Project

General

Profile

« Previous | Next » 

Revision c167aac2

Added by Andreas Kohlbecker over 6 years ago

ref #6026 importing Basionyms

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/app/iapt/IAPTActivator.java
40 40 
    public static final String DATA_ENCODING_PROBLEMS = "encoding-problems.xls";
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 
    public static final String DATA_FILE = DATA_TYPE_LEG_100;
43 
    public static final String DATA_FILE = DATA_FILE_0_100;
44 44 

  		




  45
  45
  
    
    //database validation status (create, update, validate ...)


  		




  46
  46
  
    
    static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;


  		












  

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





  176
  176
  
    
        String notesTxt = getValue(record, NOTESTXT, true);


  		




  177
  177
  
    
        String caveats = getValue(record, CAVEATS, true);


  		




  178
  178
  
    
        String fullSynSubstStr = getValue(record, FULLSYNSUBST, true);


  		




  
  179
  
    
        String fullBasionymStr = getValue(record, FULLBASIONYM, true);


  		




  
  180
  
    
        String basionymNameStr = getValue(record, FULLBASIONYM, true);


  		




  179
  181
  
    
        String synSubstStr = getValue(record, SYNSUBSTSTR, true);


  		




  180
  182
  
    
        String typeStr = getValue(record, TYPE, true);


  		




  181
  183
  
    

  		




  ......




  226
  228
  
    
            caveats = caveats.replace("Caveats: ", "").trim();


  		




  227
  229
  
    
            taxonName.addAnnotation(Annotation.NewInstance(caveats, annotationTypeCaveats(), Language.DEFAULT()));


  		




  228
  230
  
    
        }


  		




  229
  
  
    
        //


  		




  
  231
  
    

  		




  
  232
  
    
        getNameService().save(taxonName);


  		




  230
  233
  
    

  		




  231
  234
  
    
        // Namerelations


  		




  232
  235
  
    
        if(!StringUtils.isEmpty(authorsSpelling)){


  		




  ......




  265
  268
  
    
        Reference sec = state.getConfig().getSecReference();


  		




  266
  269
  
    
        Taxon taxon = Taxon.NewInstance(taxonName, sec);


  		




  267
  270
  
    

  		




  
  271
  
    
        // Basionym


  		




  
  272
  
    
        if(fullBasionymStr != null){


  		




  
  273
  
    
            fullBasionymStr = fullBasionymStr.replaceAll("^\\w*:\\s", ""); // Strip off the leading 'Basionym: "


  		




  
  274
  
    
            BotanicalName basionym = makeBotanicalName(state, regNumber, fullBasionymStr, basionymNameStr, null, null);


  		




  
  275
  
    
            getNameService().save(basionym);


  		




  
  276
  
    
            taxonName.addBasionym(basionym);


  		




  
  277
  
    

  		




  
  278
  
    
            Synonym syn = Synonym.NewInstance(basionym, sec);


  		




  
  279
  
    
            taxon.addSynonym(syn, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF());


  		




  
  280
  
    
            getTaxonService().save(syn);


  		




  
  281
  
    
        }


  		




  
  282
  
    

  		




  268
  283
  
    
        // Markers


  		




  269
  284
  
    
        if(isFossil){


  		




  270
  285
  
    
            taxon.addMarker(Marker.NewInstance(markerTypeFossil(), true));


  		




  ......




  654
  669
  
    
        if(titleCacheStr.endsWith(ANNOTATION_MARKER_STRING) || (authorStr != null && authorStr.endsWith(ANNOTATION_MARKER_STRING))){


  		




  655
  670
  
    
            nameAnnotations.put("Author abbreviation not checked.", AnnotationType.EDITORIAL());


  		




  656
  671
  
    
            titleCacheStr = titleCacheStr.replace(ANNOTATION_MARKER_STRING, "").trim();


  		




  657
  
  
    
            authorStr = authorStr.replace(ANNOTATION_MARKER_STRING, "").trim();


  		




  
  672
  
    
            if(authorStr != null) {


  		




  
  673
  
    
                authorStr = authorStr.replace(ANNOTATION_MARKER_STRING, "").trim();


  		




  
  674
  
    
            }


  		




  658
  675
  
    
        }


  		




  659
  676
  
    

  		




  660
  677
  
    
        // parse the full taxon name


  		












Also available in:  Unified diff