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Revision 8a133607

Added by Andreas Müller over 4 years ago

ref #1444, ref #8508 add Monera filter handling in ERMS validation and for import

View differences:

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsTaxonImport.java
80 80 

  		




  81
  81
  
    
	@Override


  		




  82
  82
  
    
	protected String getIdQuery() {


  		




  83
  
  
    
		String strQuery = " SELECT id FROM tu WHERE id NOT IN (147415) " ;  //for now we exclude Monera as it has no children and is unclear what classification it has. In ERMS it is alternative accepted name, but according to https://en.wikipedia.org/wiki/Monera it is a super taxon to bacteria.


  		




  
  83
  
    
		String strQuery = " SELECT id FROM tu " ;  //WHERE id NOT IN (147415) for now we exclude Monera as it has no children and is unclear what classification it has. In ERMS it is alternative accepted name (in https://en.wikipedia.org/wiki/Monera it might be a super taxon to bacteria).


  		




  84
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		return strQuery;


  		




  85
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	}


  		




  86
  86
  
    

  		












  

    
      cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/validation/PesiErmsValidator.java
    
  





  36
  36
  
    

  		




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    private Source source = defaultSource;


  		




  38
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    private Source destination = defaultDestination;


  		




  
  39
  
    
    private String moneraFilter = " NOT IN (-1)"; // 147415;


  		




  39
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  40
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    private String origErms = "OriginalDB = 'ERMS' ";


  		




  41
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  ......




  123
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        return success;


  		




  124
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    }


  		




  125
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  126
  
  
    
    private final String countAddtionalTaxonSource = "SELECT count(*) FROM tu_sources ts WHERE ts.tu_id <>  147415 ";


  		




  
  127
  
    
    private final String countAddtionalTaxonSource = "SELECT count(*) FROM tu_sources ts WHERE ts.tu_id " + moneraFilter;


  		




  127
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    private boolean testAdditionalTaxonSourcesCount() {


  		




  128
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        int countSrc = source.getUniqueInteger(countAddtionalTaxonSource);


  		




  129
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        int countDest = destination.getUniqueInteger("SELECT count(*) FROM AdditionalTaxonSource ");


  		




  ......




  138
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        countSrc = source.getUniqueInteger("SELECT count(*) FROM tu "


  		




  140
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                + " WHERE (tu_marine IS NOT NULL OR tu_brackish IS NOT NULL OR tu_fresh IS NOT NULL OR tu_terrestrial IS NOT NULL) "


  		




  141
  
  
    
                + "     AND tu.id <>  147415 ");


  		




  
  142
  
    
                + "     AND tu.id " + moneraFilter );


  		




  142
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        countDest = destination.getUniqueInteger("SELECT count(*) FROM Note "


  		




  143
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                + " WHERE (NoteCategoryFk = 4 AND LastAction IS NULL) ");


  		




  144
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        result &= equals("Notes ecology count ", countSrc, countDest, String.valueOf(-1));


  		




  ......




  163
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        return equals("CommonName count ", countSrc, countDest, String.valueOf(-1));


  		




  164
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    }


  		




  165
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  166
  
  
    
    private final String countTaxonRelation = "SELECT count(*) FROM tu WHERE  tu_acctaxon <> id AND id NOT IN (147415) ";


  		




  
  167
  
    
    private final String countTaxonRelation = "SELECT count(*) FROM tu WHERE  tu_acctaxon <> id AND id " + moneraFilter;


  		




  167
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    private boolean testTaxonRelationCount() {


  		




  168
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         int countSrc = source.getUniqueInteger(countTaxonRelation);


  		




  169
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         int countDest = destination.getUniqueInteger("SELECT count(*) FROM RelTaxon ");


  		




  ......




  171
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     }


  		




  172
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  173
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  174
  
  
    
    private final String countTaxon = "SELECT count(*) FROM tu WHERE id NOT IN (147415)";


  		




  
  175
  
    
    private final String countTaxon = "SELECT count(*) FROM tu WHERE id " + moneraFilter;


  		




  175
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    private boolean testTaxaCount() {


  		




  176
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         int countSrc = source.getUniqueInteger(countTaxon);


  		




  177
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         int countDest = destination.getUniqueInteger("SELECT count(*) FROM Taxon ");


  		




  ......




  192
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                + " LEFT JOIN tu type ON type.id = t.tu_typetaxon "


  		




  193
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                + " LEFT JOIN fossil fo ON t.tu_fossil = fo.fossil_id "


  		




  194
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                + " LEFT JOIN qualitystatus qs ON t.tu_qualitystatus = qs.id "


  		




  195
  
  
    
                + " WHERE t.id NOT IN (147415) "


  		




  
  196
  
    
                + " WHERE t.id " + moneraFilter


  		




  196
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                + " ORDER BY CAST(t.id as nvarchar(20)) ");


  		




  197
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        ResultSet destRS = destination.getResultSet("SELECT t.*, "


  		




  198
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                + "     pt.GenusOrUninomial p_GenusOrUninomial, pt.InfraGenericEpithet p_InfraGenericEpithet, pt.SpecificEpithet p_SpecificEpithet, "


  		




  ......




  403
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        ResultSet srcRS = source.getResultSet(""


  		




  404
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                + " SELECT t.* "


  		




  405
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                + " FROM tu t "


  		




  406
  
  
    
                + " WHERE t.id NOT IN (147415) AND tu_acctaxon <> id "


  		




  
  407
  
    
                + " WHERE t.id "+ moneraFilter + " AND tu_acctaxon <> id "


  		




  407
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                + " ORDER BY CAST(t.id as nvarchar(20)) ");


  		




  408
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        ResultSet destRS = destination.getResultSet("SELECT rel.*, t1.IdInSource t1Id, t2.IdInSource t2Id "


  		




  409
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                + " FROM RelTaxon rel "


  		




  ......




  438
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                + " FROM tu_sources MN INNER JOIN tu ON MN.tu_id = tu.id "


  		




  439
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                + "    LEFT JOIN sources s ON s.id = MN.source_id "


  		




  440
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                + "    LEFT JOIN sourceuses su ON MN.sourceuse_id = su.sourceuse_id "


  		




  441
  
  
    
                + " WHERE MN.tu_id NOT IN (147415)  "


  		




  
  442
  
    
                + " WHERE MN.tu_id  " + moneraFilter


  		




  442
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                + " ORDER BY CAST(tu.id as nvarchar(20)), MN.sourceuse_id, s.id ");  //, no.note (not possible because ntext


  		




  443
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        ResultSet destRs = destination.getResultSet("SELECT t.IdInSource, ats.*, s.*, su.* "


  		




  444
  445
  
    
                + " FROM AdditionalTaxonSource ats INNER JOIN Taxon t ON t.TaxonId = ats.TaxonFk "


  		












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