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Revision 1d5daa79

Added by Patrick Plitzner over 7 years ago

#5448 Import rank "SAM"

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java
34 34 
import eu.etaxonomy.cdm.model.common.AnnotationType;
35 35 
import eu.etaxonomy.cdm.model.common.CdmBase;
36 36 
import eu.etaxonomy.cdm.model.common.Language;
37 
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
37 38 
import eu.etaxonomy.cdm.model.description.CommonTaxonName;
38 39 
import eu.etaxonomy.cdm.model.description.TaxonDescription;
39 40 
import eu.etaxonomy.cdm.model.name.BotanicalName;
......
43 44 
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
44 45 
import eu.etaxonomy.cdm.model.name.NonViralName;
45 46 
import eu.etaxonomy.cdm.model.name.Rank;
47 
import eu.etaxonomy.cdm.model.name.RankClass;
46 48 
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
47 49 
import eu.etaxonomy.cdm.model.taxon.Synonym;
48 50 
import eu.etaxonomy.cdm.model.taxon.Taxon;
......
136 138 
        importAuthors(state, rs, name);
137 139 

  		




  138
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        //---TAXON---


  		




  139
  
  
    
        TaxonBase<?> taxonBase = importTaxon(rs, name);


  		




  
  141
  
    
        TaxonBase<?> taxonBase = importTaxon(rs, name, state);


  		




  140
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        if(taxonBase==null){


  		




  141
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            RedListUtil.logMessage(id, "Taxon for name "+name+" could not be created.", logger);


  		




  142
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            return;


  		




  ......




  189
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        }


  		




  190
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    }


  		




  191
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  192
  
  
    
    private TaxonBase<?> importTaxon(ResultSet rs, NonViralName<?> name) throws SQLException {


  		




  
  194
  
    
    private TaxonBase<?> importTaxon(ResultSet rs, NonViralName<?> name, RedListGefaesspflanzenImportState state) throws SQLException {


  		




  193
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  194
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        long id = rs.getLong(RedListUtil.NAMNR);


  		




  195
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        String taxNameString = rs.getString(RedListUtil.TAXNAME);


  		




  ......




  235
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        addAnnotation(RedListUtil.WISSK+": "+wisskString, taxonBase);


  		




  236
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  237
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        //check taxon name consistency


  		




  238
  
  
    
        checkTaxonConsistency(id, taxNameString, hybString, taxonBase);


  		




  
  240
  
    
        checkTaxonConsistency(id, taxNameString, hybString, taxonBase, state);


  		




  239
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        return taxonBase;


  		




  240
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    }


  		




  241
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  ......




  500
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        }


  		




  501
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    }


  		




  502
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  503
  
  
    
    private void checkTaxonConsistency(long id, String taxNameString, String hybString, TaxonBase<?> taxonBase) {


  		




  
  505
  
    
    private void checkTaxonConsistency(long id, String taxNameString, String hybString, TaxonBase<?> taxonBase, RedListGefaesspflanzenImportState state) {


  		




  504
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        String nameCache = HibernateProxyHelper.deproxy(taxonBase.getName(), NonViralName.class).getNameCache().trim();


  		




  505
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        taxNameString = taxNameString.trim();


  		




  506
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        taxNameString = taxNameString.replaceAll(" +", " ");


  		




  ......




  528
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        }


  		




  529
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  530
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        taxNameString = taxNameString.replace("[ranglos]", "[unranked]");


  		




  531
  
  
    
        if(taxonBase.getName().getRank()!=null && taxonBase.getName().getRank().equals(Rank.PROLES())){


  		




  532
  
  
    
            taxNameString = taxNameString.replace("proles", "prol.");


  		




  
  533
  
    
        if(taxonBase.getName().getRank()!=null){


  		




  
  534
  
    
            if(taxonBase.getName().getRank().equals(Rank.PROLES())){


  		




  
  535
  
    
                taxNameString = taxNameString.replace("proles", "prol.");


  		




  
  536
  
    
            }


  		




  
  537
  
    
            else if(taxonBase.getName().getRank().equals(state.getRank(RedListUtil.uuidRankCollectionSpecies))){


  		




  
  538
  
    
                taxNameString = taxNameString.replace("\"Sammelart\"", "\"Coll. Species\"");


  		




  
  539
  
    
            }


  		




  533
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        }


  		




  534
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        if(STRICT_TITLE_CHECK){


  		




  535
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            if(!taxNameString.trim().equals(nameCache)){


  		




  ......




  555
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                    return Rank.UNRANKED_INFRAGENERIC();


  		




  556
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                }


  		




  557
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            }


  		




  
  565
  
    
            else if(rankStr.equals("SAM")){


  		




  
  566
  
    
                return getRank(state, RedListUtil.uuidRankCollectionSpecies, "Collective Species", "Collective Species", "\"Coll. Species\"", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.SpeciesGroup);


  		




  
  567
  
    
            }


  		




  558
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            else{


  		




  559
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                rank = state.getTransformer().getRankByKey(rankStr);


  		




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            }


  		












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