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Revision 7ec0eb3f

Added by Andreas Müller over 11 years ago

caryophyllales import final version

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/CaryoActivator.java
43 43 
//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
44 44 
//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest();
45 45
46 
	static final String classificationName = "Caryophyllales";
46 47
47 48 
	//classification
48 49 
	static final UUID classificationUuid = UUID.fromString("9edc58b5-de3b-43aa-9f31-1ede7c009c2b");
......
52 53
53 54 
	//taxa
54 55 
	static final boolean doTaxa = true;
55 
	static final boolean doDeduplicate = false;
56 
	static final boolean doDeduplicate = true;
56 57
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	private void doImport(ICdmDataSource cdmDestination){
......
64 65 
		config.setDoTaxa(doTaxa);
65 66 
		config.setDbSchemaValidation(hbm2dll);
66 67 
		config.setSourceReferenceTitle("NCU - Caryophyllales, v0.4");
68 
		config.setClassificationName(classificationName);
67 69
68 70 
		CdmDefaultImport<CaryoImportConfigurator> myImport = new CdmDefaultImport<CaryoImportConfigurator>();
69 71 

  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoTaxonImport.java
    
  





  26
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import eu.etaxonomy.cdm.model.agent.Person;


  		




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import eu.etaxonomy.cdm.model.agent.Team;


  		




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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;


  		




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


  		




  29
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import eu.etaxonomy.cdm.model.common.CdmBase;


  		




  30
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import eu.etaxonomy.cdm.model.common.Language;


  		




  31
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import eu.etaxonomy.cdm.model.common.TimePeriod;


  		




  ......




  196
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		}


  		




  197
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	}


  		




  198
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  199
  
  
    
	


  		




  200
  
  
    
	private INonViralNameParser parser = NonViralNameParserImpl.NewInstance();


  		




  201
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	private void handleBasionym(CaryoImportState state, ResultSet rs, Taxon taxon, String basioStr, Integer id) {


  		




  202
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		if (StringUtils.isNotBlank(basioStr)){


  		




  203
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			BotanicalName name = (BotanicalName) taxon.getName();


  		




  204
  
  
    
			BotanicalName basionym = BotanicalName.PARSED_NAME(basioStr);


  		




  
  203
  
    
			BotanicalName basionym = BotanicalName.PARSED_REFERENCE(basioStr);


  		




  
  204
  
    
			if (basionym.hasProblem()){


  		




  
  205
  
    
				logger.warn("Problem when parsing basionym ("+id+"): " +  basioStr);


  		




  
  206
  
    
			}


  		




  205
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			name.addBasionym(basionym);


  		




  206
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			Synonym syn = Synonym.NewInstance(basionym, state.getTransactionalSourceReference());


  		




  207
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			taxon.addSynonym(syn, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF());


  		




  ......




  216
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	private void handleTypes(CaryoImportState state, ResultSet rs, Taxon taxon, String origType, Integer id) {


  		




  217
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		NameTypeDesignation desig = NameTypeDesignation.NewInstance();


  		




  218
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		String type = origType;


  		




  219
  
  
    
		if (StringUtils.isBlank(type) ){


  		




  
  221
  
    
		if (StringUtils.isBlank(type) || "to be designated".equalsIgnoreCase(type)){


  		




  220
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			return;


  		




  221
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		}else{


  		




  222
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			BotanicalName name = (BotanicalName)taxon.getName();


  		




  ......




  229
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				if (! type.startsWith(genus.substring(0,1) + ". " )){


  		




  230
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					int i = type.indexOf(" ");


  		




  231
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					String genusOrig = type.substring(0, i);


  		




  232
  
  
    
					logger.warn("First genus letter not recognized: " + genusOrig + "-" + genus + ":"+  id);


  		




  
  234
  
    
					logger.info("First genus letter not recognized: " + genusOrig + "-" + genus + ":"+  id);


  		




  233
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					typeName.setGenusOrUninomial(genusOrig);


  		




  234
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					type = type.substring(i + 1).trim();


  		




  235
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				}else{


  		




  ......




  246
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					int posBracket = type.indexOf("(", 2);


  		




  247
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					if (posBracket > 0){


  		




  248
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						String bracket = type.substring(posBracket);


  		




  249
  
  
    
						//TODO


  		




  250
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//						logger.warn("Type has bracket("+id+"): " + bracket);


  		




  251
  
  
    
						//TODO Annotation


  		




  
  252
  
    
						taxon.addAnnotation(Annotation.NewInstance("Type-bracket: " + bracket, Language.DEFAULT()));


  		




  252
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						type = type.substring(0, posBracket).trim();


  		




  
  254
  
    
					}else{


  		




  
  255
  
    
						Taxon speciesTaxon = Taxon.NewInstance(typeName, state.getTransactionalSourceReference());


  		




  
  256
  
    
						classification.addParentChild(taxon, speciesTaxon, null, null);


  		




  253
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					}


  		




  254
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					type = makeTypeNomStatus(typeName, type);


  		




  255
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  ......




  289
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			} catch (UnknownCdmTypeException e) {


  		




  290
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				if (nomStatusStr.startsWith("nom. rej. prop.")){


  		




  291
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					nomStatusType = NomenclaturalStatusType.REJECTED_PROP();


  		




  292
  
  
    
					logger.warn("in favour not supported ("+id+"): " + nomStatusStr);


  		




  
  296
  
    
					logger.info("in favour not supported ("+id+"): " + nomStatusStr);


  		




  293
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				}else if (nomStatusStr.startsWith("nom. rej. in favour")){


  		




  294
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					nomStatusType = NomenclaturalStatusType.REJECTED();


  		




  295
  
  
    
					logger.warn("in favour not supported ("+id+"): " + nomStatusStr);


  		




  
  299
  
    
					logger.info("in favour not supported ("+id+"): " + nomStatusStr);


  		




  296
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				}else if (nomStatusStr.startsWith("nom. cons. against")){


  		




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					nomStatusType = NomenclaturalStatusType.CONSERVED();


  		




  298
  
  
    
					logger.warn("against not supported ("+id+"): " + nomStatusStr);


  		




  
  302
  
    
					logger.info("against not supported ("+id+"): " + nomStatusStr);


  		




  299
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				}else if (nomStatusStr.startsWith("nom. cons. prop. against")){


  		




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					nomStatusType = NomenclaturalStatusType.CONSERVED_PROP();


  		




  301
  
  
    
					logger.warn("against not supported ("+id+"): " + nomStatusStr);


  		




  
  305
  
    
					logger.info("against not supported ("+id+"): " + nomStatusStr);


  		




  302
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				}else{


  		




  303
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					logger.warn("Unknown status type ("+id+"): " + nomStatusStr);


  		




  304
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					nomStatusType = NomenclaturalStatusType.DOUBTFUL();


  		




  ......




  369
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  370
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		tp.setStartYear(year1.intValue());


  		




  371
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		Integer[] preDate1 = getDay(pre1,id);


  		




  372
  
  
    
		tp.setStartMonth(preDate1[1]);


  		




  373
  
  
    
		tp.setStartDay(preDate1[0]);


  		




  
  376
  
    
//		tp.setStartMonth(preDate1[1]);


  		




  
  377
  
    
//		tp.setStartDay(preDate1[0]);


  		




  374
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		if (year2 != null){


  		




  375
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			tp.setEndYear(year2.intValue());


  		




  376
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		}


  		




  377
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		Integer[] preDate2 = getDay(pre2, id);


  		




  378
  
  
    
		tp.setEndMonth(preDate2[1]);


  		




  379
  
  
    
		tp.setEndDay(preDate2[0]);


  		




  
  382
  
    
//		tp.setEndMonth(preDate2[1]);


  		




  
  383
  
    
//		tp.setEndDay(preDate2[0]);


  		




  380
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  381
  
  
    
		if (StringUtils.isNotBlank(modi1) || StringUtils.isNotBlank(modi2)){


  		




  382
  
  
    
			tp.setFreeText(date);


  		




  383
  
  
    
		}


  		




  
  385
  
    
//		if (StringUtils.isNotBlank(modi1) || StringUtils.isNotBlank(modi2)){


  		




  
  386
  
    
//			tp.setFreeText(date);


  		




  
  387
  
    
//		}


  		




  384
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		ref.setDatePublished(tp);


  		




  385
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	}


  		




  386
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  ......




  685
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		if (author != null){


  		




  686
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			String[]  split = author.split("\\sex\\s");


  		




  687
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			if (split.length > 1){


  		




  688
  
  
    
				//TODO richtige Reihenfolge ?


  		




  689
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				result[0] = split[1].trim();


  		




  690
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				result[1] = split[0].trim();


  		




  691
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			}else{


  		












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