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Revision 495cebda

Added by Andreas Müller about 11 years ago

updates to globis import

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisCurrentSpeciesImport.java
29 29 
import eu.etaxonomy.cdm.model.description.Distribution;
30 30 
import eu.etaxonomy.cdm.model.description.PresenceTerm;
31 31 
import eu.etaxonomy.cdm.model.description.TaxonDescription;
32 
import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
32 
import eu.etaxonomy.cdm.model.location.NamedArea;
33 33 
import eu.etaxonomy.cdm.model.name.Rank;
34 34 
import eu.etaxonomy.cdm.model.name.ZoologicalName;
35 35 
import eu.etaxonomy.cdm.model.reference.Reference;
......
116 116
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        		Integer taxonId = rs.getInt("IDcurrentspec");
118 118
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        		//String dtSpcJahr -> ignore !
121 120 
        		//empty: fiSpcLiteratur
122 121
......
134 133 
					boolean hasNewParent = false; //true if any parent is new
135 134
136 135 
					//species
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					Taxon species = createObject(rs, state);
136 
					Taxon species = createObject(rs, state, taxonId);
138 137
139 138
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					String familyStr = rs.getString("dtSpcFamakt");
......
142 141 
					String tribeStr = rs.getString("dtSpcTribakt");
143 142
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					//family
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					Taxon family = getTaxon(state, rs, familyStr, null, Rank.FAMILY(), null, taxonMap);
144 
					Taxon family = getTaxon(state, rs, familyStr, null, Rank.FAMILY(), null, taxonMap, taxonId);
146 145
147 146 
					//subfamily
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					Taxon subFamily = getTaxon(state, rs, subFamilyStr, null, Rank.SUBFAMILY(), null, taxonMap);
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					Taxon subFamily = getTaxon(state, rs, subFamilyStr, null, Rank.SUBFAMILY(), null, taxonMap, taxonId);
149 148 
					Taxon subFamilyParent = getParent(subFamily, classification);
150 149 
					if (subFamilyParent != null){
151 150 
						if (! compareTaxa(family, subFamilyParent)){
......
157 156 
					nextHigherTaxon = subFamily;
158 157
159 158 
					//tribe
160 
					Taxon tribe = getTaxon(state, rs, tribeStr, null, Rank.TRIBE(), null, taxonMap);
159 
					Taxon tribe = getTaxon(state, rs, tribeStr, null, Rank.TRIBE(), null, taxonMap, taxonId);
161 160 
					if (tribe != null){
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						Taxon tribeParent = getParent(tribe, classification);
163 162 
						if (tribeParent != null){
......
174 173 
					//genus
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					String genusStr = rs.getString("dtSpcGenusakt");
176 175 
					String genusAuthorStr = rs.getString("dtSpcGenusaktauthor");
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					Taxon genus = getTaxon(state, rs, genusStr, null, Rank.GENUS(), genusAuthorStr, taxonMap);
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					Taxon genus = getTaxon(state, rs, genusStr, null, Rank.GENUS(), genusAuthorStr, taxonMap, taxonId);
178 177 
					Taxon genusParent = getParent(genus, classification);
179 178
180 179 
					if (genusParent != null){
......
191 190 
					String subGenusAuthorStr = rs.getString("dtSpcSubgenaktauthor");
192 191 
					boolean hasSubgenus = StringUtils.isNotBlank(subGenusStr) || StringUtils.isNotBlank(subGenusAuthorStr);
193 192 
					if (hasSubgenus){
194 
						Taxon subGenus = getTaxon(state, rs, genusStr, subGenusStr, Rank.SUBGENUS(), subGenusAuthorStr, taxonMap);
193 
						Taxon subGenus = getTaxon(state, rs, genusStr, subGenusStr, Rank.SUBGENUS(), subGenusAuthorStr, taxonMap, taxonId);
195 194 
						classification.addParentChild(nextHigherTaxon, subGenus, sourceRef, null);
196 195 
						nextHigherTaxon = subGenus;
197 196 
					}
......
256 255
257 256 
			countryStr = normalizeCountry(countryStr);
258 257
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			WaterbodyOrCountry country = getCountry(state, countryStr);
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			NamedArea country = getCountry(state, countryStr);
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261 260 
			PresenceTerm status;
262 261 
			if (isDoubtful){
......
348 347 

  		




  349
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  350
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  351
  
  
    
	private Taxon getTaxon(GlobisImportState state, ResultSet rs, String uninomial, String infraGenericEpi, Rank rank, String author, Map<String, Taxon> taxonMap) {


  		




  
  350
  
    
	private Taxon getTaxon(GlobisImportState state, ResultSet rs, String uninomial, String infraGenericEpi, Rank rank, String author, Map<String, Taxon> taxonMap, Integer taxonId) {


  		




  352
  351
  
    
		if (isBlank(uninomial)){


  		




  353
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			return null;


  		




  354
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		}


  		




  ......




  366
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			taxon = Taxon.NewInstance(name, state.getTransactionalSourceReference());


  		




  367
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  368
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			taxonMap.put(key, taxon);


  		




  369
  
  
    
			handleAuthorAndYear(author, name);


  		




  
  368
  
    
			handleAuthorAndYear(author, name, taxonId);


  		




  370
  369
  
    
			getTaxonService().save(taxon);


  		




  371
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		}


  		




  372
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  ......




  392
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	/* (non-Javadoc)


  		




  393
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	 * @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet, eu.etaxonomy.cdm.io.common.ImportStateBase)


  		




  394
  393
  
    
	 */


  		




  395
  
  
    
	public Taxon createObject(ResultSet rs, GlobisImportState state)


  		




  
  394
  
    
	public Taxon createObject(ResultSet rs, GlobisImportState state, Integer taxonId)


  		




  396
  395
  
    
			throws SQLException {


  		




  397
  396
  
    
		String speciesEpi = rs.getString("dtSpcSpcakt");


  		




  398
  397
  
    
		String subGenusEpi = rs.getString("dtSpcSubgenakt");


  		




  ......




  406
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			zooName.setInfraGenericEpithet(subGenusEpi);


  		




  407
  406
  
    
		}


  		




  408
  407
  
    
		zooName.setGenusOrUninomial(genusEpi);


  		




  409
  
  
    
		handleAuthorAndYear(author, zooName);


  		




  
  408
  
    
		handleAuthorAndYear(author, zooName, taxonId);


  		




  410
  409
  
    
		


  		




  411
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		Taxon taxon = Taxon.NewInstance(zooName, state.getTransactionalSourceReference());


  		




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