Revision ad6b62ca
Added by Patrick Plitzner almost 7 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java | ||
|---|---|---|
| 91 | 91 |
@Override |
| 92 | 92 |
public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
|
| 93 | 93 |
ResultSet rs = partitioner.getResultSet(); |
| 94 |
Set<TaxonNameBase<?,?>> namesToSave = new HashSet<TaxonNameBase<?,?>>();
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| 95 |
Set<TaxonBase<?>> taxaToSave = new HashSet<TaxonBase<?>>();
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| 94 |
Set<TaxonNameBase> namesToSave = new HashSet<TaxonNameBase>();
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| 95 |
Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
|
|
| 96 | 96 |
try {
|
| 97 | 97 |
while (rs.next()){
|
| 98 | 98 |
makeSingleNameAndTaxon(state, rs, namesToSave, taxaToSave); |
| ... | ... | |
| 102 | 102 |
e.printStackTrace(); |
| 103 | 103 |
} |
| 104 | 104 |
|
| 105 |
getNameService().saveOrUpdate((TaxonNameBase) namesToSave);
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|
| 106 |
getTaxonService().saveOrUpdate((TaxonBase) taxaToSave);
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| 105 |
getNameService().saveOrUpdate(namesToSave); |
|
| 106 |
getTaxonService().saveOrUpdate(taxaToSave); |
|
| 107 | 107 |
return true; |
| 108 | 108 |
} |
| 109 | 109 |
|
| 110 |
private void makeSingleNameAndTaxon(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase<?,?>> namesToSave, Set<TaxonBase<?>> taxaToSave)
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| 110 |
private void makeSingleNameAndTaxon(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave, Set<TaxonBase> taxaToSave)
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| 111 | 111 |
throws SQLException {
|
| 112 | 112 |
long id = rs.getLong(RedListUtil.NAMNR); |
| 113 | 113 |
String clTaxonString = rs.getString(RedListUtil.CL_TAXON); |
| ... | ... | |
| 139 | 139 |
TaxonBase<?> checklistTaxon = null; |
| 140 | 140 |
if(CdmUtils.isNotBlank(clTaxonString) && !clTaxonString.trim().equals("-")){
|
| 141 | 141 |
checklistTaxon = (TaxonBase<?>) taxonBase.clone(); |
| 142 |
//TODO what to do with synonyms? |
|
| 143 | 142 |
if(checklistTaxon.isInstanceOf(Taxon.class)){
|
| 144 | 143 |
TaxonRelationship relation = HibernateProxyHelper.deproxy(checklistTaxon, Taxon.class).addTaxonRelation(HibernateProxyHelper.deproxy(taxonBase, Taxon.class), TaxonRelationshipType.CONGRUENT_TO(), null, null); |
| 145 | 144 |
relation.setDoubtful(true); |
| ... | ... | |
| 163 | 162 |
taxaToSave.add(taxonBase); |
| 164 | 163 |
} |
| 165 | 164 |
|
| 166 |
private void addConceptRelation(String relationString, String classificationNamespace, TaxonBase<?> gesamtListeTaxon, TaxonBase<?> checkListenTaxon, Set<TaxonBase<?>> taxaToSave, long id, RedListGefaesspflanzenImportState state){
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| 165 |
private void addConceptRelation(String relationString, String classificationNamespace, TaxonBase<?> gesamtListeTaxon, TaxonBase<?> checkListenTaxon, Set<TaxonBase> taxaToSave, long id, RedListGefaesspflanzenImportState state){
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|
| 167 | 166 |
if(CdmUtils.isNotBlank(relationString) && !relationString.equals(".")){
|
| 168 | 167 |
String substring = relationString.substring(relationString.length()-1, relationString.length()); |
| 169 | 168 |
TaxonRelationshipType taxonRelationshipTypeByKey = new RedListGefaesspflanzenTransformer().getTaxonRelationshipTypeByKey(substring); |
| ... | ... | |
| 189 | 188 |
* This can be changed with parameter <i>reverseRelation</i> |
| 190 | 189 |
* @return cloned taxon |
| 191 | 190 |
*/ |
| 192 |
private Taxon cloneTaxon(final TaxonBase<?> gesamtListeTaxon, final TaxonBase<?> checklisteTaxon, TaxonRelationshipType relationFromCloneToTaxon, Set<TaxonBase<?>> taxaToSave, long id, String sourceNameSpace, boolean reverseRelation, boolean doubtful, RedListGefaesspflanzenImportState state){
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| 191 |
private Taxon cloneTaxon(final TaxonBase<?> gesamtListeTaxon, final TaxonBase<?> checklisteTaxon, TaxonRelationshipType relationFromCloneToTaxon, Set<TaxonBase> taxaToSave, long id, String sourceNameSpace, boolean reverseRelation, boolean doubtful, RedListGefaesspflanzenImportState state){
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|
| 193 | 192 |
Taxon acceptedGesamtListeTaxon = getAcceptedTaxon(gesamtListeTaxon); |
| 194 | 193 |
Taxon acceptedChecklistTaxon = getAcceptedTaxon(checklisteTaxon); |
| 195 | 194 |
Taxon clonedTaxon = null; |
| ... | ... | |
| 346 | 345 |
checkAuthorShipConsistency(id, nomZusatzString, taxZusatzString, zusatzString, authorString, authorshipCache); |
| 347 | 346 |
} |
| 348 | 347 |
|
| 349 |
private NonViralName<?> importName(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase<?,?>> namesToSave) throws SQLException {
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| 348 |
private NonViralName<?> importName(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave) throws SQLException {
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|
| 350 | 349 |
|
| 351 | 350 |
long id = rs.getLong(RedListUtil.NAMNR); |
| 352 | 351 |
String taxNameString = rs.getString(RedListUtil.TAXNAME); |
| ... | ... | |
| 370 | 369 |
} |
| 371 | 370 |
name.setGenusOrUninomial(ep1String); |
| 372 | 371 |
if(CdmUtils.isNotBlank(ep2String)){
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| 373 |
name.setSpecificEpithet(ep2String); |
|
| 372 |
if(rank!=null && rank.isInfraGeneric()){
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| 373 |
name.setInfraGenericEpithet(ep2String); |
|
| 374 |
} |
|
| 375 |
else{
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| 376 |
name.setSpecificEpithet(ep2String); |
|
| 377 |
} |
|
| 374 | 378 |
} |
| 375 | 379 |
if(CdmUtils.isNotBlank(ep3String)){
|
| 376 | 380 |
name.setInfraSpecificEpithet(ep3String); |
| ... | ... | |
| 480 | 484 |
taxNameString = taxNameString.replace(RedListUtil.HYB_SIGN+" ", RedListUtil.HYB_SIGN);//hybrid sign has no space after it in titleCache for binomial hybrids |
| 481 | 485 |
} |
| 482 | 486 |
if(taxNameString.endsWith("- Gruppe")){
|
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taxNameString.replaceAll("- Gruppe", "species group");
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| 487 |
taxNameString = taxNameString.replaceAll("- Gruppe", "species group");
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| 484 | 488 |
} |
| 485 | 489 |
if(taxNameString.endsWith("- group")){
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| 486 |
taxNameString.replaceAll("- group", "species group");
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| 490 |
taxNameString = taxNameString.replaceAll("- group", "species group");
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| 487 | 491 |
} |
| 488 | 492 |
taxNameString = taxNameString.replace("[ranglos]", "[unranked]");
|
| 489 | 493 |
if(!taxNameString.trim().equals(nameCache)){
|
Also available in: Unified diff
Fix ClassCastException, improve taxon name check, fix rank evaluation
#5448