Revision 1030c26a
Added by Andreas Müller over 4 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java | ||
|---|---|---|
| 13 | 13 |
import java.sql.ResultSet; |
| 14 | 14 |
import java.sql.SQLException; |
| 15 | 15 |
import java.sql.Types; |
| 16 |
import java.util.ArrayList; |
|
| 17 | 16 |
import java.util.BitSet; |
| 18 | 17 |
import java.util.HashMap; |
| 19 | 18 |
import java.util.HashSet; |
| ... | ... | |
| 109 | 108 |
private PreparedStatement parentTaxonFkStmt; |
| 110 | 109 |
private PreparedStatement rankTypeExpertsUpdateStmt; |
| 111 | 110 |
private PreparedStatement rankUpdateStmt; |
| 112 |
private NomenclaturalCode nomenclaturalCode; |
|
| 113 | 111 |
private Integer kingdomFk; |
| 114 |
private final HashMap<Rank, Rank> rank2endRankMap = new HashMap<>(); |
|
| 115 |
private final List<Rank> rankList = new ArrayList<>(); |
|
| 116 |
private static final UUID uuidTreeIndex = UUID.fromString("28f4e205-1d02-4d3a-8288-775ea8413009");
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|
| 117 | 112 |
private AnnotationType treeIndexAnnotationType; |
| 118 | 113 |
private static ExtensionType lastActionExtensionType; |
| 119 | 114 |
private static ExtensionType lastActionDateExtensionType; |
| ... | ... | |
| 124 | 119 |
public static TaxonNameDefaultCacheStrategy nonViralNameStrategy = TaxonNameDefaultCacheStrategy.NewInstance(); |
| 125 | 120 |
private static int currentTaxonId; |
| 126 | 121 |
|
| 127 |
|
|
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/** |
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* @return the treeIndexAnnotationType |
|
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*/ |
|
| 131 | 122 |
protected AnnotationType getTreeIndexAnnotationType() {
|
| 132 | 123 |
return treeIndexAnnotationType; |
| 133 | 124 |
} |
| 134 | 125 |
|
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/** |
|
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* @param treeIndexAnnotationType the treeIndexAnnotationType to set |
|
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*/ |
|
| 138 | 126 |
protected void setTreeIndexAnnotationType(AnnotationType treeIndexAnnotationType) {
|
| 139 | 127 |
this.treeIndexAnnotationType = treeIndexAnnotationType; |
| 140 | 128 |
} |
| ... | ... | |
| 356 | 344 |
private void validatePhaseOne(TaxonBase<?> taxon, TaxonName taxonName) {
|
| 357 | 345 |
|
| 358 | 346 |
// Check whether some rules are violated |
| 359 |
nomenclaturalCode = taxonName.getNameType(); |
|
| 347 |
NomenclaturalCode nomenclaturalCode = taxonName.getNameType();
|
|
| 360 | 348 |
String genusOrUninomial = taxonName.getGenusOrUninomial(); |
| 361 | 349 |
String specificEpithet = taxonName.getSpecificEpithet(); |
| 362 | 350 |
String infraSpecificEpithet = taxonName.getInfraSpecificEpithet(); |
| ... | ... | |
| 667 | 655 |
|
| 668 | 656 |
//TODO why are expertFks needed? (Andreas M.) |
| 669 | 657 |
// if (expertFk != null || speciesExpertFk != null) {
|
| 670 |
invokeRankDataAndTypeNameFkAndKingdomFk(taxonName, nomenclaturalCode, state.getDbId(taxon), |
|
| 658 |
NomenclaturalCode nomCode = taxonName.getNameType(); |
|
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//is there a reason why we do pass nomCode separately? Before nomCode was class variable, but not clear why and when it was set |
|
| 660 |
invokeRankDataAndTypeNameFkAndKingdomFk(taxonName, nomCode, state.getDbId(taxon), |
|
| 671 | 661 |
typeNameFk, kingdomFk, state); |
| 672 | 662 |
// } |
| 673 | 663 |
} |
| ... | ... | |
| 727 | 717 |
} |
| 728 | 718 |
return kingdomID; |
| 729 | 719 |
} else {
|
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NomenclaturalCode nomenclaturalCode = taxon.getName().getNameType(); |
|
| 730 | 721 |
logger.warn("The taxon has no nodes: " + taxon.getTitleCache() + ". The kingdom is taken from the nomenclatural code: " + PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode));
|
| 731 | 722 |
return PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode); |
| 732 | 723 |
} |
| 733 | 724 |
} else{
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NomenclaturalCode nomenclaturalCode = taxonBase.getName().getNameType(); |
|
| 734 | 726 |
logger.warn("Taxon is synonym with no accepted taxon attached: " + taxonBase.getTitleCache() + ". The kingdom is taken from the nomenclatural code: " + PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode) );
|
| 735 | 727 |
return PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode); |
| 736 | 728 |
} |
| ... | ... | |
| 783 | 775 |
|
| 784 | 776 |
// Save Rank Data and KingdomFk for inferred synonyms |
| 785 | 777 |
for (Integer taxonFk : inferredSynonymsDataToBeSaved.keySet()) {
|
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invokeRankDataAndKingdomFk(inferredSynonymsDataToBeSaved.get(taxonFk), nomenclaturalCode, taxonFk, kingdomFk, state); |
|
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TaxonName taxonName = inferredSynonymsDataToBeSaved.get(taxonFk); |
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NomenclaturalCode nomCode = taxonName.getNameType(); //nomCode was class variable before, not sure if this was important |
|
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invokeRankDataAndKingdomFk(inferredSynonymsDataToBeSaved.get(taxonFk), nomCode, taxonFk, kingdomFk, state); |
|
| 787 | 781 |
} |
| 788 | 782 |
|
| 789 | 783 |
// Start transaction |
| ... | ... | |
| 810 | 804 |
|
| 811 | 805 |
// Save Rank Data and KingdomFk for inferred synonyms |
| 812 | 806 |
for (Integer taxonFk : inferredSynonymsDataToBeSaved.keySet()) {
|
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invokeRankDataAndKingdomFk(inferredSynonymsDataToBeSaved.get(taxonFk), nomenclaturalCode, taxonFk, kingdomFk, state); |
|
| 807 |
TaxonName taxonName = inferredSynonymsDataToBeSaved.get(taxonFk); |
|
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NomenclaturalCode nomCode = taxonName.getNameType(); //nomCode was class variable before, not sure if this was important |
|
| 809 |
invokeRankDataAndKingdomFk(inferredSynonymsDataToBeSaved.get(taxonFk), nomCode, taxonFk, kingdomFk, state); |
|
| 814 | 810 |
} |
| 815 | 811 |
|
| 816 | 812 |
// Start transaction |
| ... | ... | |
| 864 | 860 |
TaxonName taxonName = acceptedTaxon.getName(); |
| 865 | 861 |
|
| 866 | 862 |
if (taxonName.isZoological()) {
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nomenclaturalCode = taxonName.getNameType(); |
|
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NomenclaturalCode nomenclaturalCode = taxonName.getNameType();
|
|
| 868 | 864 |
kingdomFk = PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode); |
| 869 | 865 |
|
| 870 | 866 |
Set<TaxonNode> taxonNodes = acceptedTaxon.getTaxonNodes(); |
Also available in: Unified diff
ref #8509 cleanup and handle nomCode not as class variable