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Revision 17d546a5

Added by Katja Luther over 4 years ago

ref #1445: smaller changes in activators

View differences:

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;
7 6 
import java.util.Iterator;
8 7 
import java.util.List;
9 8 
import java.util.Map;
10 9 
import java.util.Set;
11 10 
import java.util.UUID;
12 11 

  		




  13
  
  
    
import com.sun.media.jfxmedia.logging.Logger;


  		




  
  12
  
    
import org.apache.log4j.Logger;


  		




  14
  13
  
    

  		




  15
  14
  
    
import eu.etaxonomy.cdm.api.application.CdmApplicationController;


  		




  16
  15
  
    
import eu.etaxonomy.cdm.app.common.CdmDestinations;


  		




  17
  
  
    
import eu.etaxonomy.cdm.app.util.TestDatabase;


  		




  
  16
  
    
import eu.etaxonomy.cdm.app.pesi.ErmsImportActivator;


  		




  18
  17
  
    
import eu.etaxonomy.cdm.database.DbSchemaValidation;


  		




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


  		




  20
  19
  
    
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;


  		




  ......




  27
  26
  
    
import eu.etaxonomy.cdm.model.name.TaxonName;


  		




  28
  27
  
    
import eu.etaxonomy.cdm.model.reference.Reference;


  		




  29
  28
  
    
import eu.etaxonomy.cdm.model.taxon.Classification;


  		




  
  29
  
    
import eu.etaxonomy.cdm.model.taxon.Synonym;


  		




  30
  30
  
    
import eu.etaxonomy.cdm.model.taxon.Taxon;


  		




  31
  31
  
    
import eu.etaxonomy.cdm.model.taxon.TaxonBase;


  		




  32
  32
  
    
import eu.etaxonomy.cdm.model.taxon.TaxonNode;


  		




  33
  33
  
    
import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;


  		




  34
  34
  
    

  		




  35
  35
  
    
public class FaunaEuErmsFindIdenticalNamesActivator {


  		




  36
  
  
    

  		




  
  36
  
    
	private static final Logger logger = Logger.getLogger(FaunaEuErmsFindIdenticalNamesActivator.class);


  		




  37
  37
  
    
	//static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.localH2();


  		




  38
  38
  
    
	static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.cdm_test_local_faunaEu_mysql();


  		




  39
  39
  
    
	static Reference faunaSec;


  		




  ......




  83
  83
  
    
		faunaSec = appCtrFaunaEu.getReferenceService().load(UUID.fromString("6786d863-75d4-4796-b916-c1c3dff4cb70"));


  		




  84
  84
  
    
		ermsSec = appCtrFaunaEu.getReferenceService().load(UUID.fromString("7744bc26-f914-42c4-b54a-dd2a030a8bb7"));


  		




  85
  85
  
    
		Map<String, List<TaxonName>> namesOfIdenticalTaxa = appCtrFaunaEu.getTaxonService().findIdenticalTaxonNameIds(ermsSec, faunaSec, propertyPaths);


  		




  86
  
  
    
		//List<UUID> namesOfIdenticalTaxa = appCtrFaunaEu.getTaxonService().findIdenticalTaxonNameIds(propertyPaths);


  		




  87
  
  
    

  		




  88
  
  
    
		System.err.println("first name: " + namesOfIdenticalTaxa.get(0) + " " + namesOfIdenticalTaxa.size());


  		




  89
  
  
    
		//TaxonName zooName = namesOfIdenticalTaxa.get(0);


  		




  90
  
  
    
		//System.err.println(zooName + " nr of taxa " + namesOfIdenticalTaxa.size());


  		




  91
  
  
    
		//TaxonNameComparator taxComp = new TaxonNameComparator();


  		




  92
  
  
    

  		




  93
  
  
    
		//Collections.sort(namesOfIdenticalTaxa,taxComp);


  		




  94
  
  
    
		System.err.println(namesOfIdenticalTaxa.get(0) + " - " + namesOfIdenticalTaxa.get(1) + " - " + namesOfIdenticalTaxa.get(2));


  		




  
  86
  
    
			


  		




  95
  87
  
    
		List<FaunaEuErmsMerging> mergingObjects = new ArrayList<>();


  		




  96
  88
  
    
		FaunaEuErmsMerging mergeObject;


  		




  97
  89
  
    
		TaxonName faunaEuTaxName;


  		




  98
  90
  
    
		TaxonName ermsTaxName;


  		




  99
  
  
    

  		




  
  91
  
    
		System.err.println("Start creating merging objects");


  		




  100
  92
  
    
		mergingObjects= sc.createMergeObjects(namesOfIdenticalTaxa, appCtrFaunaEu);


  		




  
  93
  
    
		boolean resultOK = true;


  		




  
  94
  
    
		System.err.println("Start creating csv files");


  		




  
  95
  
    
		resultOK = resultOK && sc.writeSameNamesdifferentAuthorToCsv(mergingObjects, sFileName + "_authors.csv");


  		




  
  96
  
    
		resultOK = resultOK &&sc.writeSameNamesdifferentStatusToCsv(mergingObjects, sFileName + "_status.csv");


  		




  
  97
  
    
		resultOK = resultOK &&sc.writeSameNamesToCsVFile(mergingObjects, sFileName + "_names.csv");


  		




  
  98
  
    
		resultOK = resultOK &&sc.writeSameNamesdifferentPhylumToCsv(mergingObjects, sFileName + "_phylum.csv");


  		




  
  99
  
    
		resultOK = resultOK &&sc.writeSameNamesDifferentParentToCsv(mergingObjects, sFileName + "parent.csv");


  		




  101
  100
  
    

  		




  102
  
  
    
		sc.writeSameNamesdifferentAuthorToCsv(mergingObjects, sFileName + "_authors.csv");


  		




  103
  
  
    
		sc.writeSameNamesdifferentStatusToCsv(mergingObjects, sFileName + "_status.csv");


  		




  104
  
  
    
		sc.writeSameNamesToCsVFile(mergingObjects, sFileName + "_names.csv");


  		




  105
  
  
    
		sc.writeSameNamesdifferentPhylumToCsv(mergingObjects, sFileName + "_phylum.csv");


  		




  106
  
  
    

  		




  107
  
  
    

  		




  108
  
  
    
		System.out.println("End merging Fauna Europaea and Erms");


  		




  
  101
  
    
		System.err.println("End merging Fauna Europaea and Erms" + resultOK);


  		




  
  102
  
    
		System.exit(0);


  		




  109
  103
  
    

  		




  110
  104
  
    
	}


  		




  111
  105
  
    

  		




  ......




  157
  151
  
    
		}


  		




  158
  152
  
    
		return true;


  		




  159
  153
  
    
	}


  		




  
  154
  
    
	


  		




  
  155
  
    
	private boolean writeSameNamesDifferentParentToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){


  		




  
  156
  
    
		try


  		




  
  157
  
    
		{


  		




  
  158
  
    
		    FileWriter writer = new FileWriter(sfileName);


  		




  
  159
  
    

  		




  
  160
  
    
		    //create Header


  		




  
  161
  
    
		   String firstLine = "same names but different parent";


  		




  
  162
  
    
		   createHeader(writer, firstLine);


  		




  
  163
  
    

  		




  
  164
  
    
			//write data


  		




  
  165
  
    
			for (FaunaEuErmsMerging merging : mergingObjects){


  		




  
  166
  
    
		    	//TODO


  		




  
  167
  
    
				if ((merging.getParentStringInErms()== null )^ (merging.getParentStringInFaunaEu()== null)){


  		




  
  168
  
    
					writeCsvLine(writer, merging) ;


  		




  
  169
  
    
				}else if(!((merging.getParentStringInErms()==null) && (merging.getParentStringInFaunaEu()==null))){


  		




  
  170
  
    
					if(!merging.getParentStringInErms().equals(merging.getParentStringInFaunaEu())){


  		




  
  171
  
    
						writeCsvLine(writer, merging) ;


  		




  
  172
  
    
					}


  		




  
  173
  
    
				}


  		




  
  174
  
    
			}


  		




  
  175
  
    
			writer.flush();


  		




  
  176
  
    
			writer.close();


  		




  
  177
  
    
		}


  		




  
  178
  
    
		catch(IOException e)


  		




  
  179
  
    
		{


  		




  
  180
  
    
		 return false;


  		




  
  181
  
    
		}


  		




  
  182
  
    
		return true;


  		




  
  183
  
    
	}


  		




  160
  184
  
    

  		




  161
  185
  
    
	private boolean writeSameNamesdifferentRankToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){


  		




  162
  186
  
    
		try


  		




  ......




  264
  288
  
    
			//write data


  		




  265
  289
  
    
			for (FaunaEuErmsMerging merging : mergingObjects){


  		




  266
  290
  
    

  		




  267
  
  
    
				if (!merging.getAuthorInErms().equals(merging.getAuthorInFaunaEu())){


  		




  
  291
  
    
				if (merging.getAuthorInErms() != null && merging.getAuthorInFaunaEu() != null && !merging.getAuthorInErms().equals(merging.getAuthorInFaunaEu())){


  		




  268
  292
  
    
					 writeCsvLine(writer, merging);


  		




  
  293
  
    
				}else if ((merging.getAuthorInErms() == null && merging.getAuthorInFaunaEu() != null) || (merging.getAuthorInErms() != null && merging.getAuthorInFaunaEu() == null)) {


  		




  
  294
  
    
					writeCsvLine(writer, merging);


  		




  269
  295
  
    
				}


  		




  270
  296
  
    
			}


  		




  271
  297
  
    

  		




  ......




  298
  324
  
    
			writer.append("synonym");


  		




  299
  325
  
    
		}


  		




  300
  326
  
    
		writer.append(';');


  		




  301
  
  
    
		writer.append(merging.getPhylumInFaunaEu().getTaxonTitleCache());


  		




  
  327
  
    
		writer.append(merging.getPhylumInFaunaEu() != null? merging.getPhylumInFaunaEu().getTaxonTitleCache(): "");


  		




  302
  328
  
    
		writer.append(';');


  		




  303
  329
  
    
		writer.append(merging.getParentStringInFaunaEu());


  		




  304
  330
  
    
		writer.append(';');


  		




  ......




  322
  348
  
    
		}


  		




  323
  349
  
    

  		




  324
  350
  
    
		writer.append(';');


  		




  325
  
  
    
		writer.append(merging.getPhylumInErms().getTaxonTitleCache());


  		




  
  351
  
    
		writer.append(merging.getPhylumInErms() != null? merging.getPhylumInErms().getTaxonTitleCache():"");


  		




  326
  352
  
    
		writer.append(';');


  		




  327
  353
  
    
		writer.append(merging.getParentStringInErms());


  		




  328
  354
  
    
		writer.append(';');


  		




  ......




  332
  358
  
    

  		




  333
  359
  
    

  		




  334
  360
  
    
	private List<FaunaEuErmsMerging> createMergeObjects(Map<String,List<TaxonName>> names, CdmApplicationController appCtr){


  		




  335
  
  
    

  		




  
  361
  
    
		Classification faunaEuClassification = appCtr.getClassificationService().load(UUID.fromString("44d8605e-a7ce-41e1-bee9-99edfec01e7c"));


  		




  
  362
  
    
		Classification ermsClassification = appCtr.getClassificationService().load(UUID.fromString("6fa988a9-10b7-48b0-a370-2586fbc066eb"));


  		




  336
  363
  
    
		List<FaunaEuErmsMerging> merge = new ArrayList<>();


  		




  337
  
  
    
		TaxonName zooName, zooName2;


  		




  
  364
  
    
		


  		




  338
  365
  
    
		FaunaEuErmsMerging mergeObject;


  		




  339
  366
  
    
		String idInSource1;


  		




  340
  367
  
    
		List<TaxonName> identicalNames;


  		




  
  368
  
    
		


  		




  341
  369
  
    
		for (String nameCache: names.keySet()){


  		




  342
  370
  
    
			identicalNames = names.get(nameCache);


  		




  343
  371
  
    
			


  		




  344
  372
  
    
			mergeObject = new FaunaEuErmsMerging();


  		




  345
  
  
    
			//TODO:überprüfen, ob die beiden Namen identisch sind und aus unterschiedlichen DB kommen


  		




  346
  
  
    
			Classification faunaEuClassification = appCtr.getClassificationService().load(UUID.fromString("44d8605e-a7ce-41e1-bee9-99edfec01e7c"));


  		




  347
  
  
    
			Classification ermsClassification = appCtr.getClassificationService().load(UUID.fromString("6fa988a9-10b7-48b0-a370-2586fbc066eb"));


  		




  
  373
  
    
			


  		




  
  374
  
    
			


  		




  348
  375
  
    
			//getPhylum


  		




  349
  376
  
    
			TaxonNodeDto phylum1 = null;


  		




  350
  377
  
    
			TaxonName faunaEuName = null;


  		




  ......




  366
  393
  
    
					//TODO: find the two correct names


  		




  367
  394
  
    
				}


  		




  368
  395
  
    
			}else {


  		




  369
  
  
    
				System.err.println(nameCache + " has more than two identical namecaches");


  		




  370
  
  
    
				return null;


  		




  
  396
  
    
				logger.debug(nameCache + " has more than two identical namecaches");


  		




  
  397
  
    
				continue;


  		




  371
  398
  
    
			}


  		




  372
  399
  
    
			phylum1 = null;


  		




  373
  
  
    
			if (faunaEuName != null && !faunaEuName.getRank().isHigher(Rank.PHYLUM())){


  		




  
  400
  
    
			if (faunaEuName.getRank().equals(Rank.PHYLUM())) {


  		




  
  401
  
    
				Taxon taxon = null;


  		




  
  402
  
    
				taxon = getAcceptedTaxon(faunaEuName);


  		




  
  403
  
    
				if (taxon != null) {


  		




  
  404
  
    
					phylum1 = new TaxonNodeDto(taxon.getTaxonNode(faunaEuClassification));


  		




  
  405
  
    
				}


  		




  
  406
  
    
				


  		




  
  407
  
    
			}


  		




  
  408
  
    
			if (phylum1 == null && faunaEuName != null && !faunaEuName.getRank().isHigher(Rank.PHYLUM())){


  		




  374
  409
  
    
					phylum1 =appCtr.getTaxonNodeService().taxonNodeDtoParentRank(faunaEuClassification, Rank.PHYLUM(), faunaEuName);


  		




  375
  410
  
    
			}


  		




  376
  411
  
    

  		




  377
  412
  
    
			TaxonNodeDto phylum2 = null;


  		




  378
  
  
    
			if (ermsName != null && !ermsName.getRank().isHigher(Rank.PHYLUM())){


  		




  
  413
  
    
			if (ermsName.getRank().equals(Rank.PHYLUM())) {


  		




  
  414
  
    
				Taxon taxon = null;


  		




  
  415
  
    
				taxon = getAcceptedTaxon(ermsName);


  		




  
  416
  
    
				if (taxon != null) {


  		




  
  417
  
    
					phylum2 = new TaxonNodeDto(taxon.getTaxonNode(ermsClassification));


  		




  
  418
  
    
				}


  		




  
  419
  
    
				


  		




  
  420
  
    
			}


  		




  
  421
  
    
			if (phylum2 == null && ermsName != null && !ermsName.getRank().isHigher(Rank.PHYLUM())){


  		




  379
  422
  
    
				phylum2 = appCtr.getTaxonNodeService().taxonNodeDtoParentRank(ermsClassification, Rank.PHYLUM(), ermsName);


  		




  380
  423
  
    
			}


  		




  381
  424
  
    
			mergeObject.setPhylumInErms(phylum1);


  		




  ......




  429
  472
  
    
					String parentNameCache = parentName.getNameCache();


  		




  430
  473
  
    
					mergeObject.setParentStringInErms(parentNameCache);


  		




  431
  474
  
    
					mergeObject.setParentRankStringInErms(parentName.getRank().getLabel());


  		




  432
  
  
    
					//System.err.println("parentName: " + parentNameCache);


  		




  
  475
  
    
					


  		




  433
  476
  
    
				}


  		




  434
  477
  
    
			}else{


  		




  435
  478
  
    
				mergeObject.setStatInErms(false);


  		




  
  479
  
    
				TaxonNode parentNode = getAcceptedNode(ermsName);


  		




  
  480
  
    
				//TODO: ändern mit erweitertem Initializer..


  		




  
  481
  
    
				if (parentNode != null){


  		




  
  482
  
    
				    TaxonName parentName = HibernateProxyHelper.deproxy(parentNode.getTaxon().getName());


  		




  
  483
  
    
					String parentNameCache = parentName.getNameCache();


  		




  
  484
  
    
					mergeObject.setParentStringInErms(parentNameCache);


  		




  
  485
  
    
					mergeObject.setParentRankStringInErms(parentName.getRank().getLabel());


  		




  
  486
  
    
					


  		




  
  487
  
    
				}


  		




  436
  488
  
    
			}


  		




  437
  489
  
    
			taxa = faunaEuName.getTaxa();


  		




  438
  490
  
    
			if (!taxa.isEmpty()){


  		




  ......




  462
  514
  
    
    					String parentNameCache = parentName.getNameCache();


  		




  463
  515
  
    
    					mergeObject.setParentStringInFaunaEu(parentNameCache);


  		




  464
  516
  
    
    					mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel());


  		




  465
  
  
    
    					System.err.println("parentName: " + parentNameCache);


  		




  
  517
  
    
    					


  		




  466
  518
  
    
					}else{


  		




  467
  
  
    
						System.err.println("no zoologicalName: " + parentNode.getTaxon().getName().getTitleCache() +" . "+parentNode.getTaxon().getName().getUuid());


  		




  
  519
  
    
						logger.debug("no zoologicalName: " + parentNode.getTaxon().getName().getTitleCache() +" . "+parentNode.getTaxon().getName().getUuid());


  		




  468
  520
  
    
					}


  		




  469
  521
  
    

  		




  470
  522
  
    
				}


  		




  471
  
  
    
			}else{


  		




  472
  
  
    
				mergeObject.setStatInErms(false);


  		




  473
  
  
    
			}


  		




  474
  
  
    
			taxa = faunaEuName.getTaxa();


  		




  475
  
  
    
			if (!taxa.isEmpty()){


  		




  476
  
  
    
				mergeObject.setStatInFaunaEu(true);


  		




  477
  523
  
    
			}else{


  		




  478
  524
  
    
				mergeObject.setStatInFaunaEu(false);


  		




  479
  
  
    

  		




  
  525
  
    
				TaxonNode parentNode = getAcceptedNode(faunaEuName);


  		




  
  526
  
    
				//TODO: ändern mit erweitertem Initializer..


  		




  
  527
  
    
				if (parentNode != null){


  		




  
  528
  
    
				    TaxonName parentName = HibernateProxyHelper.deproxy(parentNode.getTaxon().getName());


  		




  
  529
  
    
					String parentNameCache = parentName.getNameCache();


  		




  
  530
  
    
					mergeObject.setParentStringInFaunaEu(parentNameCache);


  		




  
  531
  
    
					mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel());


  		




  
  532
  
    
					


  		




  
  533
  
    
				}


  		




  480
  534
  
    
			}


  		




  
  535
  
    
			


  		




  481
  536
  
    

  		




  482
  537
  
    
			mergeObject.setRankInErms(ermsName.getRank().getLabel());


  		




  483
  538
  
    
			mergeObject.setRankInFaunaEu(faunaEuName.getRank().getLabel());


  		




  ......




  513
  568
  
    
		return merge;


  		




  514
  569
  
    

  		




  515
  570
  
    
	}


  		




  
  571
  
    

  		




  
  572
  
    

  		




  
  573
  
    
	/**


  		




  
  574
  
    
	 * @param ermsName


  		




  
  575
  
    
	 * @return


  		




  
  576
  
    
	 */


  		




  
  577
  
    
	private TaxonNode getAcceptedNode(TaxonName ermsName) {


  		




  
  578
  
    
		Set<TaxonBase> taxonBases = ermsName.getTaxonBases();


  		




  
  579
  
    
		Taxon taxon = null;


  		




  
  580
  
    
		if (taxonBases != null && !taxonBases.isEmpty()) {


  		




  
  581
  
    
			TaxonBase taxonBase = taxonBases.iterator().next();


  		




  
  582
  
    
			if (taxonBase instanceof Synonym) {


  		




  
  583
  
    
				taxon = ((Synonym)taxonBase).getAcceptedTaxon();


  		




  
  584
  
    
			}


  		




  
  585
  
    
		}


  		




  
  586
  
    
		


  		




  
  587
  
    
		


  		




  
  588
  
    
		Set<TaxonNode> nodes = taxon.getTaxonNodes();


  		




  
  589
  
    
		


  		




  
  590
  
    
		TaxonNode node, parentNode = null;


  		




  
  591
  
    
		if (nodes != null && !nodes.isEmpty()) {


  		




  
  592
  
    
			parentNode = nodes.iterator().next();


  		




  
  593
  
    
		}


  		




  
  594
  
    
		return parentNode;


  		




  
  595
  
    
	}


  		




  
  596
  
    

  		




  
  597
  
    

  		




  
  598
  
    
	/**


  		




  
  599
  
    
	 * @param ermsName


  		




  
  600
  
    
	 * @param taxon


  		




  
  601
  
    
	 * @return


  		




  
  602
  
    
	 */


  		




  
  603
  
    
	private Taxon getAcceptedTaxon(TaxonName ermsName) {


  		




  
  604
  
    
		Taxon taxon = null;


  		




  
  605
  
    
		if (ermsName.getTaxa() != null && !ermsName.getTaxa().isEmpty()){


  		




  
  606
  
    
			taxon = ermsName.getTaxa().iterator().next();


  		




  
  607
  
    
			


  		




  
  608
  
    
		}else if (ermsName.getTaxonBases() != null && !ermsName.getTaxonBases().isEmpty()){


  		




  
  609
  
    
			TaxonBase taxonBase = ermsName.getTaxonBases().iterator().next();


  		




  
  610
  
    
			if (taxonBase instanceof Synonym) {


  		




  
  611
  
    
				Synonym syn = (Synonym)taxonBase;


  		




  
  612
  
    
				taxon = syn.getAcceptedTaxon();


  		




  
  613
  
    
			}


  		




  
  614
  
    
		}


  		




  
  615
  
    
		return taxon;


  		




  
  616
  
    
	}


  		




  516
  617
  
    
}


  		












  

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





  71
  71
  
    
		FaunaEuErmsMergeActivator sc = new FaunaEuErmsMergeActivator();


  		




  72
  72
  
    

  		




  73
  73
  
    
		sc.initDb(faunaEuropaeaSource);


  		




  74
  
  
    

  		




  
  74
  
    
//we also need to merge names completely identical!


  		




  75
  75
  
    
		sc.mergeAuthors();


  		




  76
  76
  
    

  		




  77
  77
  
    
		//set the ranks of Agnatha and Gnathostomata to 50 instead of 45


  		




  ......




  142
  142
  
    
			UUID uuidErms = UUID.fromString(row.get(ermsUuid));


  		




  143
  143
  
    
			taxonFaunaEu = appCtrInit.getTaxonService().find(uuidFaunaEu);


  		




  144
  144
  
    
			taxonErms = appCtrInit.getTaxonService().find(uuidErms);


  		




  145
  
  
    

  		




  
  145
  
    
// which information should be used can be found in last row -> needs to be done manually


  		




  146
  146
  
    
			if (Integer.parseInt(row.get(18)) == 1){


  		




  147
  147
  
    
				//isFaunaEu = 1 -> copy the author of Fauna Europaea to Erms


  		




  148
  148
  
    
				if (((IZoologicalName)taxonFaunaEu.getName()).getBasionymAuthorship()!= null){


  		




  ......




  219
  219
  
    
		// update nameRelationships -> if the nameRelationship does not exist, then create a new one with ermsAcc as relatedTo TaxonName


  		




  220
  220
  
    
		updateNameRelationships(ermsAccFaEuSyn);


  		




  221
  221
  
    

  		




  222
  
  
    
		//delete all synonyms of FaunaEu Syn


  		




  
  222
  
    
		//delete all synonyms of FaunaEu Syn TODO: move sources and additional informations to erms taxon


  		




  223
  223
  
    
		for (List<String> rowList: ermsAccFaEuSyn){


  		




  224
  224
  
    
			UUID faunaUUID = UUID.fromString(rowList.get(faunaEuUuid));


  		




  225
  225
  
    
			//UUID ermsUUID = UUID.fromString(rowList.get(ermsUuid));


  		




  226
  226
  
    
			Synonym syn = (Synonym)appCtrInit.getTaxonService().find(faunaUUID);


  		




  
  227
  
    
			// remove synonym from taxon then delete


  		




  227
  228
  
    
			appCtrInit.getTaxonService().deleteSynonym(syn, null);


  		




  228
  229
  
    
		}


  		




  229
  230
  
    

  		




  ......




  231
  232
  
    
	}


  		




  232
  233
  
    

  		




  233
  234
  
    
	private  void mergeErmsSynFaunaEuAcc (List<List<String>> ermsAccFaEuSyn){


  		




  234
  
  
    
		//occurence: verknüpfe statt dem Fauna Europaea Taxon das akzeptierte Taxon, des Synonyms mit der Occurence (CDM -> distribution)


  		




  235
  
  
    
		//suche distribution (über das Taxon der TaxonDescription), dessen Taxon, das entsprechende Fauna Eu Taxon ist und verkn�pfe es mit dem akzeptieren Taxon des Erms Syn


  		




  
  235
  
    
		//occurence: verkn?pfe statt dem Fauna Europaea Taxon das akzeptierte Taxon, des Synonyms mit der Occurence (CDM -> distribution)


  		




  
  236
  
    
		//suche distribution (?ber das Taxon der TaxonDescription), dessen Taxon, das entsprechende Fauna Eu Taxon ist und verkn?pfe es mit dem akzeptieren Taxon des Erms Syn


  		




  236
  237
  
    
		for (List<String> row: ermsAccFaEuSyn){


  		




  237
  238
  
    
		    Taxon taxonFaunaEu = (Taxon)appCtrInit.getTaxonService().find(UUID.fromString(row.get(faunaEuUuid)));


  		




  238
  239
  
    
			Synonym synErms = (Synonym)appCtrInit.getTaxonService().find(UUID.fromString(row.get(ermsUuid)));


  		




  ......




  284
  285
  
    
				}


  		




  285
  286
  
    

  		




  286
  287
  
    
			}


  		




  
  288
  
    
			//the fauna eu taxon should now only contain synonyms not existing in erms


  		




  287
  289
  
    
			moveFaunaEuSynonymsToErmsTaxon(taxonFaunaEu, taxonErms);


  		




  288
  290
  
    
			moveAllInformationsFromFaunaEuToErms(taxonFaunaEu, taxonErms);


  		




  289
  291
  
    
			moveOriginalDbToErmsTaxon(taxonFaunaEu, taxonErms);


  		




  ......




  302
  304
  
    
	private void updateNameRelationships(List<List<String>> ermsAccFaEuSyn){


  		




  303
  305
  
    
		//suche alle NameRelationships aus FaunaEu und Erms, wo (faunaEu)relatedFrom.name.titleCache = (erms)relatedFrom.name.titleCache und ersetze in der faunaEu Relationship den relatedTo.name durch den relatedTo.name der erms-relationship


  		




  304
  306
  
    
		//wenn es diese relationship noch nicht gibt und der typ der gleiche ist!!


  		




  305
  
  
    
		//wenn der relatedTo Name zu einem Erms Taxon und einem FaunaEu Synonym gehört


  		




  
  307
  
    
		//wenn der relatedTo Name zu einem Erms Taxon und einem FaunaEu Synonym geh?rt


  		




  306
  308
  
    

  		




  307
  309
  
    
		Synonym synFaunaEu;


  		




  308
  310
  
    
		Taxon taxonErms;


  		












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