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Revision a2a0c1de

Added by Andreas Müller over 4 years ago

ref #2717 some fixes E+M Pesi export

View differences:

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiDescriptionExport.java
13 13 
import java.sql.SQLException;
14 14 
import java.sql.Types;
15 15 
import java.util.Arrays;
16 
import java.util.EnumSet;
16 17 
import java.util.HashSet;
17 18 
import java.util.List;
18 19 
import java.util.Map;
......
34 35 
import eu.etaxonomy.cdm.io.common.mapping.out.DbDistributionStatusMapper;
35 36 
import eu.etaxonomy.cdm.io.common.mapping.out.DbExportIgnoreMapper;
36 37 
import eu.etaxonomy.cdm.io.common.mapping.out.DbLanguageMapper;
38 
import eu.etaxonomy.cdm.io.common.mapping.out.DbNullMapper;
37 39 
import eu.etaxonomy.cdm.io.common.mapping.out.DbObjectMapper;
38 40 
import eu.etaxonomy.cdm.io.common.mapping.out.DbOriginalNameMapper;
39 41 
import eu.etaxonomy.cdm.io.common.mapping.out.DbSimpleFilterMapper;
......
46 48 
import eu.etaxonomy.cdm.model.common.ExtensionType;
47 49 
import eu.etaxonomy.cdm.model.common.Language;
48 50 
import eu.etaxonomy.cdm.model.common.LanguageString;
49 
import eu.etaxonomy.cdm.model.common.Marker;
50 
import eu.etaxonomy.cdm.model.common.MarkerType;
51 51 
import eu.etaxonomy.cdm.model.description.CommonTaxonName;
52 52 
import eu.etaxonomy.cdm.model.description.DescriptionBase;
53 53 
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
......
62 62 
import eu.etaxonomy.cdm.model.media.MediaRepresentation;
63 63 
import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
64 64 
import eu.etaxonomy.cdm.model.name.TaxonName;
65 
import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
65 66 
import eu.etaxonomy.cdm.model.taxon.Taxon;
66 67 
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
67 68 
import eu.etaxonomy.cdm.profiler.ProfilerController;
......
98 99 
	//debugging
99 100 
	private static int countDescriptions;
100 101 
	private static int countTaxa;
101 
	private static int countDistribution;
102 
	private static int countDistributionFiltered;
102 103 
	private static int countAdditionalSources;
103 104 
	private static int countImages;
104 105 
	private static int countNotes;
......
229 230 
		logger.info("Partition: " + partitionCount);
230 231 
		logger.info("Taxa: " + countTaxa);
231 232 
		logger.info("Desc: " + countDescriptions);
232 
		logger.info("Distr: " + countDistribution);
233 
		logger.info("Occur: " + countOccurrence);
233 
		logger.info("Distr: " + countOccurrence);
234 
		logger.info("Distr(Pesi): " + countDistributionFiltered);
234 235 
		logger.info("Commons: " + countCommonName);
235 236 
		logger.info("AddSrc: " + countAdditionalSources);
236 237 
		logger.info("Images: " + countImages);
......
305 306 
		logger.info("Partition: " + partitionCount);
306 307 
		logger.info("Taxa: " + countTaxa);
307 308 
		logger.info("Desc: " + countDescriptions);
308 
		logger.info("Distr: " + countDistribution);
309 309 
		logger.info("Occur: " + countOccurrence);
310 
		logger.info("Distr(Pesi): " + countDistributionFiltered);
310 311 
		logger.info("Commons: " + countCommonName);
311 312 
		logger.info("AddSrc: " + countAdditionalSources);
312 313 
		logger.info("Images: " + countImages);
......
364 365 
			}else if (isOccurrence(element)){
365 366 
				countOccurrence++;
366 367 
				Distribution distribution = CdmBase.deproxy(element, Distribution.class);
367 
				MarkerType markerType = getUuidMarkerType(PesiTransformer.uuidMarkerTypeHasNoLastAction, state);
368 
				distribution.addMarker(Marker.NewInstance(markerType, true));
368 
//				MarkerType markerType = getUuidMarkerType(PesiTransformer.uuidMarkerTypeHasNoLastAction, state);
369 
//				distribution.addMarker(Marker.NewInstance(markerType, true));
369 370 
				if (!isPesiDistribution(state, distribution)){
370 371 
				    logger.debug("Distribution is not PESI distribution: " + distribution.toString());
371 372 
				}else{
372 
					countDistribution++;
373 
					countDistributionFiltered++;
373 374 
					try{
374 375 
					    success &=occurrenceMapping.invoke(distribution);
375 376 
					}catch(Exception e){
......
872 873 
		//TODO
873 874 
		mapping.addMapper(MethodMapper.NewInstance("Note_2", this, standardMethodParameter));
874 875 
		mapping.addMapper(MethodMapper.NewInstance("NoteCategoryFk", this, standardMethodParameter ));
875 

  		




  876
  876
  
    
		mapping.addMapper(MethodMapper.NewInstance("NoteCategoryCache", this, standardMethodParameter, PesiExportState.class ));


  		




  
  877
  
    

  		




  877
  878
  
    
		mapping.addMapper(MethodMapper.NewInstance("LanguageFk", this));


  		




  878
  879
  
    
		mapping.addMapper(MethodMapper.NewInstance("LanguageCache", this, standardMethodParameter, PesiExportState.class));


  		




  879
  880
  
    

  		




  880
  881
  
    
//		mapping.addMapper(MethodMapper.NewInstance("Region", this));


  		




  881
  882
  
    
		mapping.addMapper(DbDescriptionElementTaxonMapper.NewInstance("taxonFk"));


  		




  
  883
  
    

  		




  882
  884
  
    
		mapping.addMapper(ExpertsAndLastActionMapper.NewInstance());


  		




  
  885
  
    

  		




  883
  886
  
    
		mapping.addCollectionMapping(getNoteSourceMapping());


  		




  884
  887
  
    
		return mapping;


  		




  885
  888
  
    
	}


  		




  ......




  892
  895
  
    
        CollectionExportMapping<PesiExportState, PesiExportConfigurator, PesiTransformer> mapping


  		




  893
  896
  
    
                = CollectionExportMapping.NewInstance(tableName, collectionAttribute, parentMapper);


  		




  894
  897
  
    
		mapping.addMapper(DbSimpleFilterMapper.NewSingleNullAttributeInstance("idInSource", "Sources with idInSource currently handle data lineage"));


  		




  895
  
  
    
		mapping.addMapper(DbObjectMapper.NewInstance("Citation", "SourceFk"));


  		




  
  898
  
    
		mapping.addMapper(DbObjectMapper.NewNotNullInstance("Citation", "SourceFk"));


  		




  896
  899
  
    
		mapping.addMapper(DbObjectMapper.NewInstance("Citation", "SourceNameCache", IS_CACHE));


  		




  897
  900
  
    
		mapping.addMapper(DbStringMapper.NewInstance("CitationMicroReference", "SourceDetail"));


  		




  898
  901
  
    
		return mapping;


  		




  ......




  915
  918
  
    
		mapping.addMapper(DbDistributionStatusMapper.NewInstance("OccurrenceStatusCache", IS_CACHE));


  		




  916
  919
  
    

  		




  917
  920
  
    
//		Use OccurrenceSource table instead


  		




  918
  
  
    
		mapping.addMapper(DbExportIgnoreMapper.NewInstance("SourceFk", "Use OccurrenceSource table for sources instead"));


  		




  919
  
  
    
		mapping.addMapper(DbExportIgnoreMapper.NewInstance("SourceCache", "Use OccurrenceSource table for sources instead"));


  		




  
  921
  
    
		mapping.addMapper(DbNullMapper.NewIntegerInstance("SourceFk"));


  		




  
  922
  
    
		mapping.addMapper(DbNullMapper.NewStringInstance("SourceCache"));


  		




  920
  923
  
    

  		




  921
  924
  
    
		mapping.addMapper(DbAnnotationMapper.NewExludedInstance(getLastActionAnnotationTypes(), "Notes"));


  		




  922
  925
  
    
		mapping.addMapper(ExpertsAndLastActionMapper.NewInstance());


  		




  
  926
  
    

  		




  923
  927
  
    
		mapping.addCollectionMapping(getOccurrenceSourceMapping());


  		




  924
  928
  
    

  		




  925
  929
  
    
		return mapping;


  		




  ......




  934
  938
  
    
		        = CollectionExportMapping.NewInstance(tableName, collectionAttribute, parentMapper);


  		




  935
  939
  
    
		mapping.addMapper(DbSimpleFilterMapper.NewSingleNullAttributeInstance("idInSource",


  		




  936
  940
  
    
		        "Sources with idInSource currently handle data lineage"));


  		




  937
  
  
    
		mapping.addMapper(DbObjectMapper.NewInstance("Citation", "SourceFk"));


  		




  
  941
  
    
        mapping.addMapper(DbSimpleFilterMapper.NewAllowedValueInstance("idInSource",


  		




  
  942
  
    
              EnumSet.of(OriginalSourceType.PrimaryTaxonomicSource, OriginalSourceType.PrimaryMediaSource, OriginalSourceType.Aggregation),


  		




  
  943
  
    
              null, "Only primary taxonomic sources should be exported"));


  		




  
  944
  
    
		mapping.addMapper(DbObjectMapper.NewNotNullInstance("Citation", "SourceFk"));


  		




  938
  945
  
    
		mapping.addMapper(DbObjectMapper.NewInstance("Citation", "SourceNameCache", IS_CACHE));


  		




  939
  946
  
    
		mapping.addMapper(DbStringMapper.NewInstance("CitationMicroReference", "SourceDetail"));


  		




  940
  947
  
    
        mapping.addMapper(DbOriginalNameMapper.NewInstance("OldTaxonName", IS_CACHE, null));


  		




  ......




  1000
  1007
  
    
		mapping.addMapper(DbLanguageMapper.NewInstance(CommonTaxonName.class, "Language", "LanguageFk", ! IS_CACHE));


  		




  1001
  1008
  
    
		mapping.addMapper(DbLanguageMapper.NewInstance(CommonTaxonName.class, "Language", "LanguageCache", IS_CACHE));


  		




  1002
  1009
  
    

  		




  1003
  
  
    
//      Use OccurrenceSource table instead


  		




  1004
  
  
    
        mapping.addMapper(DbExportIgnoreMapper.NewInstance("SourceFk", "Use CommonNameSource table for sources instead"));


  		




  1005
  
  
    
        mapping.addMapper(DbExportIgnoreMapper.NewInstance("SourceNameCache", "Use CommonNameSource table for sources instead"));


  		




  
  1010
  
    
//      Use CommonNameSource table instead


  		




  
  1011
  
    
        mapping.addMapper(DbNullMapper.NewIntegerInstance("SourceFk"));


  		




  
  1012
  
    
        mapping.addMapper(DbNullMapper.NewStringInstance("SourceNameCache"));


  		




  1006
  1013
  
    
        //OLD


  		




  1007
  1014
  
    
//		mapping.addMapper(DbSingleSourceMapper.NewInstance("SourceFk", of ( DbSingleSourceMapper.EXCLUDE.WITH_ID) , ! IS_CACHE));


  		




  1008
  1015
  
    
//		mapping.addMapper(DbSingleSourceMapper.NewInstance("SourceNameCache", of ( DbSingleSourceMapper.EXCLUDE.WITH_ID) , IS_CACHE));


  		




  1009
  1016
  
    

  		




  1010
  
  
    
		mapping.addMapper(ExpertsAndLastActionMapper.NewInstance());


  		




  
  1017
  
    
		//no SpeciesExpertGUID and SpeciesExpertName for E+M according to SQL


  		




  
  1018
  
    
        mapping.addMapper(ExpertsAndLastActionMapper.NewInstance());


  		




  
  1019
  
    

  		




  1011
  1020
  
    
	    mapping.addCollectionMapping(getCommonNameSourceMapping());


  		




  1012
  1021
  
    
		return mapping;


  		




  1013
  1022
  
    
	}


  		












  

    
      cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiExportBase.java
    
  





  399
  399
  
    

  		




  400
  400
  
    
    private static boolean isPesiSynonym(Synonym synonym) {


  		




  401
  401
  
    
        boolean hasAcceptedPesiTaxon = false;


  		




  402
  
  
    
        hasAcceptedPesiTaxon = isPesiTaxon(synonym.getAcceptedTaxon());


  		




  403
  402
  
    

  		




  
  403
  
    
        hasAcceptedPesiTaxon = isPesiTaxon(synonym.getAcceptedTaxon());


  		




  404
  404
  
    
        if (!hasAcceptedPesiTaxon) {if (logger.isDebugEnabled()){logger.debug("Synonym has no accepted PESI taxon: " +  synonym.getUuid() + ", (" +  synonym.getTitleCache() + ")");}}


  		




  405
  
  
    
        synonym = null;


  		




  406
  
  
    
        return hasAcceptedPesiTaxon;


  		




  
  405
  
    

  		




  
  406
  
    
        return hasAcceptedPesiTaxon && synonym.isPublish();


  		




  407
  407
  
    
    }


  		




  408
  408
  
    

  		




  409
  409
  
    
    private static boolean isPesiAcceptedTaxon(boolean excludeMisappliedNames, Taxon taxon) {


  		




  410
  410
  
    
        if (! taxon.isPublish()){


  		




  411
  
  
    
        	taxon = null;


  		




  412
  411
  
    
        	return false;


  		




  413
  412
  
    
        }


  		




  414
  413
  
    
        for (Marker marker : taxon.getMarkers()){


  		




  415
  414
  
    
        	//probably not needed anymore after #1780 was fixed, also #4046 interesting


  		




  416
  415
  
    
        	if (marker.getValue() == false && marker.getMarkerType().equals(MarkerType.PUBLISH())){


  		




  417
  
  
    
        		taxon = null;


  		




  418
  416
  
    
        		return false;


  		




  419
  417
  
    
        	//probably not needed any more after #2786 was fixed


  		




  420
  418
  
    
        	}else if (marker.getValue() == true && marker.getMarkerType().getUuid().equals(BerlinModelTransformer.uuidMisappliedCommonName)){


  		




  421
  419
  
    
        		logger.warn("Misapplied common name still exists");


  		




  422
  
  
    
        		taxon = null;


  		




  423
  420
  
    
        		return false;


  		




  424
  421
  
    
        	}


  		




  425
  422
  
    
        }


  		




  ......




  428
  425
  
    
        if (! taxon.isMisapplication()){


  		




  429
  426
  
    
        	for (Marker marker : taxon.getMarkers()){


  		




  430
  427
  
    
        		if (marker.getValue() == false && marker.getMarkerType().equals(MarkerType.PUBLISH())){


  		




  431
  
  
    
        			taxon = null;


  		




  432
  428
  
    
        			return false;


  		




  433
  429
  
    
        		}


  		




  434
  430
  
    
        	}


  		




  ......




  436
  432
  
    
        //handle misapplied names


  		




  437
  433
  
    
        }else{


  		




  438
  434
  
    
        	if (excludeMisappliedNames){


  		




  439
  
  
    
        		taxon = null;


  		




  440
  435
  
    
        		return false;


  		




  441
  436
  
    
        	}


  		




  442
  437
  
    
        	for (Marker marker : taxon.getMarkers()){


  		




  443
  438
  
    
        		//probably not needed any more after #2786 was fixed


  		




  444
  439
  
    
        		if (marker.getValue() == true && marker.getMarkerType().getUuid().equals(BerlinModelTransformer.uuidMisappliedCommonName)){


  		




  445
  440
  
    
        			logger.warn("Misapplied common name still exists");


  		




  446
  
  
    
        			taxon = null;


  		




  447
  441
  
    
        			return false;


  		




  448
  442
  
    
        		}


  		




  449
  443
  
    
        	}


  		




  450
  444
  
    
        	for (TaxonRelationship taxRel : taxon.getRelationsFromThisTaxon()){


  		




  451
  
  
    
        		if (taxRel.getType().equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())){


  		




  
  445
  
    
        		if (taxRel.getType().isAnyMisappliedName()){


  		




  452
  446
  
    
//						logger.warn(taxRel.getUuid() + "; " + taxRel.getToTaxon().getUuid() + " + " + taxRel.getToTaxon().getTitleCache());


  		




  453
  447
  
    
        			if (isPesiTaxon(taxRel.getToTaxon(), true)){


  		




  454
  
  
    
        				taxon = null;


  		




  455
  448
  
    
        				return true;


  		




  456
  449
  
    
        			}


  		




  457
  450
  
    
        		}


  		




  458
  451
  
    
        	}


  		




  459
  452
  
    
        	if (logger.isDebugEnabled()){ logger.debug("Misapplied name has no accepted PESI taxon: " +  taxon.getUuid() + ", (" +  taxon.getTitleCache() + ")");}


  		




  460
  
  
    
        	taxon = null;


  		




  461
  453
  
    
        	return false;


  		




  462
  454
  
    
        }


  		




  463
  455
  
    
    }


  		












  

    
      cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTransformer.java
    
  





  114
  114
  
    
	private static int REF_PUBLICATION = 11;


  		




  115
  115
  
    
	public static String REF_STR_UNRESOLVED = "unresolved";


  		




  116
  116
  
    

  		




  
  117
  
    
	private static int LANG_UNKNOWN = -99;


  		




  117
  118
  
    
	private static int LANG_VALENCIAN = 65;


  		




  118
  119
  
    
	private static int LANG_HIGH_ARAGONES = 66;


  		




  119
  120
  
    
	private static int LANG_MAJORCAN = 67;


  		




  120
  121
  
    

  		




  121
  
  
    

  		




  122
  
  
    

  		




  123
  122
  
    
	// NameStatus


  		




  124
  123
  
    
    public static UUID uuidNomStatusTemporaryName = UUID.fromString("aa6ada5a-ca21-4fef-b76f-9ae237e9c4ae");


  		




  125
  124
  
    

  		




  ......




  994
  993
  
    
			else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidLt)) { return AREA_LITHUANIA; }


  		




  995
  994
  
    
			else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidLu)) { return AREA_PORTUGUESE_MAINLAND; }


  		




  996
  995
  
    
			else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidMa)) { return AREA_MOROCCO; }


  		




  997
  
  
    
			else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidMd)) { return AREA_MADEIRA; }


  		




  
  996
  
    
			else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidMd)) { return AREA_MADEIRA_ARCHIPELAGO; }


  		




  998
  997
  
    
			else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidMd_D)) { return AREA_DESERTAS; }


  		




  999
  998
  
    
			else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidMd_M)) { return AREA_MADEIRA; }


  		




  1000
  999
  
    
			else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidMd_P)) { return AREA_PORTO_SANTO; }


  		




  ......




  1326
  1325
  
    
		}else if (language.getUuid().equals(BerlinModelTransformer.uuidLangValencian)){return LANG_VALENCIAN;


  		




  1327
  1326
  
    
        }else if (language.getUuid().equals(BerlinModelTransformer.uuidLangHighAragonese)){return LANG_HIGH_ARAGONES;


  		




  1328
  1327
  
    
        }else if (language.getUuid().equals(BerlinModelTransformer.uuidLangMajorcan)){return LANG_MAJORCAN;


  		




  1329
  
  
    
		} else {


  		




  
  1328
  
    
        //some common names from ILDIS have no defined language


  		




  
  1329
  
    
        }else if (language.equals(Language.UNKNOWN_LANGUAGE())){return LANG_UNKNOWN;


  		




  
  1330
  
    
        } else {


  		




  1330
  1331
  
    
			logger.warn("Unknown Language: " + language.getTitleCache());


  		




  1331
  1332
  
    
			return null;


  		




  1332
  1333
  
    
		}


  		












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