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Revision b0b606e6

Added by Andreas Müller over 8 years ago

Latest updates to Cuba import

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/app/cuba/CubaActivator.java
41 41 

  		




  42
  42
  
    
	boolean invers = true;


  		




  43
  43
  
    
	boolean include = !invers;


  		




  
  44
  
    

  		




  44
  45
  
    
    boolean doAsteraceae = include;


  		




  45
  46
  
    
    boolean doConvolvulaceae = include;


  		




  46
  
  
    
    boolean doCyperaceae = include;


  		




  
  47
  
    
    boolean doCyperaceae = ! include;


  		




  47
  48
  
    
    boolean doDicotA_C = include;


  		




  48
  49
  
    
    boolean doDicotD_M = include;


  		




  49
  50
  
    
    boolean doDicotN_Z = include;


  		




  50
  51
  
    
    boolean doEuphorbiaceae = include;


  		




  51
  
  
    
    boolean doFabaceae = include;


  		




  
  52
  
    
    boolean doFabaceae = ! include;


  		




  52
  53
  
    
    boolean doGymnospermae = include;


  		




  53
  54
  
    
    boolean doLamVerbenaceae = include;


  		




  54
  
  
    
    boolean doMalpighiaceae = include;


  		




  
  55
  
    
    boolean doMalpighiaceae = ! include;


  		




  55
  56
  
    
    boolean doMelastomataceae = ! include;


  		




  56
  
  
    
    boolean doMonocots = include ;


  		




  
  57
  
    
    boolean doMonocots = ! include ;


  		




  57
  58
  
    
    boolean doMyrtaceae = include;


  		




  58
  59
  
    
    boolean doOrchidaceae = include;


  		




  59
  60
  
    
    boolean doRubiaceae = include;


  		




  60
  
  
    
    boolean doUrticaceae = include;


  		




  
  61
  
    
    boolean doUrticaceae = ! include;


  		




  61
  62
  
    

  		




  62
  63
  
    

  		




  63
  64
  
    

  		




  64
  
  
    
    static final ICdmDataSource cdmDestination = CdmDestinations.localH2();


  		




  
  65
  
    
//    static final ICdmDataSource cdmDestination = CdmDestinations.localH2();


  		




  65
  66
  
    
//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();


  		




  66
  67
  
    
//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_dev();


  		




  67
  
  
    
//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cuba_production();


  		




  
  68
  
    
	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cuba_production();


  		




  68
  69
  
    

  		




  69
  70
  
    

  		




  70
  71
  
    
	//feature tree uuid


  		




  ......




  79
  80
  
    
	//check - import


  		




  80
  81
  
    
	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;


  		




  81
  82
  
    

  		




  82
  
  
    
	static boolean doVocabularies = (hbm2dll == DbSchemaValidation.CREATE);


  		




  
  83
  
    
	boolean doVocabularies = (hbm2dll == DbSchemaValidation.CREATE);


  		




  83
  84
  
    
	static final boolean doTaxa = true;


  		




  84
  85
  
    
	static final boolean doDeduplicate = false;


  		




  85
  86
  
    

  		




  ......




  189
  190
  
    
        if (doVocabularies){


  		




  190
  191
  
    
            FeatureTree tree = makeFeatureNodes(myImport.getCdmAppController().getTermService());


  		




  191
  192
  
    
            myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);


  		




  
  193
  
    
            this.doVocabularies = false;


  		




  192
  194
  
    
        }


  		




  193
  195
  
    
        System.out.println("End import from ("+ source.toString() + ")...");


  		




  194
  196
  
    
    }


  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/io/cuba/CubaExcelImport.java
    
  





  270
  270
  
    
                                                     +"(\\((.{6,})\\))?";


  		




  271
  271
  
    
    private static final String heterotypicRegExStr_TEST = "([^\\(]{5,}" +"(\\(.+\\))?" + "[^\\)\\(]{2,})"


  		




  272
  272
  
    
            +"(\\((.{6,})\\))?";


  		




  273
  
  
    
    private static final String missapliedRegExStr = "“(.*{5,})”\\s+(auct\\.(\\sFC\\-S)?(\\s+p\\.\\s*p\\.)?|sensu\\s+.{2,})";


  		




  
  273
  
    
    private static final String auctRegExStr = "auct\\."


  		




  
  274
  
    
            +"((\\sFC(\\-S)?(\\s&\\sA&S)?)|(\\sA&S))?(\\s+p\\.\\s*p\\.)?";


  		




  
  275
  
    
    private static final String missapliedRegExStr = "“(.*{5,})”\\s+(" + auctRegExStr + "|sensu\\s+.{2,})";


  		




  274
  276
  
    
    private static final String nomInvalRegExStr = "“(.*{5,})”\\s+nom\\.\\s+inval\\.";


  		




  275
  277
  
    
    private static final String homonymRegExStr = "\\s*(\\[.*\\])*\\s*";


  		




  276
  278
  
    

  		




  ......




  321
  323
  
    
                Team team = Team.NewTitledInstance(secondPart, null);


  		




  322
  324
  
    
                sensu.setAuthorship(team);


  		




  323
  325
  
    
                misappliedNameTaxon.setSec(sensu);


  		




  324
  
  
    
            }else if (secondPart.matches("auct.((\\s+p\\.\\s*p\\.)|(\\sFC\\-S))?")){


  		




  
  326
  
    
            }else if (secondPart.matches(auctRegExStr)){


  		




  325
  327
  
    
                secondPart = secondPart.replace("p. p.", "p.p.");


  		




  326
  328
  
    
                misappliedNameTaxon.setAppendedPhrase(secondPart);


  		




  327
  329
  
    
            }else{


  		




  ......




  692
  694
  
    
        TaxonNode familyTaxon = getFamilyTaxon(record, state);


  		




  693
  695
  
    
        if (familyTaxon == null){


  		




  694
  696
  
    
            if (record.get("Taxón") != null){


  		




  695
  
  
    
                logger.warn(line + ": Family not recognized but taxon exists:" + record.get("Taxón"));


  		




  
  697
  
    
                logger.warn(line + ": Family not recognized but taxon exists: " + record.get("Taxón"));


  		




  696
  698
  
    
                return;


  		




  697
  699
  
    
            }else if (record.get("Syn.") == null){


  		




  698
  700
  
    
                logger.warn(line + ": Family not recognized but also no synonym exists");


  		












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