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Revision 5cdaf78e

Added by Andreas Müller about 8 years ago

Latest cuba import changes

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/app/cuba/CubaActivator.java
39 39 
	//database validation status (create, update, validate ...)
40 40 
	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
41 41 

  		




  42
  
  
    
//    static final ICdmDataSource cdmDestination = CdmDestinations.localH2();


  		




  
  42
  
    
    static final ICdmDataSource cdmDestination = CdmDestinations.localH2();


  		




  43
  43
  
    
//  static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();


  		




  44
  
  
    
    static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cuba_production();


  		




  45
  
  
    

  		




  46
  
  
    
	boolean invers = false;


  		




  47
  
  
    

  		




  48
  
  
    
	boolean include = !invers;


  		




  49
  
  
    
	boolean exists = true;


  		




  50
  
  
    

  		




  51
  
  
    
    boolean doAsteraceae = include && false;


  		




  52
  
  
    
    boolean doConvolvulaceae = include && exists;   //x


  		




  53
  
  
    
    boolean doCyperaceae = include && exists;   //x


  		




  54
  
  
    
    boolean doDicotA_C = include && false;


  		




  55
  
  
    
    boolean doDicotD_M = include && false;


  		




  56
  
  
    
    boolean doDicotN_Z = include && false;


  		




  57
  
  
    
    boolean doEuphorbiaceae = include && false;


  		




  58
  
  
    
    boolean doFabaceae = include && exists;


  		




  59
  
  
    
    boolean doGymnospermae = include && false;


  		




  60
  
  
    
    boolean doLamVerbenaceae = include && false;


  		




  61
  
  
    
    boolean doMalpighiaceae = include && exists;


  		




  62
  
  
    
    boolean doMelastomataceae = include && exists;


  		




  63
  
  
    
    boolean doMonocots = include && exists;


  		




  64
  
  
    
    boolean doMyrtaceae = include && exists;


  		




  65
  
  
    
    boolean doOrchidaceae = include && false;


  		




  66
  
  
    
    boolean doRubiaceae = include && exists;


  		




  67
  
  
    
    boolean doUrticaceae = include && exists;


  		




  
  44
  
    
//    static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cuba_production();


  		




  
  45
  
    

  		




  
  46
  
    
	static boolean invers = false;


  		




  
  47
  
    

  		




  
  48
  
    
    boolean doAsteraceae = include;


  		




  
  49
  
    
    boolean doConvolvulaceae = include;


  		




  
  50
  
    
    boolean doCyperaceae = include;


  		




  
  51
  
    
    boolean doDicotA_C = include;


  		




  
  52
  
    
    boolean doDicotD_M = include;


  		




  
  53
  
    
    boolean doDicotN_Z = include;


  		




  
  54
  
    
    boolean doEuphorbiaceae = include;


  		




  
  55
  
    
    boolean doFabaceae = include;


  		




  
  56
  
    
    boolean doGymnospermae = include;


  		




  
  57
  
    
    boolean doLamVerbenaceae = include;


  		




  
  58
  
    
    boolean doMalpighiaceae = include;


  		




  
  59
  
    
    boolean doMelastomataceae = include;


  		




  
  60
  
    
    boolean doMonocots = include;


  		




  
  61
  
    
    boolean doMyrtaceae = include;


  		




  
  62
  
    
    boolean doOrchidaceae = include;


  		




  
  63
  
    
    boolean doRubiaceae = include;


  		




  
  64
  
    
    boolean doUrticaceae = include;


  		




  
  65
  
    

  		




  
  66
  
    
    static boolean include = !invers;


  		




  68
  67
  
    

  		




  69
  68
  
    

  		




  70
  69
  
    

  		












  

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





  61
  61
  
    
    private static final long serialVersionUID = -747486709409732371L;


  		




  62
  62
  
    
    private static final Logger logger = Logger.getLogger(CubaExcelImport.class);


  		




  63
  63
  
    

  		




  64
  
  
    
    private static final String HOMONYM_MARKER = ".*\\s+homon.?$";


  		




  
  64
  
    
    private static final String HOMONYM_MARKER = "\\s+homon.?$";


  		




  65
  65
  
    
    private static final String DOUBTFUL_MARKER = "^\\?\\s?";


  		




  66
  66
  
    

  		




  67
  67
  
    

  		




  ......




  302
  302
  
    
    private static final String heterotypicRegExStr_TEST = "([^\\(]{5,}" +"(\\(.+\\))?" + "[^\\)\\(]{2,})"


  		




  303
  303
  
    
            +"(\\((.{6,})\\))?";


  		




  304
  304
  
    
    private static final String auctRegExStr = "auct\\."


  		




  305
  
  
    
            +"((\\sFC(\\-S)?(\\s&\\sA&S)?)|(\\sA&S))?(\\s+p\\.\\s*p\\.)?";


  		




  306
  
  
    
    private static final String missapliedRegExStr = "“(.*{5,})”\\s+(" + auctRegExStr + "|sensu\\s+.{2,})";


  		




  
  305
  
    
            +"((\\sFC(\\-S)?(\\s&\\sA&S)?)|(\\sA&S)|\\sSagra|\\sBritton|\\sGriseb\\.|\\sWright|\\sFRC|\\sCoL|\\sUrb\\.)?(\\s+p\\.\\s*p\\.)?";


  		




  
  306
  
    
    private static final String missapliedRegExStr = "(\\?\\s)?“(.*{5,})”\\s+(" + auctRegExStr + "|sensu\\s+.{2,})";


  		




  307
  307
  
    
    private static final String nomInvalRegExStr = "“(.*{5,})”\\s+nom\\.\\s+inval\\.";


  		




  308
  308
  
    
    private static final String homonymRegExStr = "\\s*(\\[.*\\])*\\s*";


  		




  309
  309
  
    

  		




  ......




  340
  340
  
    

  		




  341
  341
  
    
        List<BotanicalName> homonyms = new ArrayList<>();


  		




  342
  342
  
    
        if (missapliedMatcher.matches()){


  		




  343
  
  
    
            String firstPart = missapliedMatcher.group(1);


  		




  
  343
  
    
            boolean doubtful = missapliedMatcher.group(1) != null;


  		




  
  344
  
    
            String firstPart = missapliedMatcher.group(2);


  		




  344
  345
  
    
            BotanicalName name = (BotanicalName)nameParser.parseSimpleName(firstPart, state.getConfig().getNomenclaturalCode(), Rank.SPECIES());


  		




  345
  346
  
    

  		




  346
  
  
    
            String secondPart = missapliedMatcher.group(2);


  		




  
  347
  
    
            String secondPart = missapliedMatcher.group(3);


  		




  347
  348
  
    
            Taxon misappliedNameTaxon = Taxon.NewInstance(name, null);


  		




  
  349
  
    
            misappliedNameTaxon.setDoubtful(doubtful);


  		




  348
  350
  
    
            if (secondPart.startsWith("sensu")){


  		




  349
  351
  
    
                secondPart = secondPart.substring(5).trim();


  		




  350
  352
  
    
                if (secondPart.contains(" ")){


  		




  351
  
  
    
                    logger.warn(line + "Second part contains more than 1 word. Check if this is correct: " + secondPart);


  		




  
  353
  
    
                    logger.warn(line + "CHECK: Second part contains more than 1 word. Check if this is correct: " + secondPart);


  		




  352
  354
  
    
                }


  		




  353
  355
  
    
                Reference<?> sensu = ReferenceFactory.newGeneric();


  		




  354
  356
  
    
                Team team = Team.NewTitledInstance(secondPart, null);


  		




  ......




  378
  380
  
    
            String secondPart = heterotypicMatcher.groupCount() < 3 ? null : heterotypicMatcher.group(3);


  		




  379
  381
  
    
            String homonymPart = heterotypicMatcher.groupCount() < 4 ? null : heterotypicMatcher.group(4);


  		




  380
  382
  
    
            boolean isDoubtful = firstPart.matches("^\\?\\s*.*");


  		




  381
  
  
    
            boolean isHomonym = firstPart.trim().matches(HOMONYM_MARKER);


  		




  
  383
  
    
            boolean isHomonym = firstPart.trim().matches(".*" + HOMONYM_MARKER);


  		




  382
  384
  
    
            firstPart = normalizeStatus(firstPart);


  		




  383
  385
  
    
            BotanicalName synName = (BotanicalName)nameParser.parseReferencedName(firstPart, state.getConfig().getNomenclaturalCode(), Rank.SPECIES());


  		




  384
  386
  
    
            if (synName.isProtectedTitleCache()){


  		




  ......




  423
  425
  
    
        BotanicalName currentBasionym = homotypicName;


  		




  424
  426
  
    
        String[] splits = homotypicStr.split("\\s*,\\s*");


  		




  425
  427
  
    
        for (String split : splits){


  		




  426
  
  
    
            boolean isHomonym = split.trim().matches(HOMONYM_MARKER);


  		




  
  428
  
    
            boolean isHomonym = split.trim().matches(".*" + HOMONYM_MARKER);


  		




  427
  429
  
    
            String singleName = normalizeStatus(split);


  		




  428
  430
  
    
            BotanicalName newName = (BotanicalName)nameParser.parseReferencedName(singleName, state.getConfig().getNomenclaturalCode(), Rank.SPECIES());


  		




  429
  431
  
    
            if (newName.isProtectedTitleCache()){


  		




  ......




  492
  494
  
    
            basionymName = name2;


  		




  493
  495
  
    
            newCombination = currentBasionym;


  		




  494
  496
  
    
        }


  		




  
  497
  
    
//        newCombination.getHomotypicalGroup().removeGroupBasionym(xxx);


  		




  495
  498
  
    
        if (matchAuthor(basionymName.getCombinationAuthorship(), newCombination.getBasionymAuthorship())){


  		




  496
  499
  
    
            newCombination.getHomotypicalGroup().setGroupBasionym(basionymName);


  		




  497
  500
  
    
        }


  		




  ......




  591
  594
  
    

  		




  592
  595
  
    

  		




  593
  596
  
    
    private static final String[] nomStatusStrings = new String[]{"nom. cons.", "ined.", "nom. illeg.",


  		




  594
  
  
    
            "nom. rej.","nom. cons. prop.","nom. altern."};


  		




  
  597
  
    
            "nom. rej.","nom. cons. prop.","nom. altern.","nom. confus.","nom. dub."};


  		




  595
  598
  
    
    /**


  		




  596
  599
  
    
     * @param taxonStr


  		




  597
  600
  
    
     * @return


  		












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