Revision 8419d12a
Added by Andreas Müller over 4 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/validate/PesiErmsValidator.java | ||
|---|---|---|
| 31 | 31 |
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| 32 | 32 |
private static final Logger logger = Logger.getLogger(PesiErmsValidator.class); |
| 33 | 33 |
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private static final Source defaultSource = PesiSources.PESI2019_ERMS_2018();
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private static final Source defaultSource = PesiSources.PESI2019_ERMS_2019();
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// private static final Source defaultDestination = PesiDestinations.pesi_test_local_CDM_ERMS2PESI(); |
| 36 | 36 |
private static final Source defaultDestination = PesiDestinations.pesi_test_local_CDM_ERMS2PESI_2(); |
| 37 | 37 |
|
| ... | ... | |
| 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
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success &= testTaxonRelations(); //name relations count!, Implement single compare tests |
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| 54 | 54 |
// success &= testCommonNames(); //source(s) discuss VLIZ, exact duplicates (except for sources), Anus(Korur) |
| 55 | 55 |
// success &= testDistributions(); //>1000 duplicates in "dr", sources (OccurrenceSource table), area spellings(Baelt Sea), 1 long note |
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// success &= testNotes(); //ecology & link notes test (only count tested), sources untested (NoteSource table), few duplicates,
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success &= testAdditionalTaxonSources(); //ready |
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// success &= testNotes(); //ecology & link notes test (only count tested), sources untested (NoteSource table)
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// success &= testAdditionalTaxonSources(); //ready
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} catch (Exception e) {
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e.printStackTrace(); |
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success = false; |
| ... | ... | |
| 266 | 266 |
+ " type.tu_displayname typename, type.tu_authority typeauthor, " |
| 267 | 267 |
+ " fo.fossil_name, qs.qualitystatus_name " |
| 268 | 268 |
+ " FROM tu t " |
| 269 |
+ " LEFT JOIN tu as tu1 on t.tu_parent = tu1.id" |
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+ " LEFT JOIN (SELECT DISTINCT rank_id, rank_name FROM ranks WHERE NOT(rank_id = 40 AND rank_name = 'Subdivision' OR rank_id = 122 AND rank_name='Subsection')) as r ON t.tu_rank = r.rank_id "
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+ " LEFT JOIN tu as tu1 on t.tu_parent = tu1.id "
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+ " LEFT JOIN (SELECT DISTINCT rank_id, rank_name FROM ranks WHERE NOT(rank_id = 30 AND rank_name = 'Phylum (Division)' OR rank_id = 40 AND rank_name = 'Subphylum (Subdivision)' OR rank_id = 122 AND rank_name='Subsection')) as r ON t.tu_rank = r.rank_id "
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| 271 | 271 |
+ " LEFT JOIN tu acc ON acc.id = t.tu_acctaxon " |
| 272 | 272 |
+ " LEFT JOIN status st ON st.status_id = t.tu_status " |
| 273 | 273 |
+ " LEFT JOIN tu type ON type.id = t.tu_typetaxon " |
| ... | ... | |
| 295 | 295 |
int i = 0; |
| 296 | 296 |
while (srcRS.next() && destRS.next()){
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| 297 | 297 |
success &= testSingleTaxon(srcRS, destRS); |
| 298 |
//TODO success &= testLastAction(srcRsLastAction, destRS, String.valueOf(srcRS.getInt("id")), "Taxon");
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success &= testLastAction(srcRsLastAction, destRS, String.valueOf(srcRS.getInt("id")), "Taxon");
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i++; |
| 300 | 300 |
} |
| 301 | 301 |
success &= equals("Taxon count for single compare", n, i, String.valueOf(-1));
|
| ... | ... | |
| 314 | 314 |
success &= compareNameParts(srcRS, destRS, id); |
| 315 | 315 |
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| 316 | 316 |
success &= equals("Taxon websearchname", srcRS.getString("tu_displayname"), destRS.getString("WebSearchName"), id);
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// success &= equals("Taxon WebShowName", srcRS.getString("tu_displayname"), destRS.getString("WebShowName"), id);
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//TODO success &= equals("Taxon WebShowName", srcRS.getString("tu_displayname"), destRS.getString("WebShowName"), id);
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| 318 | 318 |
success &= equals("Taxon authority", srcRS.getString("tu_authority"), destRS.getString("AuthorString"), id);
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// success &= equals("Taxon FullName", srcFullName(srcRS), destRS.getString("FullName"), id);
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success &= equals("Taxon FullName", srcFullName(srcRS), destRS.getString("FullName"), id);
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| 320 | 320 |
success &= isNull("NomRefString", destRS);
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| 321 | 321 |
// success &= equals("Taxon DisplayName", srcDisplayName(srcRS), destRS.getString("DisplayName"), id); //according to SQL script same as FullName, no nom.ref. information attached
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| 322 | 322 |
|
| ... | ... | |
| 402 | 402 |
private String srcFullName(ResultSet srcRs) throws SQLException {
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| 403 | 403 |
String result = null; |
| 404 | 404 |
String epi = srcRs.getString("tu_name");
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epi = " a" + epi; |
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| 406 | 405 |
String display = srcRs.getString("tu_displayname");
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| 407 | 406 |
String sp = srcRs.getString("tu_sp");
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if (display.indexOf(epi) != display.lastIndexOf(epi) && !sp.startsWith("#2#")){ //homonym, animal
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result = srcRs.getString("tu_displayname").replaceFirst(epi+" ", CdmUtils.concat(" ", " "+epi, srcRs.getString("tu_authority")))+" ";
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if (display.indexOf(epi) != display.lastIndexOf(epi) && !sp.startsWith("#2#")){ //autonym, !animal
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String authority = srcRs.getString("tu_authority");
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result = srcRs.getString("tu_displayname").replaceFirst(epi+" ", CdmUtils.concat(" ", epi, authority)+" ");
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| 410 | 410 |
}else{
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| 411 | 411 |
result = CdmUtils.concat(" ", srcRs.getString("tu_displayname"), srcRs.getString("tu_authority"));
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| 412 | 412 |
} |
| ... | ... | |
| 796 | 796 |
return success; |
| 797 | 797 |
} |
| 798 | 798 |
|
| 799 |
//NOTE: there could be better parsing of source_year during import, this may also need better normalizing in the database |
|
| 799 | 800 |
private String normalizeYear(String yearStr) {
|
| 800 | 801 |
if (StringUtils.isBlank(yearStr)){
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| 801 | 802 |
return yearStr; |
| ... | ... | |
| 804 | 805 |
if (yearStr.matches("\\d{4}-\\d{2}")){
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yearStr = yearStr.substring(0, 5)+yearStr.substring(0, 2)+yearStr.substring(5); |
| 806 | 807 |
} |
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if (yearStr.equals("20 Mar 1891")){
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yearStr = "20.3.1891"; |
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} |
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if (yearStr.equals("July 1900")){
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yearStr = "7.1900"; |
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} |
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return yearStr; |
| 808 | 815 |
} |
| 809 | 816 |
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Also available in: Unified diff
ref #8508 latest changes to ERMS validation