Revision ba5dcea5
Added by Andreas Müller almost 6 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightClassificationExport.java | ||
|---|---|---|
| 76 | 76 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 77 | 77 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 78 | 78 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
| 79 |
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship; |
|
| 80 |
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; |
|
| 79 | 81 |
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; |
| 80 | 82 |
|
| 81 | 83 |
/** |
| ... | ... | |
| 145 | 147 |
|
| 146 | 148 |
@SuppressWarnings("unchecked")
|
| 147 | 149 |
TaxonNodeOutStreamPartitioner<XmlExportState> partitioner |
| 148 |
= TaxonNodeOutStreamPartitioner.NewInstance( |
|
| 149 |
this, state, state.getConfig().getTaxonNodeFilter(), |
|
| 150 |
100, monitor, null); |
|
| 150 |
= TaxonNodeOutStreamPartitioner.NewInstance(
|
|
| 151 |
this, state, state.getConfig().getTaxonNodeFilter(),
|
|
| 152 |
100, monitor, null);
|
|
| 151 | 153 |
|
| 152 | 154 |
|
| 153 | 155 |
monitor.subTask("Start partitioning");
|
| 154 | 156 |
|
| 155 | 157 |
TaxonNode node = partitioner.next(); |
| 156 | 158 |
while (node != null){
|
| 157 |
handleTaxonNode(state, node); |
|
| 158 |
node = partitioner.next(); |
|
| 159 |
handleTaxonNode(state, node);
|
|
| 160 |
node = partitioner.next();
|
|
| 159 | 161 |
} |
| 160 | 162 |
|
| 161 | 163 |
|
| ... | ... | |
| 175 | 177 |
* @param classificationUuid |
| 176 | 178 |
*/ |
| 177 | 179 |
private void handleTaxonNode(CdmLightExportState state, TaxonNode taxonNode) {
|
| 178 |
try {
|
|
| 179 |
// TaxonNode taxonNode = getTaxonNodeService().find(taxonNodeUuid); |
|
| 180 | 180 |
|
| 181 | 181 |
if (taxonNode == null){
|
| 182 | 182 |
String message = "TaxonNode for given taxon node UUID not found. "; |
| 183 | 183 |
//TODO |
| 184 | 184 |
state.getResult().addWarning(message); |
| 185 | 185 |
}else{
|
| 186 |
TaxonNode root = taxonNode; |
|
| 187 |
if (root.hasTaxon()){
|
|
| 188 |
handleTaxon(state, root); |
|
| 189 |
}else{
|
|
| 190 |
// for (TaxonNode child : root.getChildNodes()){
|
|
| 191 |
// handleTaxon(state, child); |
|
| 192 |
// //TODO progress monitor |
|
| 193 |
// } |
|
| 186 |
try {
|
|
| 187 |
TaxonNode root = taxonNode; |
|
| 188 |
if (root.hasTaxon()){
|
|
| 189 |
handleTaxon(state, root); |
|
| 190 |
}else{
|
|
| 191 |
// for (TaxonNode child : root.getChildNodes()){
|
|
| 192 |
// handleTaxon(state, child); |
|
| 193 |
// //TODO progress monitor |
|
| 194 |
// } |
|
| 195 |
} |
|
| 196 |
} catch (Exception e) {
|
|
| 197 |
state.getResult().addException(e, "An unexpected error occurred when handling classification " + |
|
| 198 |
taxonNode.getUuid() + ": " + e.getMessage() + e.getStackTrace()); |
|
| 194 | 199 |
} |
| 195 | 200 |
} |
| 196 |
} catch (Exception e) {
|
|
| 197 |
state.getResult().addException(e, "An unexpected error occurred when handling classification " + |
|
| 198 |
taxonNode.getUuid() + ": " + e.getMessage() + e.getStackTrace()); |
|
| 199 |
} |
|
| 200 | 201 |
} |
| 201 | 202 |
|
| 202 | 203 |
/** |
| ... | ... | |
| 223 | 224 |
for (Synonym syn : taxon.getSynonyms()){
|
| 224 | 225 |
handleSynonym(state, syn); |
| 225 | 226 |
} |
| 226 |
|
|
| 227 |
for (TaxonRelationship rel : taxon.getProParteAndPartialSynonymRelations()){
|
|
| 228 |
handleProPartePartialMisapplied(state, rel); |
|
| 229 |
} |
|
| 230 |
for (TaxonRelationship rel : taxon.getMisappliedNameRelations()){
|
|
| 231 |
handleProPartePartialMisapplied(state, rel); |
|
| 232 |
} |
|
| 227 | 233 |
|
| 228 | 234 |
CdmLightExportTable table = CdmLightExportTable.TAXON; |
| 229 | 235 |
String[] csvLine = new String[table.getSize()]; |
| ... | ... | |
| 256 | 262 |
} |
| 257 | 263 |
} |
| 258 | 264 |
|
| 265 |
|
|
| 259 | 266 |
/** |
| 260 | 267 |
* @param state |
| 261 | 268 |
* @param taxon |
| ... | ... | |
| 704 | 711 |
csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name); |
| 705 | 712 |
csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, synonym.getSec()); |
| 706 | 713 |
csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(synonym.getSec()); |
| 707 |
if (synonym.isProParte()) {
|
|
| 708 |
csvLine[table.getIndex(CdmLightExportTable.IS_PRO_PARTE)] = "1"; |
|
| 709 |
}else {
|
|
| 710 |
csvLine[table.getIndex(CdmLightExportTable.IS_PRO_PARTE)] = "0"; |
|
| 711 |
} |
|
| 712 | 714 |
|
| 713 | 715 |
state.getProcessor().put(table, synonym, csvLine); |
| 714 | 716 |
} catch (Exception e) {
|
| ... | ... | |
| 718 | 720 |
} |
| 719 | 721 |
|
| 720 | 722 |
|
| 723 |
/** |
|
| 724 |
* Handles Misapplied names (including pro parte and partial as well as |
|
| 725 |
* pro parte and partial synonyms |
|
| 726 |
* @param state |
|
| 727 |
* @param rel |
|
| 728 |
*/ |
|
| 729 |
private void handleProPartePartialMisapplied(CdmLightExportState state, TaxonRelationship rel) {
|
|
| 730 |
try {
|
|
| 731 |
Taxon ppSyonym = rel.getFromTaxon(); |
|
| 732 |
if (isUnpublished(state.getConfig(), ppSyonym)){
|
|
| 733 |
return; |
|
| 734 |
} |
|
| 735 |
TaxonName name = ppSyonym.getName(); |
|
| 736 |
handleName(state, name); |
|
| 737 |
|
|
| 738 |
CdmLightExportTable table = CdmLightExportTable.SYNONYM; |
|
| 739 |
String[] csvLine = new String[table.getSize()]; |
|
| 740 |
|
|
| 741 |
csvLine[table.getIndex(CdmLightExportTable.SYNONYM_ID)] = getId(state, rel); |
|
| 742 |
csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, rel.getToTaxon()); |
|
| 743 |
csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name); |
|
| 744 |
|
|
| 745 |
//TODO pro parte synonyms have to references, the synonym relationship reference |
|
| 746 |
//and the sec reference of the Taxon representing the synonym. |
|
| 747 |
//As we currently do have only 1 reference column in CDM light the synonym relationship |
|
| 748 |
//reference is used here. This is according to how pro parte synonyms were mapped to |
|
| 749 |
//concept relationships in #7334 |
|
| 750 |
Reference secRef = rel.getCitation(); |
|
| 751 |
csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, secRef); |
|
| 752 |
csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(secRef); |
|
| 753 |
|
|
| 754 |
// Reference secRef = ppSyonym.getSec(); |
|
| 755 |
// csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, secRef); |
|
| 756 |
// csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(secRef); |
|
| 757 |
// Reference synSecRef = rel.getCitation(); |
|
| 758 |
// csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE_FK)] = getId(state, secRef); |
|
| 759 |
// csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE)] = getTitleCache(secRef); |
|
| 760 |
|
|
| 761 |
//pro parte type |
|
| 762 |
TaxonRelationshipType type = rel.getType(); |
|
| 763 |
csvLine[table.getIndex(CdmLightExportTable.IS_PRO_PARTE)] = type.isProParte()? "1":"0"; |
|
| 764 |
csvLine[table.getIndex(CdmLightExportTable.IS_PARTIAL)] = type.isPartial()? "1":"0"; |
|
| 765 |
csvLine[table.getIndex(CdmLightExportTable.IS_MISAPPLIED)] = type.isAnyMisappliedName()? "1":"0"; |
|
| 766 |
if (type.isPartial()) {
|
|
| 767 |
String message = "Partial synonyms/misapplied names not yet handled by CDM light. Created " |
|
| 768 |
+ "pro parte synonym/misapplied name instead for " + rel.getId(); |
|
| 769 |
state.getResult().addWarning(message, "handleProParteSynonym", ppSyonym.getTitleCache()); |
|
| 770 |
csvLine[table.getIndex(CdmLightExportTable.IS_PRO_PARTE)] = "1"; |
|
| 771 |
} |
|
| 772 |
|
|
| 773 |
state.getProcessor().put(table, ppSyonym, csvLine); |
|
| 774 |
} catch (Exception e) {
|
|
| 775 |
state.getResult().addException(e, "An unexpected error occurred when handling " |
|
| 776 |
+ "pro parte/partial synonym relationship " + |
|
| 777 |
cdmBaseStr(rel) + ": " + e.getMessage()); |
|
| 778 |
} |
|
| 779 |
|
|
| 780 |
} |
|
| 781 |
|
|
| 782 |
|
|
| 721 | 783 |
/** |
| 722 | 784 |
* @param state |
| 723 | 785 |
* @param name |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightExportTable.java | ||
|---|---|---|
| 46 | 46 |
protected static final String SEC_REFERENCE_FK = "SecReference_FK"; |
| 47 | 47 |
protected static final String SEC_REFERENCE = "SecReference"; |
| 48 | 48 |
protected static final String IS_PRO_PARTE = "IsProParteSynonym"; |
| 49 |
protected static final String IS_PARTIAL = "IsPartial"; |
|
| 50 |
protected static final String IS_MISAPPLIED = "IsMisapplied"; |
|
| 49 | 51 |
//Reference |
| 50 | 52 |
protected static final String REFERENCE_ID = "Reference_ID"; |
| 51 | 53 |
protected static final String BIBLIO_SHORT_CITATION = "BibliographicShortCitation"; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/CdmExportBase.java | ||
|---|---|---|
| 184 | 184 |
|| config.getTaxonNodeFilter().isIncludeUnpublished()); |
| 185 | 185 |
} |
| 186 | 186 |
|
| 187 |
|
|
| 188 |
/** |
|
| 189 |
* <code>true</code> if neither pro parte synonym or misapplied name has state publish nor |
|
| 190 |
* taxon node filter includes unpublished taxa. |
|
| 191 |
*/ |
|
| 192 |
protected boolean isUnpublished(CONFIG config, Taxon relatedSynonymOrMisappliedName) {
|
|
| 193 |
return ! (relatedSynonymOrMisappliedName.isPublish() |
|
| 194 |
|| config.getTaxonNodeFilter().isIncludeUnpublished()); |
|
| 195 |
} |
|
| 196 |
|
|
| 187 | 197 |
} |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTaxonExport.java | ||
|---|---|---|
| 80 | 80 |
TaxonName basionym = name.getBasionym(); |
| 81 | 81 |
Classification classification = node.getClassification(); |
| 82 | 82 |
if (! state.recordExists(file, taxon)){
|
| 83 |
handleTaxonBase(state, record, taxon, name, taxon, parent, basionym, classification, null, false, false);
|
|
| 83 |
handleTaxonBase(state, record, taxon, name, taxon, parent, basionym, classification, null); |
|
| 84 | 84 |
PrintWriter writer = createPrintWriter(state, file); |
| 85 | 85 |
record.write(state, writer); |
| 86 | 86 |
state.addExistingRecord(file, taxon); |
| ... | ... | |
| 90 | 90 |
//synonyms |
| 91 | 91 |
if (state.getConfig().isDoSynonyms()){
|
| 92 | 92 |
handleSynonyms(state, taxon, file, classification, metaRecord); |
| 93 |
//pro parte syonyms |
|
| 94 |
handleProparteSynonyms(state, taxon, file, classification, metaRecord); |
|
| 93 | 95 |
} |
| 94 | 96 |
|
| 95 | 97 |
//misapplied names |
| ... | ... | |
| 97 | 99 |
handleMisapplication(state, taxon, file, classification, metaRecord); |
| 98 | 100 |
} |
| 99 | 101 |
|
| 102 |
|
|
| 103 |
|
|
| 100 | 104 |
} catch (Exception e) {
|
| 101 | 105 |
String message = "Unexpected exception: " + e.getMessage(); |
| 102 | 106 |
state.getResult().addException(e, message); |
| ... | ... | |
| 117 | 121 |
|
| 118 | 122 |
DwcaTaxonRecord record = new DwcaTaxonRecord(metaRecord, state.getConfig()); |
| 119 | 123 |
SynonymType type = synonym.getType(); |
| 120 |
boolean isProParte = synonym.isProParte(); |
|
| 121 |
boolean isPartial = synonym.isPartial(); |
|
| 122 | 124 |
if (type == null){ // should not happen
|
| 123 | 125 |
type = SynonymType.SYNONYM_OF(); |
| 124 | 126 |
} |
| ... | ... | |
| 128 | 130 |
TaxonName basionym = name.getBasionym(); |
| 129 | 131 |
|
| 130 | 132 |
if (! state.recordExists(file, synonym)){
|
| 131 |
handleTaxonBase(state, record, synonym, name, taxon, parent, basionym, classification, type, isProParte, isPartial);
|
|
| 133 |
handleTaxonBase(state, record, synonym, name, taxon, parent, basionym, classification, type); |
|
| 132 | 134 |
PrintWriter writer = createPrintWriter(state, file); |
| 133 | 135 |
record.write(state, writer); |
| 134 | 136 |
state.addExistingRecord(file, synonym); |
| ... | ... | |
| 150 | 152 |
|
| 151 | 153 |
if (! state.recordExists(file, misappliedName)){
|
| 152 | 154 |
handleTaxonBase(state, record, misappliedName, name, taxon, parent, basionym, classification, |
| 153 |
misappliedNameRel.getType(), false, false);
|
|
| 155 |
misappliedNameRel.getType()); |
|
| 154 | 156 |
PrintWriter writer = createPrintWriter(state, file); |
| 155 | 157 |
record.write(state, writer); |
| 156 | 158 |
state.addExistingRecord(file, misappliedName); |
| ... | ... | |
| 158 | 160 |
} |
| 159 | 161 |
} |
| 160 | 162 |
|
| 163 |
private void handleProparteSynonyms(DwcaTaxExportState state, Taxon taxon, |
|
| 164 |
DwcaTaxExportFile file, Classification classification, DwcaMetaDataRecord metaRecord) throws FileNotFoundException, UnsupportedEncodingException, IOException {
|
|
| 165 |
|
|
| 166 |
Set<TaxonRelationship> proParteRels = taxon.getProParteAndPartialSynonymRelations(); |
|
| 167 |
for (TaxonRelationship proParteRel : proParteRels ){
|
|
| 168 |
DwcaTaxonRecord record = new DwcaTaxonRecord(metaRecord, state.getConfig()); |
|
| 169 |
Taxon proParteSynonym = proParteRel.getFromTaxon(); |
|
| 170 |
TaxonName name = proParteSynonym.getName(); |
|
| 171 |
//???? |
|
| 172 |
Taxon parent = null; |
|
| 173 |
TaxonName basionym = name.getBasionym(); |
|
| 174 |
|
|
| 175 |
if (! state.recordExists(file, proParteSynonym)){
|
|
| 176 |
handleTaxonBase(state, record, proParteSynonym, name, taxon, parent, basionym, classification, |
|
| 177 |
proParteRel.getType()); |
|
| 178 |
PrintWriter writer = createPrintWriter(state, file); |
|
| 179 |
record.write(state, writer); |
|
| 180 |
state.addExistingRecord(file, proParteSynonym); |
|
| 181 |
} |
|
| 182 |
} |
|
| 183 |
} |
|
| 184 |
|
|
| 185 |
|
|
| 186 |
|
|
| 161 | 187 |
/** |
| 162 | 188 |
* @param state |
| 163 | 189 |
* @param record |
| ... | ... | |
| 173 | 199 |
*/ |
| 174 | 200 |
private void handleTaxonBase(DwcaTaxExportState state, DwcaTaxonRecord record, TaxonBase<?> taxonBase, TaxonName name, |
| 175 | 201 |
Taxon acceptedTaxon, Taxon parent, TaxonName basionym, Classification classification, |
| 176 |
RelationshipTermBase<?> relType, boolean isProParte, boolean isPartial) {
|
|
| 202 |
RelationshipTermBase<?> relType) {
|
|
| 177 | 203 |
record.setId(taxonBase.getId()); |
| 178 | 204 |
record.setUuid(taxonBase.getUuid()); |
| 179 | 205 |
|
| ... | ... | |
| 256 | 282 |
|
| 257 | 283 |
record.setNomenclaturalCode(name.getNameType()); |
| 258 | 284 |
// ??? TODO Misapplied Names, inferred synonyms |
| 259 |
handleTaxonomicStatus(record, name, relType, isProParte, isPartial);
|
|
| 285 |
handleTaxonomicStatus(record, name, relType); |
|
| 260 | 286 |
handleNomStatus(record, taxonBase, name); |
| 261 | 287 |
|
| 262 | 288 |
// TODO we need to differentiate technical |
| ... | ... | |
| 368 | 394 |
* @param isProParte |
| 369 | 395 |
*/ |
| 370 | 396 |
private void handleTaxonomicStatus(DwcaTaxonRecord record, |
| 371 |
INonViralName name, RelationshipTermBase<?> type, |
|
| 372 |
boolean isProParte, boolean isPartial) {
|
|
| 397 |
INonViralName name, RelationshipTermBase<?> type) {
|
|
| 373 | 398 |
if (type == null){
|
| 374 | 399 |
record.setTaxonomicStatus(name.getNomenclaturalCode().acceptedTaxonStatusLabel()); |
| 375 | 400 |
}else{
|
| ... | ... | |
| 378 | 403 |
status = "heterotypicSynonym"; |
| 379 | 404 |
}else if(type.equals(SynonymType.HOMOTYPIC_SYNONYM_OF())){
|
| 380 | 405 |
status = "homotypicSynonym"; |
| 406 |
}else if(type.equals(TaxonRelationshipType.PRO_PARTE_SYNONYM_FOR())){
|
|
| 407 |
status = "proParteSynonym"; |
|
| 408 |
}else if(type.equals(TaxonRelationshipType.PARTIAL_SYNONYM_FOR())){
|
|
| 409 |
String message = "Partial synonym is not part of the gbif toxonomic status vocabulary"; |
|
| 410 |
logger.warn(message); |
|
| 411 |
status = "proParteMisapplied"; |
|
| 381 | 412 |
}else if(type.equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())){
|
| 382 | 413 |
status = "misapplied"; |
| 383 | 414 |
}else if(type.equals(TaxonRelationshipType.PRO_PARTE_MISAPPLIED_NAME_FOR())){
|
| 384 | 415 |
status = "proParteMisapplied"; |
| 416 |
}else if(type.equals(TaxonRelationshipType.PARTIAL_MISAPPLIED_NAME_FOR())){
|
|
| 417 |
String message = "Partial misapplied names are not part of the gbif toxonomic status vocabulary"; |
|
| 418 |
logger.warn(message); |
|
| 419 |
status = "partialMisapplied"; |
|
| 385 | 420 |
} |
| 386 |
if (isProParte){
|
|
| 387 |
status = "proParteSynonym"; |
|
| 388 |
}else if (isPartial){
|
|
| 389 |
String message = "Partial synonym is not part of the gbif toxonomic status vocabulary"; |
|
| 390 |
logger.warn(message); |
|
| 391 |
status = "partialSynonym"; |
|
| 392 |
} |
|
| 393 | 421 |
|
| 394 | 422 |
record.setTaxonomicStatus(status); |
| 395 | 423 |
} |
| cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/cdmLight/out/CdmLightExportTest.java | ||
|---|---|---|
| 10 | 10 |
|
| 11 | 11 |
import java.io.BufferedReader; |
| 12 | 12 |
import java.io.ByteArrayInputStream; |
| 13 |
import java.io.File; |
|
| 14 | 13 |
import java.io.FileNotFoundException; |
| 15 | 14 |
import java.io.IOException; |
| 16 | 15 |
import java.io.InputStreamReader; |
| ... | ... | |
| 160 | 159 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/BlankDataSet.xml") |
| 161 | 160 |
public void testFullTreeWithUnpublished(){
|
| 162 | 161 |
|
| 163 |
|
|
| 164 | 162 |
CdmLightExportConfigurator config = new CdmLightExportConfigurator(null); |
| 165 | 163 |
config.setTarget(TARGET.EXPORT_DATA); |
| 166 | 164 |
config.getTaxonNodeFilter().setIncludeUnpublished(true); |
| ... | ... | |
| 194 | 192 |
} |
| 195 | 193 |
Assert.assertTrue("There should be 1 synonym", count == 2);
|
| 196 | 194 |
} catch (IOException e) {
|
| 197 |
// TODO Auto-generated catch block |
|
| 198 | 195 |
e.printStackTrace(); |
| 196 |
Assert.fail("IO Exception thrown during test.");
|
|
| 199 | 197 |
} |
| 200 | 198 |
byte[] taxon = data.get(CdmLightExportTable.TAXON.getTableName()); |
| 201 | 199 |
Assert.assertNotNull("Taxon table must not be null", taxon);
|
| ... | ... | |
| 243 | 241 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/BlankDataSet.xml") |
| 244 | 242 |
public void testFullData(){
|
| 245 | 243 |
|
| 246 |
File destinationFolder = null; |
|
| 247 | 244 |
CdmLightExportConfigurator config = new CdmLightExportConfigurator(null); |
| 248 | 245 |
config.setTarget(TARGET.EXPORT_DATA); |
| 249 | 246 |
|
| ... | ... | |
| 270 | 267 |
} |
| 271 | 268 |
Assert.assertTrue("There should be 4 references", count == 5);
|
| 272 | 269 |
try{
|
| 273 |
stream = new ByteArrayInputStream(data.get(CdmLightExportTable.SYNONYM.getTableName())); |
|
| 274 |
Assert.fail("There should not be a synonym table, because the only synonym is not public.");
|
|
| 270 |
stream = new ByteArrayInputStream(data.get(CdmLightExportTable.SYNONYM.getTableName()));
|
|
| 271 |
Assert.fail("There should not be a synonym table, because the only synonym is not public.");
|
|
| 275 | 272 |
}catch(NullPointerException e){
|
| 276 |
|
|
| 273 |
//OK, should be thrown |
|
| 277 | 274 |
} |
| 278 | 275 |
|
| 279 | 276 |
} catch (IOException e) {
|
| 280 |
// TODO Auto-generated catch block |
|
| 281 |
e.printStackTrace(); |
|
| 277 |
throw new RuntimeException(e); |
|
| 282 | 278 |
} |
| 283 |
|
|
| 284 |
|
|
| 285 | 279 |
} |
| 286 | 280 |
|
| 287 | 281 |
/** |
| ... | ... | |
| 301 | 295 |
TaxonName familyName = parser.parseReferencedName("Family L., Sp. Pl. 3: 22. 1752",
|
| 302 | 296 |
NomenclaturalCode.ICNAFP, Rank.FAMILY()); |
| 303 | 297 |
setUuid(familyName,"e983cc5e-4c77-4c80-8cb0-73d43df31ef7"); |
| 304 |
setUuid((Reference)familyName.getNomenclaturalReference(), "b0dd7f4a-0c7f-4372-bc5d-3b676363bc63");
|
|
| 298 |
setUuid(familyName.getNomenclaturalReference(), "b0dd7f4a-0c7f-4372-bc5d-3b676363bc63"); |
|
| 305 | 299 |
Taxon family = Taxon.NewInstance(familyName, sec1); |
| 306 | 300 |
setUuid(family,"3162e136-f2e2-4f9a-9010-3f35908fbae1"); |
| 307 | 301 |
TaxonNode node1 = classification.addChildTaxon(family, sec1, "22"); |
| ... | ... | |
| 311 | 305 |
TaxonName genusName = parser.parseReferencedName("Genus Humb., The book of botany 3: 22. 1804",
|
| 312 | 306 |
NomenclaturalCode.ICNAFP, Rank.GENUS()); |
| 313 | 307 |
setUuid(genusName,"5e83cc5e-4c77-4d80-8cb0-73d63df35ee3"); |
| 314 |
setUuid((Reference)genusName.getNomenclaturalReference(), "5ed27f4a-6c7f-4372-bc5d-3b67636abc52");
|
|
| 308 |
setUuid(genusName.getNomenclaturalReference(), "5ed27f4a-6c7f-4372-bc5d-3b67636abc52"); |
|
| 315 | 309 |
Taxon genus = Taxon.NewInstance(genusName, sec1); |
| 316 | 310 |
setUuid(genus,"3f52e136-f2e1-4f9a-9010-2f35908fbd39"); |
| 317 | 311 |
|
| ... | ... | |
| 323 | 317 |
TaxonName speciesName = parser.parseReferencedName("Genus species Mill., The book of botany 3: 22. 1804",
|
| 324 | 318 |
NomenclaturalCode.ICNAFP, Rank.SPECIES()); |
| 325 | 319 |
setUuid(speciesName,"f983cc5e-4c77-4c80-8cb0-73d43df31ee9"); |
| 326 |
setUuid((Reference)speciesName.getNomenclaturalReference(), "a0dd7f4a-0c7f-4372-bc5d-3b676363bc0e");
|
|
| 320 |
setUuid(speciesName.getNomenclaturalReference(), "a0dd7f4a-0c7f-4372-bc5d-3b676363bc0e"); |
|
| 327 | 321 |
Taxon species = Taxon.NewInstance(speciesName, sec1); |
| 328 | 322 |
setUuid(species,"9182e136-f2e2-4f9a-9010-3f35908fb5e0"); |
| 329 | 323 |
TaxonName synonymName = parser.parseReferencedName("Genus synonym Mill., The book of botany 3: 22. 1804", NomenclaturalCode.ICNAFP, Rank.SPECIES());
|
| ... | ... | |
| 340 | 334 |
TaxonName subspeciesName = parser.parseReferencedName("Genus species subsp. subspec Mill., The book of botany 3: 22. 1804",
|
| 341 | 335 |
NomenclaturalCode.ICNAFP, Rank.SUBSPECIES()); |
| 342 | 336 |
setUuid(subspeciesName,"3483cc5e-4c77-4c80-8cb0-73d43df31ee3"); |
| 343 |
setUuid((Reference)subspeciesName.getNomenclaturalReference(), "b8dd7f4a-0c7f-4372-bc5d-3b676363bc0f");
|
|
| 337 |
setUuid(subspeciesName.getNomenclaturalReference(), "b8dd7f4a-0c7f-4372-bc5d-3b676363bc0f"); |
|
| 344 | 338 |
|
| 345 | 339 |
Taxon subspecies = Taxon.NewInstance(subspeciesName, sec1); |
| 346 | 340 |
setUuid(subspecies, "b2c86698-500e-4efb-b9ae-6bb6e701d4bc"); |
Also available in: Unified diff
ref #7334 adapt DwCA and CDM light export to new pro parte synonym handling, also add misapplied name handling to CDM light