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Revision 438dd662

Added by Andreas Kohlbecker over 7 years ago

ref #6026 speedup of import and fixing a minor bug

  • speedup by special handling for hardly to parse reference
  • minor bug during camparison of basionym names

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/app/iapt/IAPTActivator.java
41 41 
    public static final String DATA_IAPT_TYPES_100 = "iapt-types-100.xls";
42 42 
    public static final String DATA_TYPE_LEG_100 = "iapt-type-leg-100.xls";
43 43 
    public static final String DATA_NAME_TYPES = "iapt-name-types.xls";
44 
    public static final String DATA_FILE = DATA_NAME_TYPES;
44 
    public static final String DATA_SINGLE = "single.xls";
45 
    public static final String DATA_FILE = DATA_SINGLE;
45 46 

  		




  46
  47
  
    
    //database validation status (create, update, validate ...)


  		




  47
  48
  
    
    static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;


  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/io/iapt/IAPTExcelImport.java
    
  





  21
  21
  
    
import eu.etaxonomy.cdm.model.occurrence.*;


  		




  22
  22
  
    
import eu.etaxonomy.cdm.model.occurrence.Collection;


  		




  23
  23
  
    
import eu.etaxonomy.cdm.model.reference.Reference;


  		




  
  24
  
    
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;


  		




  24
  25
  
    
import eu.etaxonomy.cdm.model.reference.ReferenceType;


  		




  25
  26
  
    
import eu.etaxonomy.cdm.model.taxon.*;


  		




  26
  27
  
    
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;


  		




  ......




  167
  168
  
    
    private Rank familyIncertisSedis = null;


  		




  168
  169
  
    
    private AnnotationType annotationTypeCaveats = null;


  		




  169
  170
  
    

  		




  
  171
  
    
    private Reference bookVariedadesTradicionales = null;


  		




  
  172
  
    

  		




  170
  173
  
    
    private Taxon makeTaxon(HashMap<String, String> record, SimpleExcelTaxonImportState<CONFIG> state,


  		




  171
  174
  
    
                            TaxonNode higherTaxonNode, boolean isFossil) {


  		




  172
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  ......




  192
  195
  
    
        String nomRefIssue = null;


  		




  193
  196
  
    
        Partial pupDate = null;


  		




  194
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  198
  
    
        boolean restoreOriginalReference = false;


  		




  
  199
  
    

  		




  195
  200
  
    
        // preprocess nomRef: separate citation, reference detail, publishing date


  		




  196
  201
  
    
        if(!StringUtils.isEmpty(nomRefStr)){


  		




  197
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            nomRefStr = nomRefStr.trim();


  		




  
  203
  
    

  		




  
  204
  
    
            // handle the special case which is hard to parse:


  		




  
  205
  
    
            //


  		




  
  206
  
    
            // Las variedades tradicionales de frutales de la Cuenca del Río Segura. Catálogo Etnobotánico (1): Frutos secos, oleaginosos, frutales de hueso, almendros y frutales de pepita: 154. 1997.


  		




  
  207
  
    
            if(nomRefStr.startsWith("Las variedades tradicionales de frutales ")){


  		




  
  208
  
    

  		




  
  209
  
    
                if(bookVariedadesTradicionales == null){


  		




  
  210
  
    
                    bookVariedadesTradicionales = ReferenceFactory.newBook();


  		




  
  211
  
    
                    bookVariedadesTradicionales.setTitle("Las variedades tradicionales de frutales de la Cuenca del Río Segura. Catálogo Etnobotánico (1): Frutos secos, oleaginosos, frutales de hueso, almendros y frutales de pepita");


  		




  
  212
  
    
                    bookVariedadesTradicionales.setDatePublished(TimePeriod.NewInstance(1997));


  		




  
  213
  
    
                    getReferenceService().save(bookVariedadesTradicionales);


  		




  
  214
  
    
                }


  		




  
  215
  
    
                nomRefStr = nomRefStr.replaceAll("^.*?\\:.*?\\:", "Las variedades tradicionales:");


  		




  
  216
  
    
                restoreOriginalReference = true;


  		




  
  217
  
    
            }


  		




  
  218
  
    

  		




  198
  219
  
    
            Matcher m = nomRefTokenizeP.matcher(nomRefStr);


  		




  199
  220
  
    
            if(m.matches()){


  		




  200
  221
  
    
                nomRefTitle = m.group("title");


  		




  ......




  222
  243
  
    
                        "\n -  '" + REGISTRATION  + "': " + regStr


  		




  223
  244
  
    
                , AnnotationType.TECHNICAL(), Language.DEFAULT()));


  		




  224
  245
  
    

  		




  
  246
  
    
        if(restoreOriginalReference){


  		




  
  247
  
    
            taxonName.setNomenclaturalReference(bookVariedadesTradicionales);


  		




  
  248
  
    
        }


  		




  225
  249
  
    
        if(pupDate != null) {


  		




  226
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            taxonName.getNomenclaturalReference().setDatePublished(TimePeriod.NewInstance(pupDate));


  		




  227
  251
  
    
        }


  		




  ......




  229
  253
  
    
            ((Reference)taxonName.getNomenclaturalReference()).setVolume(nomRefIssue);


  		




  230
  254
  
    
        }


  		




  231
  255
  
    

  		




  
  256
  
    

  		




  232
  257
  
    
        if(!StringUtils.isEmpty(notesTxt)){


  		




  233
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            notesTxt = notesTxt.replace("Notes: ", "").trim();


  		




  234
  259
  
    
            taxonName.addAnnotation(Annotation.NewInstance(notesTxt, AnnotationType.EDITORIAL(), Language.DEFAULT()));


  		




  ......




  280
  305
  
    
        // Basionym


  		




  281
  306
  
    
        if(fullBasionymStr != null){


  		




  282
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            fullBasionymStr = fullBasionymStr.replaceAll("^\\w*:\\s", ""); // Strip off the leading 'Basionym: "


  		




  
  308
  
    
            basionymNameStr = basionymNameStr.replaceAll("^\\w*:\\s", ""); // Strip off the leading 'Basionym: "


  		




  283
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            BotanicalName basionym = makeBotanicalName(state, regNumber, fullBasionymStr, basionymNameStr, null, null);


  		




  284
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            getNameService().save(basionym);


  		




  285
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            taxonName.addBasionym(basionym);


  		












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