Project

General

Profile

« Previous | Next » 

Revision dd68b822

Added by Andreas Müller over 4 years ago

ref #8508 latest changes

View differences:

cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/validate/PesiErmsValidator.java
50 50 
            this.destination = destination;
51 51 
//            success &= testReferences();  //ready, few minor issues to be discussed with VLIZ
52 52 
            success &= testTaxa();
53 
            success &= testTaxonRelations();  //name relations count!,  Implement single compare tests
53 
//            success &= testTaxonRelations();  //name relations count!,  single record compare tests for synonyms and included in
54 54 
//            success &= testCommonNames();  //source(s) discuss VLIZ, exact duplicates (except for sources), Anus(Korur)
55 
//            success &= testDistributions();  //>1000 duplicates in "dr", sources (OccurrenceSource table), area spellings(Baelt Sea), 1 long note
55 
//            success &= testDistributions();  //>1000 duplicates in "dr", sources (OccurrenceSource table), 1 long note
56 56 
//            success &= testNotes();  //ecology & link notes test (only count tested), sources untested (NoteSource table)
57 57 
//            success &= testAdditionalTaxonSources();  //ready
58 58 
        } catch (Exception e) {
......
100 100 

  		




  101
  101
  
    
    int countSynonyms;


  		




  102
  102
  
    
    int countIncludedIns;


  		




  103
  
  
    
    private boolean testTaxonRelations() {


  		




  
  103
  
    
    private boolean testTaxonRelations() throws SQLException {


  		




  104
  104
  
    
        System.out.println("Start validate taxon relations");


  		




  105
  
  
    
        boolean success = testSynonymRelations();


  		




  106
  
  
    
        success &= testIncludedInRelations();


  		




  
  105
  
    
        boolean success = testSynonymRelations();  //only count, single record test still missing


  		




  
  106
  
    
        success &= testIncludedInRelations();  //only count, single record test still missing


  		




  107
  107
  
    
        success &= testTotalRelations();


  		




  108
  108
  
    
        success &= testNameRelations();


  		




  109
  109
  
    
        return success;


  		




  ......




  122
  122
  
    
        }


  		




  123
  123
  
    
    }


  		




  124
  124
  
    

  		




  125
  
  
    
    private boolean testSynonymRelations() {


  		




  
  125
  
    
    private boolean testSynonymRelations() throws SQLException {


  		




  126
  126
  
    

  		




  127
  127
  
    
        int countSrc = source.getUniqueInteger(countSynonymRelation);


  		




  128
  128
  
    
        int countDest = destination.getUniqueInteger("SELECT count(*) FROM RelTaxon WHERE RelTaxonQualifierFk > 101");


  		




  ......




  276
  276
  
    
                + " ORDER BY CAST(t.id as nvarchar(20)) ");


  		




  277
  277
  
    
        ResultSet destRS = destination.getResultSet("SELECT t.*, "


  		




  278
  278
  
    
                + "     pt.GenusOrUninomial p_GenusOrUninomial, pt.InfraGenericEpithet p_InfraGenericEpithet, pt.SpecificEpithet p_SpecificEpithet, "


  		




  
  279
  
    
                + "     pt.treeIndex pTreeIndex, "


  		




  279
  280
  
    
                + "     s.Name as sourceName, type.IdInSource typeSourceId, r.Rank "


  		




  280
  281
  
    
                + " FROM Taxon t "


  		




  281
  282
  
    
                + "    LEFT JOIN Taxon pt ON pt.TaxonId = t.ParentTaxonFk "


  		




  ......




  301
  302
  
    
        return success;


  		




  302
  303
  
    
    }


  		




  303
  304
  
    

  		




  304
  
  
    

  		




  305
  305
  
    
    private boolean testSingleTaxon(ResultSet srcRS, ResultSet destRS) throws SQLException {


  		




  306
  306
  
    
        String id = String.valueOf(srcRS.getInt("id"));


  		




  
  307
  
    
        //not complete yet


  		




  307
  308
  
    
        boolean success = equals("Taxon ID", "tu_id: " + srcRS.getInt("id"), destRS.getString("IdInSource"), id);


  		




  308
  309
  
    
        success &= equals("Taxon source", "ERMS export for PESI", destRS.getString("sourceName"), id);


  		




  309
  
  
    
//TODO some


  		




  
  310
  
    

  		




  310
  311
  
    
        success &= compareKingdom("Taxon kingdom", srcRS, destRS, id);


  		




  311
  312
  
    
        success &= equals("Taxon rank fk", srcRS.getString("tu_rank"), destRS.getString("RankFk"), id);


  		




  312
  313
  
    
        success &= equals("Taxon rank cache", normalizeRank(srcRS.getString("rank_name"), srcRS, id), destRS.getString("Rank"), id);


  		




  313
  314
  
    
        success &= compareNameParts(srcRS, destRS, id);


  		




  314
  315
  
    

  		




  315
  316
  
    
        success &= equals("Taxon websearchname", srcRS.getString("tu_displayname"), destRS.getString("WebSearchName"), id);


  		




  316
  
  
    
//TODO        success &= equals("Taxon WebShowName", srcRS.getString("tu_displayname"), destRS.getString("WebShowName"), id);


  		




  
  317
  
    
//TODO webShowName  success &= equals("Taxon WebShowName", srcRS.getString("tu_displayname"), destRS.getString("WebShowName"), id);


  		




  317
  318
  
    
        success &= equals("Taxon authority", srcRS.getString("tu_authority"), destRS.getString("AuthorString"), id);


  		




  318
  
  
    
        success &= equals("Taxon FullName", srcFullName(srcRS), destRS.getString("FullName"), id);


  		




  
  319
  
    
//        success &= equals("Taxon FullName", srcFullName(srcRS), destRS.getString("FullName"), id);


  		




  319
  320
  
    
        success &= isNull("NomRefString", destRS);


  		




  320
  321
  
    
//        success &= equals("Taxon DisplayName", srcDisplayName(srcRS), destRS.getString("DisplayName"), id);  //according to SQL script same as FullName, no nom.ref. information attached


  		




  321
  322
  
    

  		




  322
  
  
    
//TODO        success &= equals("Taxon NameStatusFk", toNameStatus(nullSafeInt(srcRS, "tu_status")),nullSafeInt( destRS,"NameStatusFk"), id);


  		




  323
  
  
    
//TODO        success &= equals("Taxon NameStatusCache", srcRS.getString("status_name"), destRS.getString("NameStatusCache"), id);


  		




  324
  
  
    

  		




  325
  
  
    
//TODO        success &= equals("Taxon TaxonStatusFk", nullSafeInt(srcRS, "tu_status"),nullSafeInt( destRS,"TaxonStatusFk"), id);


  		




  326
  
  
    
//TODO        success &= equals("Taxon TaxonStatusCache", srcRS.getString("status_name"), destRS.getString("TaxonStatusCache"), id);


  		




  
  323
  
    
//TODO nameStatusFk       success &= equals("Taxon NameStatusFk", toNameStatus(nullSafeInt(srcRS, "tu_status")),nullSafeInt( destRS,"NameStatusFk"), id);


  		




  
  324
  
    
//TODO nameStatusCache    success &= equals("Taxon NameStatusCache", srcRS.getString("status_name"), destRS.getString("NameStatusCache"), id);


  		




  327
  325
  
    

  		




  
  326
  
    
       success &= equals("Taxon TaxonStatusFk", makePesiTaxonStatus(srcRS, "tu_status"),nullSafeInt( destRS,"TaxonStatusFk"), id);


  		




  
  327
  
    
/*//TODO taxonStatusCache  success &= equals("Taxon TaxonStatusCache", srcRS.getString("status_name"), destRS.getString("TaxonStatusCache"), id);


  		




  
  328
  
    
*/


  		




  328
  329
  
    
        //TODO ParentTaxonFk


  		




  329
  330
  
    
        Integer orgigTypeNameFk = nullSafeInt(srcRS, "tu_typetaxon");


  		




  330
  331
  
    
        success &= equals("Taxon TypeNameFk", orgigTypeNameFk == null? null : "tu_id: " + orgigTypeNameFk, destRS.getString("typeSourceId"), id);


  		




  331
  332
  
    
//TODO  success &= equals("Taxon TypeFullNameCache", CdmUtils.concat(" ", srcRS.getString("typename"), srcRS.getString("typeauthor")), destRS.getString("TypeFullNameCache"), id);


  		




  332
  333
  
    
        success &= equals("Taxon QualityStatusFK", nullSafeInt(srcRS, "tu_qualitystatus"),nullSafeInt( destRS,"QualityStatusFk"), String.valueOf(id));


  		




  333
  334
  
    
        success &= equals("Taxon QualityStatusCache", srcRS.getString("qualitystatus_name"), destRS.getString("QualityStatusCache"), id);


  		




  334
  
  
    
        //TODO TreeIndex


  		




  
  335
  
    
        success &= checkTreeIndex(destRS, ("TreeIndex"), ("pTreeIndex"), id);


  		




  335
  336
  
    
        success &= equals("Taxon FossilStatusFk", nullSafeInt(srcRS, "tu_fossil"),nullSafeInt( destRS,"FossilStatusFk"), String.valueOf(id));


  		




  336
  337
  
    
        success &= equals("Taxon FossilStatusCache", srcRS.getString("fossil_name"), destRS.getString("FossilStatusCache"), id);


  		




  337
  338
  
    
        success &= equals("Taxon GUID", srcRS.getString("GUID"), destRS.getString("GUID"), id);


  		




  ......




  346
  347
  
    
        return success;


  		




  347
  348
  
    
    }


  		




  348
  349
  
    

  		




  
  350
  
    
    private Integer makePesiTaxonStatus(ResultSet srcRS, String string) throws SQLException {


  		




  
  351
  
    
        Integer status = nullSafeInt(srcRS, "tu_status");


  		




  
  352
  
    
        if(status == 1 || status == 2){   //accepted, unaccepted


  		




  
  353
  
    
            return status;


  		




  
  354
  
    
        }else if (status == 3 || status == 6 || status == 7){  //nomen nudum, nomen dubium, temporary name


  		




  
  355
  
    
            return 2;


  		




  
  356
  
    
        }


  		




  
  357
  
    
        return -1;


  		




  
  358
  
    
    }


  		




  
  359
  
    

  		




  
  360
  
    
    private boolean checkTreeIndex(ResultSet destRS, String childIndexAttr, String parentIndexAttr, String id) throws SQLException {


  		




  
  361
  
    
        boolean result;


  		




  
  362
  
    
        int taxonStatusFk = destRS.getInt("TaxonStatusFk");


  		




  
  363
  
    
        String parentTaxonId = destRS.getString("parentTaxonFk");


  		




  
  364
  
    
        int rankFk = destRS.getInt("RankFk");


  		




  
  365
  
    
        if (taxonStatusFk == 2 || rankFk <= 10){  //synonyms, Kingdom and higher


  		




  
  366
  
    
            result = isNull(childIndexAttr, destRS);


  		




  
  367
  
    
        }else{


  		




  
  368
  
    
            String childIndex = destRS.getString(childIndexAttr);


  		




  
  369
  
    
            String parentIndex = destRS.getString(parentIndexAttr);


  		




  
  370
  
    
            parentIndex = parentIndex == null? "#": parentIndex;


  		




  
  371
  
    
            result = equals("Tree index", childIndex, parentIndex + parentTaxonId + "#", id);


  		




  
  372
  
    
        }


  		




  
  373
  
    
        return result;


  		




  
  374
  
    
    }


  		




  
  375
  
    

  		




  349
  376
  
    
    boolean namePartsFirst = true;


  		




  350
  377
  
    
    private boolean compareNameParts(ResultSet srcRS, ResultSet destRS, String id) throws SQLException {


  		




  351
  378
  
    
        if (namePartsFirst){


  		












Also available in:  Unified diff