FaunaEuErmsMerging {


  		




  4
  6
  
    
	


  		




  5
  7
  
    
	private String uuidFaunaEu;


  		




  ......




  20
  22
  
    
	private String rankInFaunaEu;


  		




  21
  23
  
    
	private String rankInErms;


  		




  22
  24
  
    
	


  		




  23
  
  
    
	private String phylumInFaunaEu;


  		




  24
  
  
    
	private String phylumInErms;


  		




  
  25
  
    
	private TaxonNodeDto phylumInFaunaEu;


  		




  
  26
  
    
	private TaxonNodeDto phylumInErms;


  		




  25
  27
  
    
	


  		




  26
  28
  
    
	private String parentStringInFaunaEu;


  		




  27
  29
  
    
	private String parentStringInErms;


  		




  ......




  85
  87
  
    
		this.rankInFaunaEu = rankInFaunaEu;


  		




  86
  88
  
    
	}


  		




  87
  89
  
    

  		




  88
  
  
    
	public String getPhylumInFaunaEu() {


  		




  
  90
  
    
	public TaxonNodeDto getPhylumInFaunaEu() {


  		




  89
  91
  
    
		return phylumInFaunaEu;


  		




  90
  92
  
    
	}


  		




  91
  93
  
    

  		




  92
  
  
    
	public void setPhylumInFaunaEu(String phylumInFaunaEu) {


  		




  
  94
  
    
	public void setPhylumInFaunaEu(TaxonNodeDto phylumInFaunaEu) {


  		




  93
  95
  
    
		this.phylumInFaunaEu = phylumInFaunaEu;


  		




  94
  96
  
    
	}


  		




  95
  97
  
    

  		




  96
  
  
    
	public String getPhylumInErms() {


  		




  
  98
  
    
	public TaxonNodeDto getPhylumInErms() {


  		




  97
  99
  
    
		return phylumInErms;


  		




  98
  100
  
    
	}


  		




  99
  101
  
    

  		




  100
  
  
    
	public void setPhylumInErms(String phylumInErms) {


  		




  
  102
  
    
	public void setPhylumInErms(TaxonNodeDto phylumInErms) {


  		




  101
  103
  
    
		this.phylumInErms = phylumInErms;


  		




  102
  104
  
    
	}


  		




  103
  105
  
    

  		












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