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Revision 4772f811

Added by Andreas Müller almost 11 years ago

change return type of transformers getPresenceTerm to presenceAbsence

View differences:

cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonRelationImport.java
38 38 
import eu.etaxonomy.cdm.model.description.CommonTaxonName;
39 39 
import eu.etaxonomy.cdm.model.description.Distribution;
40 40 
import eu.etaxonomy.cdm.model.description.Feature;
41 
import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
41 42 
import eu.etaxonomy.cdm.model.description.PresenceTerm;
42 43 
import eu.etaxonomy.cdm.model.description.TaxonDescription;
43 44 
import eu.etaxonomy.cdm.model.description.TextData;
......
68 69 
public class CentralAfricaFernsTaxonRelationImport  extends CentralAfricaFernsImportBase<TaxonBase> implements IMappingImport<TaxonBase, CentralAfricaFernsImportState>{
69 70 
	private static final Logger logger = Logger.getLogger(CentralAfricaFernsTaxonRelationImport.class);
70 71
71 
	private DbImportMapping mapping;
72 
	private DbImportMapping<?,?> mapping;
72 73
73 74
74 75 
	private static final String pluralString = "taxon relations";
75 76 
	private static final String dbTableName = "[African pteridophytes]";
76 
	private static final Class cdmTargetClass = TaxonBase.class;
77 
	private static final Class<?> cdmTargetClass = TaxonBase.class;
77 78 

  		




  78
  79
  
    
	private Map<String, UUID> nameCacheTaxonMap = new HashMap<String, UUID>();


  		




  79
  80
  
    
	private Map<String, UUID> titleCacheTaxonMap = new HashMap<String, UUID>();


  		




  ......




  101
  102
  
    
	 * @see eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.CentralAfricaFernsImportBase#getMapping()


  		




  102
  103
  
    
	 */


  		




  103
  104
  
    
	@Override


  		




  104
  
  
    
	protected DbImportMapping getMapping() {


  		




  
  105
  
    
	protected DbImportMapping<?,?> getMapping() {


  		




  105
  106
  
    
		if (mapping == null){


  		




  106
  107
  
    
			mapping = new DbImportMapping();


  		




  107
  108
  
    
			


  		




  ......




  150
  151
  
    
		


  		




  151
  152
  
    
		List<Taxon> taxonList = (List)getTaxonService().list(Taxon.class, null, null, null, propPath );


  		




  152
  153
  
    
		for (Taxon taxon : taxonList){


  		




  153
  
  
    
			NonViralName nvn = CdmBase.deproxy(taxon.getName(), NonViralName.class);


  		




  
  154
  
    
			NonViralName<?> nvn = CdmBase.deproxy(taxon.getName(), NonViralName.class);


  		




  154
  155
  
    
			UUID uuid = taxon.getUuid();


  		




  155
  156
  
    
			String nameCache = nvn.getNameCache();


  		




  156
  157
  
    
			String titleCache = nvn.getTitleCache();


  		




  ......




  164
  165
  
    
	 */


  		




  165
  166
  
    
	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {


  		




  166
  167
  
    
		String nameSpace;


  		




  167
  
  
    
		Class cdmClass;


  		




  
  168
  
    
		Class<?> cdmClass;


  		




  168
  169
  
    
		Set<String> idSet;


  		




  169
  170
  
    
		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();


  		




  170
  171
  
    
		


  		




  ......




  203
  204
  
    
	 */


  		




  204
  205
  
    
	@Override


  		




  205
  206
  
    
	public TaxonBase createObject(ResultSet rs, CentralAfricaFernsImportState state) throws SQLException {


  		




  206
  
  
    
		TaxonBase result = null;


  		




  
  207
  
    
		TaxonBase<?> result = null;


  		




  207
  208
  
    
		try {


  		




  208
  209
  
    
			String status = rs.getString("Current/Synonym");


  		




  209
  210
  
    
			String taxonNumber = rs.getString("Taxon number");


  		




  ......




  267
  268
  
    
			logger.warn ("Synonym ("+synonymId+")not found.");


  		




  268
  269
  
    
			return null;


  		




  269
  270
  
    
		}


  		




  270
  
  
    
		TaxonBase taxonBase = CdmBase.deproxy(state.getRelatedObject(TAXON_NAMESPACE, accTaxonId), TaxonBase.class);


  		




  
  271
  
    
		TaxonBase<?> taxonBase = CdmBase.deproxy(state.getRelatedObject(TAXON_NAMESPACE, accTaxonId), TaxonBase.class);


  		




  271
  272
  
    
			


  		




  272
  273
  
    
		if (taxonBase != null){


  		




  273
  274
  
    
			if (taxonBase.isInstanceOf(Taxon.class)){


  		




  ......




  410
  411
  
    
	 * @param constructedHigherTaxon


  		




  411
  412
  
    
	 */


  		




  412
  413
  
    
	private Taxon mergeExistingAndConstructedTaxon(CentralAfricaFernsImportState state, Taxon existingTaxon, Taxon constructedTaxon) {


  		




  413
  
  
    
		NonViralName constructedName = CdmBase.deproxy(constructedTaxon.getName(), NonViralName.class);


  		




  414
  
  
    
		NonViralName existingName = CdmBase.deproxy(existingTaxon.getName(), NonViralName.class);


  		




  
  414
  
    
		NonViralName<?> constructedName = CdmBase.deproxy(constructedTaxon.getName(), NonViralName.class);


  		




  
  415
  
    
		NonViralName<?> existingName = CdmBase.deproxy(existingTaxon.getName(), NonViralName.class);


  		




  415
  416
  
    
		if (constructedName.hasAuthors()){


  		




  416
  417
  
    
			if (! existingName.hasAuthors()){


  		




  417
  418
  
    
				logger.warn(state.getTaxonNumber() + " - Constrcucted name ("+constructedName.getTitleCache()+") has authors but existing name ("+existingName.getTitleCache()+") has no authors");


  		




  ......




  704
  705
  
    
		


  		




  705
  706
  
    
		//persist


  		




  706
  707
  
    
//		Reference citation = state.getConfig().getSourceReference(); //throws nonUniqueObject exception


  		




  707
  
  
    
		Reference citation = null;  


  		




  
  708
  
    
		Reference<?> citation = null;  


  		




  708
  709
  
    
		String id = state.getTaxonNumber() + "-" + constructedName.getRank().getTitleCache();


  		




  709
  710
  
    
		addOriginalSource(constructedName, id, NAME_NAMESPACE, citation);


  		




  710
  711
  
    
		addOriginalSource(constructedHigherTaxon, id, TAXON_NAMESPACE, citation);


  		




  ......




  932
  933
  
    
			String province = rs.getString("Distribution - Province");


  		




  933
  934
  
    
			String distributionDetailed = rs.getString("Distribution - detailed");


  		




  934
  935
  
    
			if (taxonBase != null){


  		




  935
  
  
    
				TaxonNameBase nameUsedInSource = taxonBase.getName();


  		




  
  936
  
    
				TaxonNameBase<?,?> nameUsedInSource = taxonBase.getName();


  		




  936
  937
  
    
				Taxon taxon = getAcceptedTaxon(taxonBase);


  		




  937
  938
  
    
				if (taxon != null){


  		




  938
  939
  
    
				


  		




  ......




  1038
  1039
  
    
	private void makeSingleCountry(CentralAfricaFernsImportState state, String taxonNumber, Taxon taxon, TaxonNameBase nameUsedInSource, String country) throws UndefinedTransformerMethodException {


  		




  1039
  1040
  
    
		boolean areaDoubtful = false;


  		




  1040
  1041
  
    
		Distribution distribution = Distribution.NewInstance(null, PresenceTerm.PRESENT());


  		




  1041
  
  
    
		Reference sourceReference = this.sourceReference;


  		




  
  1042
  
    
		Reference<?> sourceReference = this.sourceReference;


  		




  1042
  1043
  
    
		distribution.addSource(taxonNumber, "Distribution_Country", sourceReference, null, nameUsedInSource, null);


  		




  1043
  1044
  
    
		NamedArea area = null;


  		




  1044
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		//empty


  		




  ......




  1115
  1116
  
    
	 * @param state


  		




  1116
  1117
  
    
	 * @return


  		




  1117
  1118
  
    
	 */


  		




  1118
  
  
    
	Reference sourceReference = null;


  		




  1119
  
  
    
	private Reference getFernsSourceReference(CentralAfricaFernsImportState state) {


  		




  
  1119
  
    
	private Reference<?> sourceReference = null;


  		




  
  1120
  
    
	private Reference<?> getFernsSourceReference(CentralAfricaFernsImportState state) {


  		




  1120
  1121
  
    
//		if (sourceReference == null || true){


  		




  1121
  
  
    
			Reference tmpReference = state.getConfig().getSourceReference();


  		




  
  1122
  
    
			Reference<?> tmpReference = state.getConfig().getSourceReference();


  		




  1122
  1123
  
    
			sourceReference = getReferenceService().find(tmpReference.getUuid());


  		




  1123
  1124
  
    
//		}


  		




  1124
  1125
  
    
		return sourceReference;


  		




  1125
  1126
  
    
	}


  		




  1126
  1127
  
    

  		




  1127
  1128
  
    

  		




  1128
  
  
    
	private String makeCountryBrackets(CentralAfricaFernsImportState state, String taxonNumber, Taxon taxon, TaxonNameBase nameUsedInSource, String country) {


  		




  
  1129
  
    
	private String makeCountryBrackets(CentralAfricaFernsImportState state, String taxonNumber, Taxon taxon, TaxonNameBase<?,?> nameUsedInSource, String country) {


  		




  1129
  1130
  
    
		String[] split = (country + " ").split("\\(.*\\)");


  		




  1130
  1131
  
    
		if (split.length == 2){


  		




  1131
  1132
  
    
			String bracket = country.substring(split[0].length()+1, country.indexOf(")"));


  		




  ......




  1140
  1141
  
    
	}


  		




  1141
  1142
  
    

  		




  1142
  1143
  
    
	private String makeCountryStatus(CentralAfricaFernsImportState state, String country, Distribution distribution) throws UndefinedTransformerMethodException {


  		




  1143
  
  
    
		PresenceTerm status = null;


  		




  
  1144
  
    
		PresenceAbsenceTermBase<?> status = null;


  		




  1144
  1145
  
    
		String[] split = country.split(" - ");


  		




  1145
  1146
  
    
		


  		




  1146
  1147
  
    
		if (split.length == 2){


  		




  ......




  1196
  1197
  
    
	 * @param existingHigherTaxon


  		




  1197
  1198
  
    
	 */


  		




  1198
  1199
  
    
	private boolean mergeAuthors_old(Taxon higherTaxon, Taxon existingHigherTaxon) {


  		




  1199
  
  
    
		NonViralName existingName = CdmBase.deproxy(higherTaxon.getName(), NonViralName.class);


  		




  1200
  
  
    
		NonViralName newName = CdmBase.deproxy(existingHigherTaxon.getName(), NonViralName.class);


  		




  
  1200
  
    
		NonViralName<?> existingName = CdmBase.deproxy(higherTaxon.getName(), NonViralName.class);


  		




  
  1201
  
    
		NonViralName<?> newName = CdmBase.deproxy(existingHigherTaxon.getName(), NonViralName.class);


  		




  1201
  1202
  
    
		if (existingName == newName){


  		




  1202
  1203
  
    
			return true;


  		




  1203
  1204
  
    
		}


  		












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