Revision 64367d00
Added by Katja Luther over 8 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/CdmApplicationAwareDefaultImport.java | ||
|---|---|---|
| 128 | 128 |
state.initialize(config); |
| 129 | 129 |
|
| 130 | 130 |
//do check for each class |
| 131 |
for (Class<ICdmImport> ioClass: config.getIoClassList()){
|
|
| 131 |
for (Class<ICdmIO> ioClass: config.getIoClassList()){
|
|
| 132 | 132 |
try {
|
| 133 | 133 |
String ioBeanName = getComponentBeanName(ioClass); |
| 134 | 134 |
ICdmIO cdmIo = applicationContext.getBean(ioBeanName, ICdmIO.class); |
| ... | ... | |
| 197 | 197 |
|
| 198 | 198 |
state.setSuccess(true); |
| 199 | 199 |
//do invoke for each class |
| 200 |
for (Class<ICdmImport> ioClass: config.getIoClassList()){
|
|
| 200 |
for (Class<ICdmIO> ioClass: config.getIoClassList()){
|
|
| 201 | 201 |
try {
|
| 202 | 202 |
String ioBeanName = getComponentBeanName(ioClass); |
| 203 |
ICdmImport cdmIo = applicationContext.getBean(ioBeanName, ICdmImport.class);
|
|
| 203 |
ICdmIO cdmIo = applicationContext.getBean(ioBeanName, ICdmIO.class);
|
|
| 204 | 204 |
if (cdmIo != null){
|
| 205 | 205 |
registerObservers(config, cdmIo); |
| 206 | 206 |
state.setCurrentIO(cdmIo); |
| 207 | 207 |
result &= cdmIo.invoke(state); |
| 208 |
importResult.addReport(cdmIo.getByteArray()); |
|
| 208 |
//importResult.addReport(cdmIo.getByteArray());
|
|
| 209 | 209 |
unRegisterObservers(config, cdmIo); |
| 210 | 210 |
}else{
|
| 211 | 211 |
logger.error("cdmIO was null");
|
| ... | ... | |
| 250 | 250 |
* @return |
| 251 | 251 |
* @throws IllegalArgumentException if the class does not have a "Component" annotation |
| 252 | 252 |
*/ |
| 253 |
public static String getComponentBeanName(Class<ICdmImport> ioClass) throws IllegalArgumentException {
|
|
| 253 |
public static String getComponentBeanName(Class<ICdmIO> ioClass) throws IllegalArgumentException {
|
|
| 254 | 254 |
Component component = ioClass.getAnnotation(Component.class); |
| 255 | 255 |
if (component == null){
|
| 256 | 256 |
throw new IllegalArgumentException("Class " + ioClass.getName() + " is missing a @Component annotation." );
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/DeleteNonReferencedReferencesConfigurator.java | ||
|---|---|---|
| 10 | 10 |
public class DeleteNonReferencedReferencesConfigurator extends ImportConfiguratorBase<DefaultImportState<DeleteNonReferencedReferencesConfigurator>, Object> implements IImportConfigurator{
|
| 11 | 11 |
|
| 12 | 12 |
private boolean doReferences = true; |
| 13 |
private boolean doAuthors = true;
|
|
| 14 |
|
|
| 13 |
private boolean doAuthors = true; |
|
| 14 |
|
|
| 15 | 15 |
public boolean isDoReferences() {
|
| 16 | 16 |
return doReferences; |
| 17 | 17 |
} |
| ... | ... | |
| 43 | 43 |
this.setSource(destination); |
| 44 | 44 |
this.setDestination(destination); |
| 45 | 45 |
this.setDbSchemaValidation(DbSchemaValidation.UPDATE); |
| 46 |
|
|
| 46 |
|
|
| 47 | 47 |
} |
| 48 | 48 |
|
| 49 | 49 |
@SuppressWarnings("unused")
|
| ... | ... | |
| 53 | 53 |
DeleteNonReferencedReferencesConfigurator result = new DeleteNonReferencedReferencesConfigurator(destination); |
| 54 | 54 |
return result; |
| 55 | 55 |
} |
| 56 |
|
|
| 57 |
|
|
| 58 |
|
|
| 56 |
|
|
| 57 |
|
|
| 58 |
|
|
| 59 | 59 |
@Override |
| 60 | 60 |
public <STATE extends ImportStateBase> STATE getNewState() {
|
| 61 | 61 |
return (STATE) new DefaultImportState(this); |
| ... | ... | |
| 65 | 65 |
protected void makeIoClassList() {
|
| 66 | 66 |
ioClassList = new Class[]{
|
| 67 | 67 |
DeleteNonReferencedreferencesUpdater.class |
| 68 |
};
|
|
| 68 |
}; |
|
| 69 | 69 |
} |
| 70 | 70 |
|
| 71 | 71 |
@Override |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/IImportConfigurator.java | ||
|---|---|---|
| 164 | 164 |
|
| 165 | 165 |
public void setNomenclaturalCode(NomenclaturalCode nomenclaturalCode); |
| 166 | 166 |
|
| 167 |
public Class<ICdmImport>[] getIoClassList();
|
|
| 167 |
public Class<ICdmIO>[] getIoClassList();
|
|
| 168 | 168 |
|
| 169 | 169 |
// public String[] getIoBeans(); |
| 170 | 170 |
// public void setIoBeans(String[] ioBeans); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/ImportConfiguratorBase.java | ||
|---|---|---|
| 76 | 76 |
private ICdmDataSource destination; |
| 77 | 77 |
private Person commentator = Person.NewTitledInstance("automatic CDM importer");
|
| 78 | 78 |
|
| 79 |
protected Class<ICdmImport>[] ioClassList;
|
|
| 79 |
protected Class<ICdmIO>[] ioClassList;
|
|
| 80 | 80 |
|
| 81 | 81 |
protected ICdmIO[] ioList; |
| 82 | 82 |
|
| ... | ... | |
| 148 | 148 |
} |
| 149 | 149 |
|
| 150 | 150 |
@Override |
| 151 |
public Class<ICdmImport>[] getIoClassList(){
|
|
| 151 |
public Class<ICdmIO>[] getIoClassList(){
|
|
| 152 | 152 |
if (ioClassList == null){
|
| 153 | 153 |
makeIoClassList(); |
| 154 | 154 |
} |
| ... | ... | |
| 158 | 158 |
/** |
| 159 | 159 |
* @param ioClassList |
| 160 | 160 |
*/ |
| 161 |
public void setIoClassList(Class<ICdmImport>[] ioClassList){
|
|
| 161 |
public void setIoClassList(Class<ICdmIO>[] ioClassList){
|
|
| 162 | 162 |
this.ioClassList = ioClassList; |
| 163 | 163 |
} |
| 164 | 164 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsrdf/TcsRdfTaxonNameImport.java | ||
|---|---|---|
| 9 | 9 |
|
| 10 | 10 |
package eu.etaxonomy.cdm.io.tcsrdf; |
| 11 | 11 |
|
| 12 |
import java.io.IOException; |
|
| 13 | 12 |
import java.io.InputStream; |
| 14 |
import java.util.List; |
|
| 15 | 13 |
import java.util.Set; |
| 16 | 14 |
|
| 17 | 15 |
import org.apache.log4j.Logger; |
| ... | ... | |
| 22 | 20 |
|
| 23 | 21 |
import com.hp.hpl.jena.rdf.model.Model; |
| 24 | 22 |
import com.hp.hpl.jena.rdf.model.ModelFactory; |
| 23 |
import com.hp.hpl.jena.rdf.model.Property; |
|
| 25 | 24 |
import com.hp.hpl.jena.rdf.model.RDFNode; |
| 26 | 25 |
import com.hp.hpl.jena.rdf.model.ResIterator; |
| 27 | 26 |
import com.hp.hpl.jena.rdf.model.Resource; |
| 28 | 27 |
import com.hp.hpl.jena.rdf.model.Statement; |
| 29 | 28 |
import com.hp.hpl.jena.rdf.model.StmtIterator; |
| 30 |
import com.hp.hpl.jena.rdf.model.Property; |
|
| 31 |
|
|
| 32 |
|
|
| 33 |
|
|
| 34 | 29 |
|
| 35 | 30 |
import eu.etaxonomy.cdm.common.XmlHelp; |
| 36 | 31 |
import eu.etaxonomy.cdm.io.common.ICdmIO; |
| ... | ... | |
| 49 | 44 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 50 | 45 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 51 | 46 |
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; |
| 47 |
import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser; |
|
| 48 |
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
|
| 52 | 49 |
|
| 53 | 50 |
/** |
| 54 | 51 |
* @author a.mueller |
| ... | ... | |
| 60 | 57 |
private static final Logger logger = Logger.getLogger(TcsRdfTaxonNameImport.class); |
| 61 | 58 |
|
| 62 | 59 |
private static int modCount = 5000; |
| 60 |
INonViralNameParser nameParser = new NonViralNameParserImpl(); |
|
| 63 | 61 |
|
| 64 | 62 |
public TcsRdfTaxonNameImport(){
|
| 65 | 63 |
super(); |
| ... | ... | |
| 127 | 125 |
Resource elTaxonName = root.getResource(taxonNameNamespace); |
| 128 | 126 |
|
| 129 | 127 |
int i = 0; |
| 130 |
|
|
| 128 |
|
|
| 131 | 129 |
TaxonNameBase name; |
| 132 | 130 |
Property property = root.getProperty(taxonNameNamespace+"authorship"); |
| 133 |
|
|
| 131 |
|
|
| 134 | 132 |
ResIterator iterator = root.listSubjectsWithProperty(property, (RDFNode) null); |
| 135 | 133 |
String id ; |
| 136 | 134 |
while (iterator.hasNext()){
|
| 137 |
|
|
| 135 |
|
|
| 138 | 136 |
Resource resource = iterator.next(); |
| 139 |
|
|
| 137 |
|
|
| 140 | 138 |
name = handleNameResource(resource, config); |
| 141 | 139 |
id = resource.getNameSpace(); |
| 142 | 140 |
taxonNameMap.put(id, name); |
| 143 | 141 |
} |
| 144 |
|
|
| 142 |
|
|
| 145 | 143 |
logger.info(i + " names handled"); |
| 146 | 144 |
getNameService().save(taxonNameMap.objects()); |
| 147 | 145 |
// makeNameSpecificData(nameMap); |
| ... | ... | |
| 156 | 154 |
protected boolean isIgnore(TcsRdfImportState state){
|
| 157 | 155 |
return ! state.getConfig().isDoTaxonNames(); |
| 158 | 156 |
} |
| 159 |
|
|
| 157 |
|
|
| 160 | 158 |
protected TaxonNameBase handleNameModel(Model model, TcsRdfImportConfigurator config, MapWrapper<TaxonNameBase> taxonNameMap, String uri){
|
| 161 | 159 |
Resource nameAbout = model.getResource(uri); |
| 162 | 160 |
TaxonNameBase result = handleNameResource(nameAbout, config); |
| 163 | 161 |
taxonNameMap.put(uri, result); |
| 164 | 162 |
return result; |
| 165 |
|
|
| 163 |
|
|
| 166 | 164 |
} |
| 167 |
|
|
| 165 |
|
|
| 168 | 166 |
private TaxonNameBase handleNameResource(Resource nameAbout, TcsRdfImportConfigurator config){
|
| 169 | 167 |
String idNamespace = "TaxonName"; |
| 170 |
|
|
| 168 |
|
|
| 171 | 169 |
StmtIterator stmts = nameAbout.listProperties(); |
| 172 | 170 |
while(stmts.hasNext()){
|
| 173 | 171 |
System.out.println(stmts.next().getPredicate().toString()); |
| 174 | 172 |
} |
| 175 |
|
|
| 173 |
|
|
| 176 | 174 |
Property prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"nomenclaturalCode"); |
| 177 | 175 |
Statement stateNomenclaturalCode = nameAbout.getProperty(prop); |
| 178 | 176 |
String strNomenclaturalCode = stateNomenclaturalCode.getObject().toString(); |
| 179 | 177 |
//Rank |
| 180 | 178 |
prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"rankString"); |
| 181 | 179 |
String strRank = nameAbout.getProperty(prop).getString(); |
| 182 |
|
|
| 183 |
|
|
| 184 |
|
|
| 180 |
|
|
| 181 |
|
|
| 182 |
|
|
| 185 | 183 |
try {
|
| 186 |
|
|
| 184 |
|
|
| 187 | 185 |
Rank rank = TcsRdfTransformer.rankString2Rank(strRank); |
| 188 | 186 |
NomenclaturalCode nomCode; |
| 189 | 187 |
if (strNomenclaturalCode != null){
|
| ... | ... | |
| 191 | 189 |
}else{
|
| 192 | 190 |
nomCode = NomenclaturalCode.ICNAFP; |
| 193 | 191 |
} |
| 194 |
|
|
| 192 |
|
|
| 195 | 193 |
TaxonNameBase<?,?> nameBase = nomCode.getNewTaxonNameInstance(rank); |
| 196 | 194 |
|
| 197 | 195 |
Set<String> omitAttributes = null; |
| 198 | 196 |
//makeStandardMapper(nameAbout, nameBase, omitAttributes, standardMappers); |
| 199 |
|
|
| 197 |
|
|
| 200 | 198 |
prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"nameComplete"); |
| 201 | 199 |
String strNameComplete = nameAbout.getProperty(prop).getString(); |
| 202 | 200 |
nameBase.setTitleCache(strNameComplete, true); |
| 203 |
|
|
| 201 |
|
|
| 204 | 202 |
prop = nameAbout.getModel().getProperty(config.getCommonNamespaceURIString()+"publishedIn"); |
| 205 | 203 |
String strPublishedIn = nameAbout.getProperty(prop).getString(); |
| 206 | 204 |
if (strPublishedIn != null && strPublishedIn != ""){
|
| ... | ... | |
| 226 | 224 |
((Reference<?>)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false)); |
| 227 | 225 |
} |
| 228 | 226 |
} |
| 229 |
|
|
| 227 |
|
|
| 230 | 228 |
if (nameBase instanceof NonViralName){
|
| 231 | 229 |
NonViralName<?> nonViralName = (NonViralName<?>)nameBase; |
| 232 | 230 |
prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"genusPart"); |
| ... | ... | |
| 237 | 235 |
prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"uninomial"); |
| 238 | 236 |
strGenusPart = nameAbout.getProperty(prop).getString(); |
| 239 | 237 |
} |
| 240 |
|
|
| 238 |
|
|
| 241 | 239 |
nonViralName.setGenusOrUninomial(strGenusPart); |
| 242 |
|
|
| 240 |
|
|
| 243 | 241 |
prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"infragenericEpithet"); |
| 244 | 242 |
try{
|
| 245 | 243 |
String strInfragenericEpithet = nameAbout.getProperty(prop).getString(); |
| 246 | 244 |
nonViralName.setInfraGenericEpithet(strInfragenericEpithet); |
| 247 | 245 |
}catch(NullPointerException e){
|
| 248 |
|
|
| 246 |
|
|
| 249 | 247 |
} |
| 250 | 248 |
try {
|
| 251 | 249 |
prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"specificEpithet"); |
| 252 | 250 |
String strSpecificEpithet = nameAbout.getProperty(prop).getString(); |
| 253 | 251 |
nonViralName.setSpecificEpithet(strSpecificEpithet); |
| 254 | 252 |
}catch(NullPointerException e){
|
| 255 |
|
|
| 253 |
|
|
| 256 | 254 |
} |
| 257 | 255 |
try{
|
| 258 | 256 |
prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"infraspecificEpithet"); |
| 259 | 257 |
String strInfraspecificEpithet = nameAbout.getProperty(prop).getString(); |
| 260 | 258 |
nonViralName.setInfraSpecificEpithet(strInfraspecificEpithet); |
| 261 | 259 |
}catch(NullPointerException e){
|
| 262 |
|
|
| 260 |
|
|
| 263 | 261 |
} |
| 264 | 262 |
//Authorships |
| 265 | 263 |
//TODO |
| ... | ... | |
| 270 | 268 |
<tm:hasMember rdf:resource="urn:lsid:ipni.org:authors:2691-1" |
| 271 | 269 |
tm:index="1" |
| 272 | 270 |
tm:role="Combination Author"/> |
| 273 |
<tm:hasMember rdf:resource="urn:lsid:ipni.org:authors:8096-1"
|
|
| 271 |
<tm:hasMember rdf:resource="urn:lsid:ipni.org:authors:8096-1" |
|
| 274 | 272 |
tm:index="1" |
| 275 | 273 |
tm:role="Basionym Author"/> |
| 276 | 274 |
</tm:Team> |
| ... | ... | |
| 290 | 288 |
try{
|
| 291 | 289 |
stateAutorTeamTeam = stateAuthorTeam.getProperty(prop); |
| 292 | 290 |
}catch(Exception e){
|
| 293 |
|
|
| 291 |
|
|
| 294 | 292 |
} |
| 295 | 293 |
try{
|
| 296 | 294 |
prop = stateAuthorTeam.getModel().getProperty(config.getTeamNamespaceURIString()+"name"); |
| 297 | 295 |
stateAutorTeamName = stateAuthorTeam.getProperty(prop); |
| 298 | 296 |
}catch(Exception e){
|
| 299 |
|
|
| 297 |
|
|
| 300 | 298 |
} |
| 301 | 299 |
try{
|
| 302 | 300 |
prop = nameAbout.getModel().getProperty(config.getTeamNamespaceURIString()+"hasMember"); |
| 303 | 301 |
stateTeamMember = ((Resource)stateAuthorTeam.getObject()).listProperties(prop); |
| 304 | 302 |
String memberString = null; |
| 305 | 303 |
Person person; |
| 306 |
for (Statement statement :stateTeamMember.toList()){
|
|
| 304 |
if (stateTeamMember.toList().size() ==1){
|
|
| 305 |
person = Person.NewTitledInstance(authorTeam.getTitleCache()); |
|
| 306 |
}else {
|
|
| 307 |
nameParser.parseAuthors(nonViralName, authorTeam.getTitleCache()); |
|
| 308 |
} |
|
| 309 |
/* for (Statement statement :stateTeamMember.toList()){
|
|
| 307 | 310 |
memberString =statement.getObject().toString(); |
| 308 | 311 |
if (memberString != null){
|
| 309 | 312 |
person = Person.NewTitledInstance(memberString); |
| 310 | 313 |
authorTeam.addTeamMember(person); |
| 311 | 314 |
} |
| 312 |
} |
|
| 315 |
}*/
|
|
| 313 | 316 |
}catch(Exception e){
|
| 314 | 317 |
System.err.println(e.getMessage()); |
| 315 | 318 |
} |
| 316 | 319 |
} |
| 317 |
|
|
| 318 |
|
|
| 319 |
|
|
| 320 |
|
|
| 321 |
|
|
| 322 |
|
|
| 320 | 323 |
nonViralName.setCombinationAuthorship(authorTeam); |
| 321 |
|
|
| 324 |
|
|
| 322 | 325 |
//Annotations: |
| 323 | 326 |
/* |
| 324 | 327 |
* <tn:hasAnnotation> |
| ... | ... | |
| 326 | 329 |
<tn:noteType rdf:resource="http://rs.tdwg.org/ontology/voc/TaxonName#replacementNameFor"/> |
| 327 | 330 |
<tn:objectTaxonName rdf:resource="urn:lsid:ipni.org:names:151538-1"/> |
| 328 | 331 |
</tn:NomenclaturalNote> |
| 329 |
</tn:hasAnnotation>
|
|
| 332 |
</tn:hasAnnotation> |
|
| 330 | 333 |
*/ |
| 331 | 334 |
/* |
| 332 | 335 |
String strInfraspecificEpithet = nameAbout.getProperty(prop).getString(); |
| ... | ... | |
| 370 | 373 |
//ImportHelper.setOriginalSource(nameBase, config.getSourceReference(), nameAbout, idNamespace); |
| 371 | 374 |
|
| 372 | 375 |
//checkAdditionalContents(elTaxonName, standardMappers, operationalMappers, unclearMappers); |
| 373 |
|
|
| 376 |
|
|
| 374 | 377 |
return nameBase; |
| 375 |
|
|
| 378 |
|
|
| 376 | 379 |
}catch(Exception e){
|
| 377 | 380 |
e.printStackTrace(); |
| 378 | 381 |
return null; |
| ... | ... | |
| 381 | 384 |
//name |
| 382 | 385 |
String strNameComplete = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "nameComplete", rdfNamespace); |
| 383 | 386 |
nameBase.setTitleCache(strNameComplete, true); |
| 384 |
|
|
| 387 |
|
|
| 385 | 388 |
//Reference |
| 386 | 389 |
//TODO |
| 387 | 390 |
String tcsElementName = "publishedIn"; |
| ... | ... | |
| 439 | 442 |
if (nameBase instanceof NonViralName){
|
| 440 | 443 |
NonViralName<?> nonViralName = (NonViralName<?>)nameBase; |
| 441 | 444 |
String strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "genusPart", rdfNamespace); |
| 442 |
|
|
| 445 |
|
|
| 443 | 446 |
//for names of rank genus the uninomial property should be used |
| 444 | 447 |
if (strGenusPart == null){
|
| 445 | 448 |
strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "uninomial", rdfNamespace); |
| 446 | 449 |
} |
| 447 | 450 |
nonViralName.setGenusOrUninomial(strGenusPart); |
| 448 |
|
|
| 451 |
|
|
| 449 | 452 |
String strInfragenericEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infragenericEpithet", rdfNamespace); |
| 450 | 453 |
nonViralName.setGenusOrUninomial(strInfragenericEpithet); |
| 451 |
|
|
| 452 |
|
|
| 453 |
|
|
| 454 |
|
|
| 455 |
|
|
| 456 |
|
|
| 454 | 457 |
String strSpecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "specificEpithet", rdfNamespace); |
| 455 | 458 |
nonViralName.setSpecificEpithet(strSpecificEpithet); |
| 456 |
|
|
| 459 |
|
|
| 457 | 460 |
String strInfraspecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infraspecificEpithet", rdfNamespace); |
| 458 | 461 |
nonViralName.setInfraSpecificEpithet(strInfraspecificEpithet); |
| 459 | 462 |
//AuthorTeams |
| ... | ... | |
| 509 | 512 |
} |
| 510 | 513 |
return null;*/ |
| 511 | 514 |
} |
| 512 |
|
|
| 515 |
|
|
| 513 | 516 |
protected TaxonNameBase handleNameElement(Element elTaxonName, Namespace rdfNamespace, Namespace taxonNameNamespace, TcsRdfImportConfigurator config, MapWrapper<TaxonNameBase> taxonNameMap){
|
| 514 | 517 |
String idNamespace = "TaxonName"; |
| 515 | 518 |
Attribute about = elTaxonName.getAttribute("about", rdfNamespace);
|
| 516 |
|
|
| 519 |
|
|
| 517 | 520 |
//create TaxonName element |
| 518 |
|
|
| 519 |
|
|
| 521 |
|
|
| 522 |
|
|
| 520 | 523 |
String nameAbout = elTaxonName.getAttributeValue("about", rdfNamespace);
|
| 521 | 524 |
if (nameAbout == null){
|
| 522 | 525 |
nameAbout = XmlHelp.getChildAttributeValue(elTaxonName, "TaxonName", taxonNameNamespace, "about", rdfNamespace); |
| 523 | 526 |
} |
| 524 |
|
|
| 525 |
|
|
| 527 |
|
|
| 528 |
|
|
| 526 | 529 |
String strRank = XmlHelp.getChildAttributeValue(elTaxonName, "rankString", taxonNameNamespace, "rankString", rdfNamespace); |
| 527 | 530 |
if (strRank == null){
|
| 528 | 531 |
strRank = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "rankString", rdfNamespace); |
| 529 |
|
|
| 532 |
|
|
| 530 | 533 |
} |
| 531 |
|
|
| 534 |
|
|
| 532 | 535 |
if (strRank == null){
|
| 533 | 536 |
strRank = XmlHelp.getChildAttributeValue(elTaxonName, "rank", taxonNameNamespace, "resource", rdfNamespace); |
| 534 |
|
|
| 537 |
|
|
| 535 | 538 |
} |
| 536 |
|
|
| 539 |
|
|
| 537 | 540 |
String strNomenclaturalCode = XmlHelp.getChildContentAttributeValue(elTaxonName, "TaxonName", taxonNameNamespace, "nomenclaturalCode", rdfNamespace); |
| 538 | 541 |
if (strNomenclaturalCode == null){
|
| 539 | 542 |
strNomenclaturalCode = XmlHelp.getChildAttributeValue(elTaxonName, "nomenclaturalCode", taxonNameNamespace, "resource", rdfNamespace); |
| 540 |
|
|
| 543 |
|
|
| 541 | 544 |
} |
| 542 | 545 |
try {
|
| 543 |
|
|
| 546 |
|
|
| 544 | 547 |
Rank rank = TcsRdfTransformer.rankString2Rank(strRank); |
| 545 | 548 |
NomenclaturalCode nomCode; |
| 546 | 549 |
if (strNomenclaturalCode != null){
|
| ... | ... | |
| 548 | 551 |
}else{
|
| 549 | 552 |
nomCode = NomenclaturalCode.ICNAFP; |
| 550 | 553 |
} |
| 551 |
|
|
| 554 |
|
|
| 552 | 555 |
TaxonNameBase<?,?> nameBase = nomCode.getNewTaxonNameInstance(rank); |
| 553 | 556 |
|
| 554 | 557 |
Set<String> omitAttributes = null; |
| 555 | 558 |
//makeStandardMapper(elTaxonName, nameBase, omitAttributes, standardMappers); |
| 556 |
|
|
| 559 |
|
|
| 557 | 560 |
//name |
| 558 | 561 |
String strNameComplete = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "nameComplete", rdfNamespace); |
| 559 | 562 |
nameBase.setTitleCache(strNameComplete, true); |
| 560 |
|
|
| 563 |
|
|
| 561 | 564 |
//Reference |
| 562 | 565 |
//TODO |
| 563 | 566 |
String tcsElementName = "publishedIn"; |
| ... | ... | |
| 615 | 618 |
if (nameBase instanceof NonViralName){
|
| 616 | 619 |
NonViralName<?> nonViralName = (NonViralName<?>)nameBase; |
| 617 | 620 |
String strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "genusPart", rdfNamespace); |
| 618 |
|
|
| 621 |
|
|
| 619 | 622 |
//for names of rank genus the uninomial property should be used |
| 620 | 623 |
if (strGenusPart == null){
|
| 621 | 624 |
strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "uninomial", rdfNamespace); |
| 622 | 625 |
} |
| 623 | 626 |
nonViralName.setGenusOrUninomial(strGenusPart); |
| 624 |
|
|
| 627 |
|
|
| 625 | 628 |
String strInfragenericEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infragenericEpithet", rdfNamespace); |
| 626 | 629 |
nonViralName.setGenusOrUninomial(strInfragenericEpithet); |
| 627 |
|
|
| 628 |
|
|
| 629 |
|
|
| 630 |
|
|
| 631 |
|
|
| 632 |
|
|
| 630 | 633 |
String strSpecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "specificEpithet", rdfNamespace); |
| 631 | 634 |
nonViralName.setSpecificEpithet(strSpecificEpithet); |
| 632 |
|
|
| 635 |
|
|
| 633 | 636 |
String strInfraspecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infraspecificEpithet", rdfNamespace); |
| 634 | 637 |
nonViralName.setInfraSpecificEpithet(strInfraspecificEpithet); |
| 635 | 638 |
//AuthorTeams |
| ... | ... | |
| 690 | 693 |
Model model = ModelFactory.createDefaultModel(); |
| 691 | 694 |
try{
|
| 692 | 695 |
model.read(is, null); |
| 693 |
|
|
| 696 |
|
|
| 694 | 697 |
config.makeNamespaces(model); |
| 695 |
|
|
| 698 |
|
|
| 696 | 699 |
String rdfNamespace = config.getRdfNamespaceURIString(); |
| 697 | 700 |
String taxonNameNamespace = config.getTnNamespaceURIString(); |
| 698 | 701 |
return handleNameModel(model, config, taxonNameMap, uri); |
| 699 |
|
|
| 700 |
|
|
| 702 |
|
|
| 703 |
|
|
| 701 | 704 |
}catch(Exception e){
|
| 702 | 705 |
logger.debug("The file was no valid rdf file");
|
| 703 | 706 |
} |
| 704 |
|
|
| 705 |
|
|
| 706 |
|
|
| 707 |
|
|
| 708 |
|
|
| 709 |
|
|
| 707 | 710 |
return null; |
| 708 | 711 |
} |
| 709 |
|
|
| 712 |
|
|
| 710 | 713 |
} |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsxml/in/TcsXmlImportBase.java | ||
|---|---|---|
| 38 | 38 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 40 | 40 |
import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
| 41 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
|
| 41 | 42 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 42 | 43 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 43 | 44 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 44 | 45 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 45 | 46 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 47 |
import eu.etaxonomy.cdm.strategy.exceptions.StringNotParsableException; |
|
| 48 |
import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser; |
|
| 49 |
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
|
| 46 | 50 |
|
| 47 | 51 |
/** |
| 48 | 52 |
* @author a.mueller |
| ... | ... | |
| 62 | 66 |
@Autowired |
| 63 | 67 |
IpniService service; |
| 64 | 68 |
|
| 69 |
INonViralNameParser nameParser = new NonViralNameParserImpl(); |
|
| 70 |
|
|
| 65 | 71 |
@Override |
| 66 | 72 |
protected abstract void doInvoke(TcsXmlImportState state); |
| 67 | 73 |
|
| ... | ... | |
| 309 | 315 |
|
| 310 | 316 |
|
| 311 | 317 |
@SuppressWarnings("unchecked")
|
| 312 |
protected TeamOrPersonBase<?> makeNameCitation(Element elNameCitation, MapWrapper<Person> authorMap, ResultWrapper<Boolean> success){
|
|
| 318 |
protected TeamOrPersonBase makeNameCitation(Element elNameCitation, MapWrapper<Person> authorMap, ResultWrapper<Boolean> success, NonViralName name,boolean isBasionymAuthor){
|
|
| 313 | 319 |
TeamOrPersonBase<?> result = null; |
| 314 | 320 |
String childName; |
| 315 | 321 |
boolean obligatory; |
| ... | ... | |
| 339 | 345 |
obligatory = true; |
| 340 | 346 |
Element elSimple = XmlHelp.getSingleChildElement(success, elNameCitation, childName, ns, obligatory); |
| 341 | 347 |
String simple = (elSimple == null)? "" : elSimple.getTextNormalize(); |
| 342 |
result = Team.NewInstance(); |
|
| 343 |
result.setNomenclaturalTitle(simple); |
|
| 348 |
result = Person.NewInstance(); |
|
| 349 |
try{
|
|
| 350 |
nameParser.parseAuthors(name, simple); |
|
| 351 |
}catch(StringNotParsableException e){
|
|
| 352 |
logger.error(e.getMessage()); |
|
| 353 |
} |
|
| 354 |
if (isBasionymAuthor){
|
|
| 355 |
result = name.getBasionymAuthorship(); |
|
| 356 |
}else{
|
|
| 357 |
result= name.getCombinationAuthorship(); |
|
| 358 |
} |
|
| 359 |
//result.setNomenclaturalTitle(simple); |
|
| 344 | 360 |
} |
| 345 | 361 |
} |
| 346 | 362 |
return result; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsxml/in/TcsXmlTaxonNameImport.java | ||
|---|---|---|
| 36 | 36 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 37 | 37 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 38 | 38 |
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; |
| 39 |
import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser; |
|
| 40 |
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
|
| 39 | 41 |
|
| 40 | 42 |
@Component("tcsXmlTaxonNameIO")
|
| 41 | 43 |
public class TcsXmlTaxonNameImport extends TcsXmlImportBase implements ICdmIO<TcsXmlImportState> {
|
| ... | ... | |
| 43 | 45 |
|
| 44 | 46 |
private static int modCount = 5000; |
| 45 | 47 |
|
| 48 |
private static INonViralNameParser parser = new NonViralNameParserImpl(); |
|
| 49 |
|
|
| 46 | 50 |
public TcsXmlTaxonNameImport(){
|
| 47 | 51 |
super(); |
| 48 | 52 |
} |
| ... | ... | |
| 295 | 299 |
obligatory = true; |
| 296 | 300 |
Element elSimple = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory); |
| 297 | 301 |
String simple = (elSimple == null)? "" : elSimple.getTextNormalize(); |
| 298 |
nameBase.setTitleCache(simple, false);
|
|
| 302 |
nameBase.setTitleCache(simple, true);
|
|
| 299 | 303 |
elementList.add(childName.toString()); |
| 300 | 304 |
|
| 301 | 305 |
childName = "CanonicalName"; |
| ... | ... | |
| 381 | 385 |
childName = "Authorship"; |
| 382 | 386 |
obligatory = false; |
| 383 | 387 |
Element elAuthorship = XmlHelp.getSingleChildElement(success, elCanonicalAuthorship, childName, ns, obligatory); |
| 384 |
TeamOrPersonBase author = makeNameCitation(elAuthorship, authorMap, success); |
|
| 388 |
TeamOrPersonBase author = makeNameCitation(elAuthorship, authorMap, success, nonViralName, false);
|
|
| 385 | 389 |
nonViralName.setCombinationAuthorship(author); |
| 386 | 390 |
//setCombinationAuthorship(author); |
| 387 | 391 |
testNoMoreElements(); |
| ... | ... | |
| 389 | 393 |
childName = "BasionymAuthorship"; |
| 390 | 394 |
obligatory = false; |
| 391 | 395 |
Element elBasionymAuthorship = XmlHelp.getSingleChildElement(success, elCanonicalAuthorship, childName, ns, obligatory); |
| 392 |
TeamOrPersonBase<?> basionymAuthor = makeNameCitation(elBasionymAuthorship, authorMap, success); |
|
| 396 |
TeamOrPersonBase<?> basionymAuthor = makeNameCitation(elBasionymAuthorship, authorMap, success, nonViralName, true);
|
|
| 393 | 397 |
nonViralName.setBasionymAuthorship(basionymAuthor); |
| 394 | 398 |
testNoMoreElements(); |
| 395 | 399 |
|
| 396 | 400 |
childName = "CombinationAuthorship"; |
| 397 | 401 |
obligatory = false; |
| 398 | 402 |
Element elCombinationAuthorship = XmlHelp.getSingleChildElement(success, elCanonicalAuthorship, childName, ns, obligatory); |
| 399 |
TeamOrPersonBase<?> combinationAuthor = makeNameCitation(elCombinationAuthorship, authorMap ,success); |
|
| 403 |
TeamOrPersonBase<?> combinationAuthor = makeNameCitation(elCombinationAuthorship, authorMap ,success, nonViralName, false);
|
|
| 400 | 404 |
if (combinationAuthor != null){
|
| 401 | 405 |
nonViralName.setCombinationAuthorship(combinationAuthor); |
| 402 | 406 |
} |
| ... | ... | |
| 546 | 550 |
private void makePublishedIn(TaxonNameBase name, Element elPublishedIn, MapWrapper<Reference> referenceMap, ResultWrapper<Boolean> success){
|
| 547 | 551 |
if (elPublishedIn != null && name != null){
|
| 548 | 552 |
Class<Reference> clazz = Reference.class; |
| 553 |
|
|
| 549 | 554 |
Reference<?> ref = makeReferenceType(elPublishedIn, clazz, referenceMap, success); |
| 550 | 555 |
if (ref instanceof Reference){
|
| 556 |
|
|
| 557 |
String titleCache = ref.getTitleCache(); |
|
| 558 |
|
|
| 559 |
ref.setAuthorship(((NonViralName)name).getCombinationAuthorship()); |
|
| 560 |
|
|
| 561 |
ref.setAbbrevTitleCache(titleCache, true); |
|
| 562 |
ref.setAbbrevTitle(titleCache); |
|
| 563 |
ref.setProtectedTitleCache(false); |
|
| 564 |
|
|
| 551 | 565 |
name.setNomenclaturalReference(ref); |
| 566 |
name.setProtectedFullTitleCache(false); |
|
| 567 |
name.getFullTitleCache(); |
|
| 568 |
name.setProtectedFullTitleCache(true); |
|
| 552 | 569 |
}else if (ref == null){
|
| 553 | 570 |
logger.warn("Nomecl. reference could not be created for '" + name.getTitleCache() + "'");
|
| 554 | 571 |
}else{
|
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/TaxonNameBase.java | ||
|---|---|---|
| 50 | 50 |
import org.hibernate.validator.constraints.NotEmpty; |
| 51 | 51 |
import org.springframework.util.ReflectionUtils; |
| 52 | 52 |
|
| 53 |
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper; |
|
| 53 | 54 |
import eu.etaxonomy.cdm.model.common.IParsable; |
| 54 | 55 |
import eu.etaxonomy.cdm.model.common.IRelated; |
| 55 | 56 |
import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
| ... | ... | |
| 339 | 340 |
if (protectedFullTitleCache){
|
| 340 | 341 |
return this.fullTitleCache; |
| 341 | 342 |
} |
| 342 |
if (fullTitleCache == null ){
|
|
| 343 |
// if (fullTitleCache == null ){
|
|
| 343 | 344 |
this.fullTitleCache = getTruncatedCache(generateFullTitle()); |
| 344 |
} |
|
| 345 |
// }
|
|
| 345 | 346 |
return fullTitleCache; |
| 346 | 347 |
} |
| 347 | 348 |
|
| ... | ... | |
| 844 | 845 |
if(!INomenclaturalReference.class.isAssignableFrom(nomenclaturalReference.getClass())){
|
| 845 | 846 |
throw new IllegalArgumentException("Parameter nomenclaturalReference is not assignable from INomenclaturalReference");
|
| 846 | 847 |
} |
| 847 |
this.nomenclaturalReference = (Reference)nomenclaturalReference;
|
|
| 848 |
this.nomenclaturalReference = HibernateProxyHelper.deproxy(nomenclaturalReference, Reference.class);
|
|
| 848 | 849 |
} else {
|
| 849 | 850 |
this.nomenclaturalReference = null; |
| 850 | 851 |
} |
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/reference/NomRefDefaultCacheStrategyBase.java | ||
|---|---|---|
| 13 | 13 |
import org.apache.log4j.Logger; |
| 14 | 14 |
|
| 15 | 15 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 16 |
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper; |
|
| 16 | 17 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
| 17 | 18 |
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference; |
| 18 | 19 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 128 | 129 |
@Override |
| 129 | 130 |
public String getNomenclaturalCitation(Reference nomenclaturalReference, String microReference) {
|
| 130 | 131 |
if (nomenclaturalReference.isProtectedAbbrevTitleCache()){
|
| 132 |
nomenclaturalReference = HibernateProxyHelper.deproxy(nomenclaturalReference, Reference.class); |
|
| 131 | 133 |
String cache = nomenclaturalReference.getAbbrevTitleCache(); |
| 132 | 134 |
return handleDetailAndYearForPreliminary(nomenclaturalReference, cache, microReference); |
| 133 | 135 |
|
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImpl.java | ||
|---|---|---|
| 516 | 516 |
* @param year |
| 517 | 517 |
* @return |
| 518 | 518 |
*/ |
| 519 |
private INomenclaturalReference parseReferenceTitle(String strReference, String year, boolean isInReference){
|
|
| 519 |
public INomenclaturalReference parseReferenceTitle(String strReference, String year, boolean isInReference){
|
|
| 520 | 520 |
IBook result = null; |
| 521 | 521 |
|
| 522 | 522 |
Matcher refSineDetailMatcher = referenceSineDetailPattern.matcher(strReference); |
| cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImpl.java | ||
|---|---|---|
| 972 | 972 |
// I think this is preferable to catching lazy initialization errors |
| 973 | 973 |
// as that solution only swallows and hides the exception, but doesn't |
| 974 | 974 |
// actually solve it. |
| 975 |
getSession().merge(taxonBase); |
|
| 975 |
//getSession().merge(taxonBase);
|
|
| 976 | 976 |
|
| 977 | 977 |
taxonBase.removeSources(); |
| 978 | 978 |
|
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonNodeServiceImpl.java | ||
|---|---|---|
| 117 | 117 |
} |
| 118 | 118 |
|
| 119 | 119 |
|
| 120 |
|
|
| 120 | 121 |
Classification classification = oldTaxonNode.getClassification(); |
| 121 |
Taxon oldTaxon = (Taxon) HibernateProxyHelper.deproxy(oldTaxonNode.getTaxon()); |
|
| 122 |
Taxon newAcceptedTaxon = (Taxon)this.taxonService.load(newAcceptedTaxonNode.getTaxon().getUuid()); |
|
| 122 |
Taxon oldTaxon = HibernateProxyHelper.deproxy(oldTaxonNode.getTaxon(), Taxon.class); |
|
| 123 |
Taxon newAcceptedTaxon = HibernateProxyHelper.deproxy(this.taxonService.load(newAcceptedTaxonNode.getTaxon().getUuid()), Taxon.class); |
|
| 124 |
|
|
| 123 | 125 |
// Move oldTaxon to newTaxon |
| 124 | 126 |
//TaxonNameBase<?,?> synonymName = oldTaxon.getName(); |
| 125 | 127 |
TaxonNameBase<?,?> synonymName = (TaxonNameBase)HibernateProxyHelper.deproxy(oldTaxon.getName()); |
| ... | ... | |
| 235 | 237 |
|
| 236 | 238 |
TaxonDeletionConfigurator conf = new TaxonDeletionConfigurator(); |
| 237 | 239 |
conf.setDeleteSynonymsIfPossible(false); |
| 240 |
conf.setDeleteNameIfPossible(false); |
|
| 238 | 241 |
DeleteResult result = taxonService.isDeletable(oldTaxon, conf); |
| 239 | 242 |
conf.setDeleteNameIfPossible(false); |
| 240 | 243 |
|
| ... | ... | |
| 248 | 251 |
result.includeResult(deleteTaxonNode(oldTaxonNode, conf)); |
| 249 | 252 |
} |
| 250 | 253 |
result.addUpdatedObject(newAcceptedTaxon); |
| 251 |
result.addUpdatedObject(oldTaxon); |
|
| 254 |
//result.addUpdatedObject(oldTaxon);
|
|
| 252 | 255 |
|
| 253 | 256 |
//oldTaxonNode.delete(); |
| 254 | 257 |
return result; |
| ... | ... | |
| 456 | 459 |
} |
| 457 | 460 |
|
| 458 | 461 |
result.setCdmEntity(node); |
| 459 |
boolean success = taxon.removeTaxonNode(node); |
|
| 460 |
dao.save(parent); |
|
| 462 |
|
|
| 463 |
boolean success = true; |
|
| 464 |
if(taxon != null){
|
|
| 465 |
success = taxon.removeTaxonNode(node); |
|
| 466 |
} |
|
| 467 |
|
|
| 461 | 468 |
taxonService.saveOrUpdate(taxon); |
| 462 | 469 |
result.addUpdatedObject(parent); |
| 463 | 470 |
|
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonServiceImpl.java | ||
|---|---|---|
| 966 | 966 |
if (config == null){
|
| 967 | 967 |
config = new TaxonDeletionConfigurator(); |
| 968 | 968 |
} |
| 969 |
Taxon taxon = (Taxon)dao.load(taxonUUID);
|
|
| 970 |
taxon = (Taxon) HibernateProxyHelper.deproxy(taxon); |
|
| 969 |
Taxon taxon = HibernateProxyHelper.deproxy(dao.load(taxonUUID), Taxon.class);
|
|
| 970 |
|
|
| 971 | 971 |
Classification classification = HibernateProxyHelper.deproxy(classificationDao.load(classificationUuid), Classification.class); |
| 972 | 972 |
DeleteResult result = isDeletable(taxon, config); |
| 973 | 973 |
|
| ... | ... | |
| 1144 | 1144 |
}else {
|
| 1145 | 1145 |
taxon.setName(null); |
| 1146 | 1146 |
} |
| 1147 |
|
|
| 1148 |
|
|
| 1147 |
this.saveOrUpdate(taxon); |
|
| 1148 |
|
|
| 1149 | 1149 |
// TaxonDescription |
| 1150 | 1150 |
/* Set<TaxonDescription> descriptions = taxon.getDescriptions(); |
| 1151 | 1151 |
|
| ... | ... | |
| 1166 | 1166 |
|
| 1167 | 1167 |
if ((taxon.getTaxonNodes() == null || taxon.getTaxonNodes().size()== 0) ){
|
| 1168 | 1168 |
try{
|
| 1169 |
//taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class); |
|
| 1169 | 1170 |
UUID uuid = dao.delete(taxon); |
| 1170 | 1171 |
|
| 1171 | 1172 |
}catch(Exception e){
|
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/UpdateResult.java | ||
|---|---|---|
| 122 | 122 |
return updatedObjects; |
| 123 | 123 |
} |
| 124 | 124 |
public void addUpdatedObject(CdmBase relatedObject) {
|
| 125 |
this.updatedObjects.add(relatedObject); |
|
| 125 |
if (relatedObject != null){
|
|
| 126 |
this.updatedObjects.add(relatedObject); |
|
| 127 |
} |
|
| 126 | 128 |
} |
| 127 | 129 |
public void addUpdatedObjects(Set<? extends CdmBase> updatedObjects) {
|
| 128 |
this.updatedObjects.addAll(updatedObjects); |
|
| 130 |
if (updatedObjects.size() >0){
|
|
| 131 |
this.updatedObjects.addAll(updatedObjects); |
|
| 132 |
} |
|
| 133 |
|
|
| 129 | 134 |
} |
| 130 | 135 |
|
| 131 | 136 |
// /** |
| ... | ... | |
| 182 | 187 |
public void includeResult(UpdateResult includedResult){
|
| 183 | 188 |
this.setMaxStatus(includedResult.getStatus()); |
| 184 | 189 |
this.addExceptions(includedResult.getExceptions()); |
| 190 |
|
|
| 185 | 191 |
this.addUpdatedObjects(includedResult.getUpdatedObjects()); |
| 192 |
|
|
| 193 |
|
|
| 186 | 194 |
} |
| 187 | 195 |
|
| 188 | 196 |
public boolean isOk(){
|
Also available in: Unified diff
minor