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Revision 99e92829

Added by Andreas Müller about 7 years ago

ref #6286 FloraHellenica import transactional

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaCommentsImport.java
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import org.apache.log4j.Logger;


  		




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import org.springframework.stereotype.Component;


  		




  
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import org.springframework.transaction.TransactionStatus;


  		




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import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;


  		




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import eu.etaxonomy.cdm.model.common.Language;


  		




  ......




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        return "comments";


  		




  54
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    }


  		




  55
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    private boolean isFirst = true;


  		




  
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    private TransactionStatus tx = null;


  		




  56
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    /**


  		




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     * {@inheritDoc}


  		




  58
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     */


  		




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    @Override


  		




  60
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    protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {


  		




  
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        if (isFirst){


  		




  
  65
  
    
            tx = this.startTransaction();


  		




  
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            isFirst = false;


  		




  
  67
  
    
        }


  		




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        String line = state.getCurrentLine() + ": ";


  		




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        HashMap<String, String> record = state.getOriginalRecord();


  		




  ......




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        makeComment(state, line, record, noStr);


  		




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    }


  		




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    @Override


  		




  
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    protected void secondPass(SimpleExcelTaxonImportState<CONFIG> state) {


  		




  
  85
  
    
        if (tx != null){


  		




  
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            this.commitTransaction(tx);


  		




  
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            tx = null;


  		




  
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        }


  		




  
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    }


  		




  
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    /**


  		




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     * @param state


  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaExcludedTaxonImport.java
    
  





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import org.apache.log4j.Logger;


  		




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import org.springframework.stereotype.Component;


  		




  
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import org.springframework.transaction.TransactionStatus;


  		




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import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;


  		




  20
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import eu.etaxonomy.cdm.model.name.BotanicalName;


  		




  ......




  60
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        return "excluded taxa";


  		




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    }


  		




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    private boolean isFirst = true;


  		




  
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    private TransactionStatus tx = null;


  		




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    /**


  		




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     * {@inheritDoc}


  		




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     */


  		




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    @Override


  		




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    protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {


  		




  
  71
  
    
        if (isFirst){


  		




  
  72
  
    
            tx = this.startTransaction();


  		




  
  73
  
    
            isFirst = false;


  		




  
  74
  
    
        }


  		




  68
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  69
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        String line = state.getCurrentLine() + ": ";


  		




  70
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        HashMap<String, String> record = state.getOriginalRecord();


  		




  ......




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        }


  		




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    }


  		




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    @Override


  		




  
  94
  
    
    protected void secondPass(SimpleExcelTaxonImportState<CONFIG> state) {


  		




  
  95
  
    
        if (tx != null){


  		




  
  96
  
    
            this.commitTransaction(tx);


  		




  
  97
  
    
            tx = null;


  		




  
  98
  
    
        }


  		




  
  99
  
    
    }


  		




  
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    /**


  		




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     * @param state


  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaImportBase.java
    
  





  81
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            String message = state.getCurrentLine()+  ": Accepted taxon could not be found: " + accStr;


  		




  82
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            logger.warn(message);


  		




  83
  83
  
    
            return null;


  		




  
  84
  
    
        }else{


  		




  
  85
  
    
            accTaxon = (Taxon)getTaxonService().find(accTaxon.getUuid());


  		




  84
  86
  
    
        }


  		




  85
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        return accTaxon;


  		




  86
  88
  
    
    }


  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaSynonymImport.java
    
  





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  18
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import org.apache.log4j.Logger;


  		




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import org.springframework.stereotype.Component;


  		




  
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import org.springframework.transaction.TransactionStatus;


  		




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import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;


  		




  22
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import eu.etaxonomy.cdm.model.name.INonViralName;


  		




  ......




  59
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        return "synonyms";


  		




  60
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    }


  		




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  63
  
    
    private boolean isFirst = true;


  		




  
  64
  
    
    private TransactionStatus tx = null;


  		




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    /**


  		




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     * {@inheritDoc}


  		




  64
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     */


  		




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    @Override


  		




  66
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    protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {


  		




  
  70
  
    
        if (isFirst){


  		




  
  71
  
    
            tx = this.startTransaction();


  		




  
  72
  
    
            isFirst = false;


  		




  
  73
  
    
        }


  		




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  68
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        String line = state.getCurrentLine() + ": ";


  		




  69
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        HashMap<String, String> record = state.getOriginalRecord();


  		




  ......




  80
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        getTaxonService().saveOrUpdate(relatedTaxon);


  		




  81
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    }


  		




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  90
  
    
    @Override


  		




  
  91
  
    
    protected void secondPass(SimpleExcelTaxonImportState<CONFIG> state) {


  		




  
  92
  
    
        if (tx != null){


  		




  
  93
  
    
            this.commitTransaction(tx);


  		




  
  94
  
    
            tx = null;


  		




  
  95
  
    
        }


  		




  
  96
  
    
    }


  		




  
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    /**


  		




  85
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     * @param state


  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaTaxonImport.java
    
  





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  19
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import org.apache.log4j.Logger;


  		




  20
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import org.springframework.stereotype.Component;


  		




  
  21
  
    
import org.springframework.transaction.TransactionStatus;


  		




  21
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import eu.etaxonomy.cdm.api.service.ITermService;


  		




  23
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import eu.etaxonomy.cdm.common.CdmUtils;


  		




  ......




  84
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  85
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  86
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   private  static List<String> expectedKeys= Arrays.asList(new String[]{


  		




  87
  
  
    
            "Unique ID","Group","Family","Genus","Species","Species Author","Subspecies","Subspecies Author",


  		




  
  88
  
    
            "Unique ID","uuid","Group","Family","Genus","Species","Species Author","Subspecies","Subspecies Author",


  		




  88
  89
  
    
            "IoI","NPi","SPi","Pe","StE","EC","NC","NE","NAe","WAe","Kik","KK","EAe",


  		




  89
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            STATUS,CHOROLOGICAL_CATEGOGY,LIFE_FORM,"A","C","G","H","M","P","R","W", "Taxon"


  		




  90
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    });


  		




  ......




  98
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        return "valid taxa names";


  		




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    }


  		




  100
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  102
  
    

  		




  
  103
  
    
    private boolean isFirst = true;


  		




  
  104
  
    
    private TransactionStatus tx = null;


  		




  101
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    /**


  		




  102
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     * {@inheritDoc}


  		




  103
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     */


  		




  104
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    @Override


  		




  105
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    protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {


  		




  
  110
  
    
        if (isFirst){


  		




  
  111
  
    
            tx = this.startTransaction();


  		




  
  112
  
    
            isFirst = false;


  		




  
  113
  
    
        }


  		




  106
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        initAreaVocabulary(state);


  		




  107
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        initLifeformVocabulary(state);


  		




  108
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        initHabitatVocabulary(state);


  		




  ......




  138
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        state.putTaxon(noStr, taxon);


  		




  139
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    }


  		




  140
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  150
  
    
    @Override


  		




  
  151
  
    
    protected void secondPass(SimpleExcelTaxonImportState<CONFIG> state) {


  		




  
  152
  
    
        if (tx != null){


  		




  
  153
  
    
            this.commitTransaction(tx);


  		




  
  154
  
    
            tx = null;


  		




  
  155
  
    
        }


  		




  
  156
  
    
    }


  		




  
  157
  
    

  		




  
  158
  
    

  		




  141
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    boolean hasFeatureTree = false;


  		




  142
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    /**


  		




  143
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     * @param state


  		




  ......




  373
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        String speciesAuthorStr = getValue(record, "Species Author");


  		




  374
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        String subSpeciesStr = getValue(record, "Subspecies");


  		




  375
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        String subSpeciesAuthorStr = getValue(record, "Subspecies Author");


  		




  
  394
  
    
        String uuidStr = getValue(record, "uuid");


  		




  
  395
  
    
        UUID uuid = UUID.fromString(uuidStr);


  		




  376
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        boolean isSubSpecies = isNotBlank(subSpeciesStr);


  		




  377
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        boolean isAutonym = isSubSpecies && speciesStr.equals(subSpeciesStr);


  		




  378
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        if (isSubSpecies && ! isAutonym && isBlank(subSpeciesAuthorStr)){


  		




  ......




  399
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        Taxon taxon = Taxon.NewInstance(name, getSecReference(state));


  		




  400
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        taxon.addImportSource(noStr, getWorksheetName(), getSourceCitation(state), null);


  		




  401
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//        String parentStr = isSubSpecies ? makeSpeciesKey(genusStr, speciesStr, speciesAuthorStr) : genusStr;


  		




  
  422
  
    
        taxon.setUuid(uuid);


  		




  402
  423
  
    
        String parentStr = genusStr;


  		




  403
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        boolean genusAsBefore = genusStr.equals(lastGenus);


  		




  404
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        boolean speciesAsBefore = speciesStr.equals(lastSpecies);


  		




  ......




  906
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        //FIXME


  		




  907
  928
  
    
//        addMapping(greece, xx "mex_adm0", "iso", "MEX");


  		




  908
  929
  
    

  		




  909
  
  
    
        addArea(state, "IoI", "Ionian Islands", FloraHellenicaTransformer.uuidAreaIoI);


  		




  910
  
  
    
        addArea(state, "NPi", "North Pindos", FloraHellenicaTransformer.uuidAreaNPi);


  		




  911
  
  
    
        addArea(state, "SPi", "South Pindos", FloraHellenicaTransformer.uuidAreaSPi);


  		




  912
  
  
    
        addArea(state, "Pe", "Peloponnisos", FloraHellenicaTransformer.uuidAreaPe);


  		




  913
  
  
    
        addArea(state, "StE", "Sterea Ellas", FloraHellenicaTransformer.uuidAreaStE);


  		




  914
  
  
    
        addArea(state, "EC", "East Central Greece", FloraHellenicaTransformer.uuidAreaEC);


  		




  915
  
  
    
        addArea(state, "NC", "North Central Greece", FloraHellenicaTransformer.uuidAreaNC);


  		




  916
  
  
    
        addArea(state, "NE", "North-East Greece", FloraHellenicaTransformer.uuidAreaNE);


  		




  917
  
  
    
        addArea(state, "NAe", "North Aegean islands", FloraHellenicaTransformer.uuidAreaNAe);


  		




  918
  
  
    
        addArea(state, "WAe", "West Aegean islands", FloraHellenicaTransformer.uuidAreaWAe);


  		




  919
  
  
    
        addArea(state, "Kik", "Kiklades", FloraHellenicaTransformer.uuidAreaKik);


  		




  920
  
  
    
        addArea(state, "KK", "Kriti and Karpathos", FloraHellenicaTransformer.uuidAreaKK);


  		




  921
  
  
    
        addArea(state, "EAe", "East Aegean islands", FloraHellenicaTransformer.uuidAreaEAe);


  		




  
  930
  
    
        addArea(state, "IoI", "Ionian Islands", 4, FloraHellenicaTransformer.uuidAreaIoI);


  		




  
  931
  
    
        addArea(state, "NPi", "North Pindos", 13, FloraHellenicaTransformer.uuidAreaNPi);


  		




  
  932
  
    
        addArea(state, "SPi", "South Pindos", 11, FloraHellenicaTransformer.uuidAreaSPi);


  		




  
  933
  
    
        addArea(state, "Pe", "Peloponnisos", 1, FloraHellenicaTransformer.uuidAreaPe);


  		




  
  934
  
    
        addArea(state, "StE", "Sterea Ellas", 12, FloraHellenicaTransformer.uuidAreaStE);


  		




  
  935
  
    
        addArea(state, "EC", "East Central Greece", 5, FloraHellenicaTransformer.uuidAreaEC);


  		




  
  936
  
    
        addArea(state, "NC", "North Central Greece", 2, FloraHellenicaTransformer.uuidAreaNC);


  		




  
  937
  
    
        addArea(state, "NE", "North-East Greece", 10, FloraHellenicaTransformer.uuidAreaNE);


  		




  
  938
  
    
        addArea(state, "NAe", "North Aegean islands", 7, FloraHellenicaTransformer.uuidAreaNAe);


  		




  
  939
  
    
        addArea(state, "WAe", "West Aegean islands", 9, FloraHellenicaTransformer.uuidAreaWAe);


  		




  
  940
  
    
        addArea(state, "Kik", "Kiklades", 8, FloraHellenicaTransformer.uuidAreaKik);


  		




  
  941
  
    
        addArea(state, "KK", "Kriti and Karpathos", 6, FloraHellenicaTransformer.uuidAreaKK);


  		




  
  942
  
    
        addArea(state, "EAe", "East Aegean islands", 3, FloraHellenicaTransformer.uuidAreaEAe);


  		




  922
  943
  
    

  		




  923
  944
  
    
        this.getVocabularyService().save(areasVoc);


  		




  924
  945
  
    
        return;


  		




  925
  946
  
    
    }


  		




  926
  947
  
    

  		




  927
  
  
    
    private void addArea(SimpleExcelTaxonImportState<CONFIG> state, String abbrevLabel, String areaLabel, UUID uuid) {


  		




  928
  
  
    
        addArea(state, abbrevLabel, areaLabel, uuid, areaLabel);  //short cut if label and mapping label are equal


  		




  
  948
  
    
    private void addArea(SimpleExcelTaxonImportState<CONFIG> state, String abbrevLabel, String areaLabel,


  		




  
  949
  
    
            Integer id, UUID uuid) {


  		




  
  950
  
    
        addArea(state, abbrevLabel, areaLabel, uuid, String.valueOf(id));  //short cut if label and mapping label are equal


  		




  929
  951
  
    
    }


  		




  930
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  931
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    private void addArea(SimpleExcelTaxonImportState<CONFIG> state, String abbrevLabel, String areaLabel,


  		




  ......




  939
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     * @param string


  		




  940
  962
  
    
     * @param uuidaguascalientes


  		




  941
  963
  
    
     */


  		




  942
  
  
    
    private void addArea(SimpleExcelTaxonImportState<CONFIG> state, String abbrevLabel, String areaLabel, UUID uuid, String mappingLabel, Integer id1) {


  		




  
  964
  
    
    private void addArea(SimpleExcelTaxonImportState<CONFIG> state, String abbrevLabel, String areaLabel,


  		




  
  965
  
    
            UUID uuid, String mappingLabel, Integer id1) {


  		




  943
  966
  
    
        NamedArea newArea = NamedArea.NewInstance(


  		




  944
  967
  
    
                areaLabel, areaLabel, abbrevLabel);


  		




  945
  968
  
    
        newArea.setIdInVocabulary(abbrevLabel);


  		




  ......




  948
  971
  
    
        newArea.setLevel(null);


  		




  949
  972
  
    
        newArea.setType(NamedAreaType.NATURAL_AREA());


  		




  950
  973
  
    
        areasVoc.addTerm(newArea);


  		




  951
  
  
    
        //FIXME


  		




  952
  
  
    
        if (id1 != null){


  		




  953
  
  
    
            addMapping(newArea, "mex_adm1", "id_1", String.valueOf(id1));


  		




  954
  
  
    
        }else if (mappingLabel != null){


  		




  955
  
  
    
            addMapping(newArea, "mex_adm1", "name_1", mappingLabel);


  		




  
  974
  
    
        if (mappingLabel != null){


  		




  
  975
  
    
            addMapping(newArea, "phytogeographical_regions_of_greece", "id", mappingLabel);


  		




  956
  976
  
    
        }


  		




  957
  977
  
    
    }


  		




  958
  978
  
    

  		












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