Revision db183545
Added by Andreas Müller almost 7 years ago
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/ipni/IpniService.java | ||
|---|---|---|
| 449 | 449 |
} |
| 450 | 450 |
|
| 451 | 451 |
|
| 452 |
private List<TaxonName<?,?>> buildNameList( InputStream content, ICdmRepository repository, IIpniServiceConfigurator iConfig) throws IOException {
|
|
| 452 |
private List<TaxonName> buildNameList( InputStream content, ICdmRepository repository, IIpniServiceConfigurator iConfig) throws IOException {
|
|
| 453 | 453 |
IpniServiceNamesConfigurator config = (IpniServiceNamesConfigurator)iConfig; |
| 454 |
List<TaxonName<?,?>> result = new ArrayList<>();
|
|
| 454 |
List<TaxonName> result = new ArrayList<>(); |
|
| 455 | 455 |
BufferedReader reader = new BufferedReader (new InputStreamReader(content)); |
| 456 | 456 |
|
| 457 | 457 |
String headerLine = reader.readLine(); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/CdmImportBase.java | ||
|---|---|---|
| 1038 | 1038 |
* |
| 1039 | 1039 |
* @see #getTaxonDescription(Taxon, boolean, boolean) |
| 1040 | 1040 |
*/ |
| 1041 |
public TaxonNameDescription getTaxonNameDescription(TaxonName<?,?> name, Reference ref, boolean isImageGallery, boolean createNewIfNotExists) {
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|
| 1041 |
public TaxonNameDescription getTaxonNameDescription(TaxonName name, Reference ref, boolean isImageGallery, boolean createNewIfNotExists) {
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|
| 1042 | 1042 |
TaxonNameDescription result = null; |
| 1043 | 1043 |
Set<TaxonNameDescription> descriptions= name.getDescriptions(); |
| 1044 | 1044 |
for (TaxonNameDescription description : descriptions){
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/out/DbDescriptionElementTaxonMapper.java | ||
|---|---|---|
| 76 | 76 |
} |
| 77 | 77 |
}else if (inDescription.isInstanceOf(TaxonNameDescription.class)){
|
| 78 | 78 |
TaxonNameDescription nameDescription = CdmBase.deproxy(inDescription, TaxonNameDescription.class); |
| 79 |
TaxonName<?,?> taxonName = nameDescription.getTaxonName();
|
|
| 79 |
TaxonName taxonName = nameDescription.getTaxonName(); |
|
| 80 | 80 |
if (isCache){
|
| 81 | 81 |
return taxonName.getTitleCache(); |
| 82 | 82 |
}else{
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/out/DbOriginalNameMapper.java | ||
|---|---|---|
| 52 | 52 |
if (cdmBase.isInstanceOf(OriginalSourceBase.class)){
|
| 53 | 53 |
OriginalSourceBase<?> source = CdmBase.deproxy(cdmBase, OriginalSourceBase.class); |
| 54 | 54 |
String nameString = source.getOriginalNameString(); |
| 55 |
TaxonName<?,?> name = null;
|
|
| 55 |
TaxonName name = null; |
|
| 56 | 56 |
if (source.isInstanceOf(DescriptionElementSource.class)){
|
| 57 | 57 |
DescriptionElementSource descSource = CdmBase.deproxy(source, DescriptionElementSource.class); |
| 58 | 58 |
name = descSource.getNameUsedInSource(); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/utils/ImportDeduplicationHelper.java | ||
|---|---|---|
| 364 | 364 |
private void initNameMap(STATE state) {
|
| 365 | 365 |
if (!nameMapIsInitialized && repository != null){
|
| 366 | 366 |
List<String> propertyPaths = Arrays.asList("");
|
| 367 |
List<TaxonName<?,?>> existingNames = repository.getNameService().list(null, null, null, null, propertyPaths);
|
|
| 368 |
for (TaxonName<?,?> name : existingNames){
|
|
| 367 |
List<TaxonName> existingNames = repository.getNameService().list(null, null, null, null, propertyPaths); |
|
| 368 |
for (TaxonName name : existingNames){
|
|
| 369 | 369 |
putName(name.getTitleCache(), name); |
| 370 | 370 |
} |
| 371 | 371 |
nameMapIsInitialized = true; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/in/DwcTaxonStreamItem2CdmTaxonConverter.java | ||
|---|---|---|
| 133 | 133 |
Rank rank = getRank(csvTaxonRecord, nomCode); |
| 134 | 134 |
|
| 135 | 135 |
//name && name published in |
| 136 |
TaxonName<?,?> name = getScientificName(csvTaxonRecord, nomCode, rank, resultList, sourceReference);
|
|
| 136 |
TaxonName name = getScientificName(csvTaxonRecord, nomCode, rank, resultList, sourceReference); |
|
| 137 | 137 |
taxonBase.setName(name); |
| 138 | 138 |
|
| 139 | 139 |
//nameAccordingTo |
| ... | ... | |
| 500 | 500 |
} |
| 501 | 501 |
|
| 502 | 502 |
|
| 503 |
private TaxonName<?,?> getScientificName(StreamItem item, NomenclaturalCode nomCode, Rank rank, List<MappedCdmBase> resultList, Reference sourceReference) {
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|
| 504 |
TaxonName<?,?> name = null;
|
|
| 503 |
private TaxonName getScientificName(StreamItem item, NomenclaturalCode nomCode, Rank rank, List<MappedCdmBase> resultList, Reference sourceReference) {
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|
| 504 |
TaxonName name = null; |
|
| 505 | 505 |
String strScientificName = getValue(item, TermUri.DWC_SCIENTIFIC_NAME); |
| 506 | 506 |
//Name |
| 507 | 507 |
if (strScientificName != null){
|
| 508 |
name = (TaxonName<?,?>)parser.parseFullName(strScientificName, nomCode, rank);
|
|
| 508 |
name = (TaxonName)parser.parseFullName(strScientificName, nomCode, rank); |
|
| 509 | 509 |
if ( rank != null && name != null && name.getRank() != null && ! rank.equals(name.getRank())){
|
| 510 | 510 |
if (config.isValidateRankConsistency()){
|
| 511 | 511 |
String message = "Parsed rank %s (%s) differs from rank %s given by fields 'taxonRank' or 'verbatimTaxonRank'"; |
| ... | ... | |
| 607 | 607 |
|
| 608 | 608 |
|
| 609 | 609 |
//TODO we may configure in configuration that scientific name never includes Authorship |
| 610 |
private void checkAuthorship(TaxonName<?,?> nameBase, StreamItem item) {
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|
| 610 |
private void checkAuthorship(TaxonName nameBase, StreamItem item) {
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|
| 611 | 611 |
if (!nameBase.isNonViral()){
|
| 612 | 612 |
return; |
| 613 | 613 |
} |
| ... | ... | |
| 677 | 677 |
* @return |
| 678 | 678 |
*/ |
| 679 | 679 |
private TaxonBase<?> getTaxonBase(StreamItem item) {
|
| 680 |
TaxonName<?,?> name = null;
|
|
| 680 |
TaxonName name = null; |
|
| 681 | 681 |
Reference sec = null; |
| 682 | 682 |
TaxonBase<?> result; |
| 683 | 683 |
String taxStatus = item.get(TermUri.DWC_TAXONOMIC_STATUS); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTypesExport.java | ||
|---|---|---|
| 241 | 241 |
return true; |
| 242 | 242 |
} |
| 243 | 243 |
|
| 244 |
private TaxonName<?,?> getScientificName(DerivedUnitFacade facade) {
|
|
| 244 |
private TaxonName getScientificName(DerivedUnitFacade facade) {
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|
| 245 | 245 |
Set<DeterminationEvent> detEvents = facade.getDeterminations(); |
| 246 | 246 |
for (DeterminationEvent detEvent : detEvents){
|
| 247 | 247 |
if (detEvent.getPreferredFlag()== true || detEvents.size()==1){
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/distribution/DistributionImport.java | ||
|---|---|---|
| 186 | 186 |
} |
| 187 | 187 |
|
| 188 | 188 |
// get the taxa for the matching names |
| 189 |
for(TaxonName<?,?> dbTaxonName: taxonNames) {
|
|
| 189 |
for(TaxonName dbTaxonName: taxonNames) {
|
|
| 190 | 190 |
|
| 191 | 191 |
Set<Taxon> taxa = dbTaxonName.getTaxa(); |
| 192 | 192 |
if (taxa.isEmpty()) {
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/taxa/NormalExplicitImport.java | ||
|---|---|---|
| 838 | 838 |
//TODO implementation must be improved when matching of taxon names with existing names is implemented |
| 839 | 839 |
//=> the assumption that the only description is the description added by this import |
| 840 | 840 |
//is wrong then |
| 841 |
private TaxonNameDescription getNameDescription(TaxonName<?,?> name) {
|
|
| 841 |
private TaxonNameDescription getNameDescription(TaxonName name) {
|
|
| 842 | 842 |
Set<TaxonNameDescription> descriptions = name.getDescriptions(); |
| 843 | 843 |
if (descriptions.size()>1){
|
| 844 | 844 |
throw new IllegalStateException("Implementation does not yet support names with multiple descriptions");
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/markup/MarkupNomenclatureImport.java | ||
|---|---|---|
| 164 | 164 |
// this a rule? |
| 165 | 165 |
TaxonName speciesName = TaxonName.castAndDeproxy( |
| 166 | 166 |
handleNom(state, reader, next, null)); |
| 167 |
for (TaxonName<?, ?> name : homotypicalGroup
|
|
| 167 |
for (TaxonName name : homotypicalGroup |
|
| 168 | 168 |
.getTypifiedNames()) {
|
| 169 | 169 |
name.addNameTypeDesignation(speciesName, null, null, |
| 170 | 170 |
null, status, false, false, false, false); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/outputmodel/OutputModelClassificationExport.java | ||
|---|---|---|
| 1074 | 1074 |
* TypeDesignatedByRef_Fk |
| 1075 | 1075 |
*/ |
| 1076 | 1076 |
|
| 1077 |
private void handleTypeDesignations(OutputModelExportState state, TaxonName name){
|
|
| 1078 |
Set<SpecimenTypeDesignation> typeDesignations = name.getTypeDesignations(); |
|
| 1077 |
private void handleSpecimenTypeDesignations(OutputModelExportState state, TaxonName name){
|
|
| 1078 |
Set<SpecimenTypeDesignation> typeDesignations = name.getSpecimenTypeDesignations();
|
|
| 1079 | 1079 |
OutputModelTable table = OutputModelTable.TYPE_DESIGNATION; |
| 1080 | 1080 |
String nameId = getId(state, name); |
| 1081 | 1081 |
String[] csvLine = new String[table.getSize()]; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/SpecimenImportBase.java | ||
|---|---|---|
| 150 | 150 |
} |
| 151 | 151 |
|
| 152 | 152 |
if(taxonName==null && atomisedTaxonName!=null){
|
| 153 |
taxonName = (TaxonName<?, ?>) atomisedTaxonName;
|
|
| 153 |
taxonName = (TaxonName) atomisedTaxonName; |
|
| 154 | 154 |
state.getReport().addName(taxonName); |
| 155 | 155 |
logger.info("Created new taxon name "+taxonName);
|
| 156 | 156 |
if(taxonName.hasProblem()){
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenCdmExcelImport.java | ||
|---|---|---|
| 845 | 845 |
if (result == null){
|
| 846 | 846 |
NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance(); |
| 847 | 847 |
NomenclaturalCode code = state.getConfig().getNomenclaturalCode(); |
| 848 |
result = (TaxonName<?,?>)parser.parseFullName(name, code, null);
|
|
| 848 |
result = (TaxonName)parser.parseFullName(name, code, null); |
|
| 849 | 849 |
|
| 850 | 850 |
} |
| 851 | 851 |
if (result != null){
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenSythesysExcelImport.java | ||
|---|---|---|
| 455 | 455 |
taxonName = TaxonNameFactory.NewNonViralInstance(null); |
| 456 | 456 |
taxonName.setTitleCache(scientificName, true); |
| 457 | 457 |
} |
| 458 |
getNameService().save((TaxonName<?,?>)taxonName);
|
|
| 458 |
getNameService().save((TaxonName)taxonName); |
|
| 459 | 459 |
taxon = Taxon.NewInstance(taxonName, ref); //sec set null |
| 460 | 460 |
getTaxonService().save(taxon); |
| 461 | 461 |
// refreshTransaction(); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx/SimpleSpecimen.java | ||
|---|---|---|
| 35 | 35 |
private DerivationEvent derivationEvent; |
| 36 | 36 |
private DerivedUnit specimen; |
| 37 | 37 |
private Collection collection; |
| 38 |
private TaxonName<?, ?> storedUnderName;
|
|
| 38 |
private TaxonName storedUnderName; |
|
| 39 | 39 |
private String titleCache; |
| 40 | 40 |
|
| 41 | 41 |
|
| ... | ... | |
| 95 | 95 |
/** |
| 96 | 96 |
* @return the storedUnderName |
| 97 | 97 |
*/ |
| 98 |
public TaxonName<?, ?> getStoredUnderName() {
|
|
| 98 |
public TaxonName getStoredUnderName() {
|
|
| 99 | 99 |
return storedUnderName; |
| 100 | 100 |
} |
| 101 | 101 |
|
| 102 | 102 |
/** |
| 103 | 103 |
* @param storedUnderName the storedUnderName to set |
| 104 | 104 |
*/ |
| 105 |
public void setStoredUnderName(TaxonName<?, ?> storedUnderName) {
|
|
| 105 |
public void setStoredUnderName(TaxonName storedUnderName) {
|
|
| 106 | 106 |
this.storedUnderName = storedUnderName; |
| 107 | 107 |
} |
| 108 | 108 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx/TaxonXNomenclatureImport.java | ||
|---|---|---|
| 512 | 512 |
String[] collectionStrings = typeLocStatus.substring(pos).split(",");
|
| 513 | 513 |
for(String collectionString : collectionStrings){
|
| 514 | 514 |
if (taxonBase != null){
|
| 515 |
TaxonName<?,?> taxonName = taxonBase.getName();
|
|
| 515 |
TaxonName taxonName = taxonBase.getName(); |
|
| 516 | 516 |
if (taxonName != null){
|
| 517 | 517 |
Reference citation = null; |
| 518 | 518 |
String citationMicroReference = null; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsxml/in/TcsXmlTaxonImport.java | ||
|---|---|---|
| 122 | 122 |
|
| 123 | 123 |
logger.info("start make TaxonConcepts ...");
|
| 124 | 124 |
MapWrapper<TaxonBase> taxonMap = (MapWrapper<TaxonBase>)state.getStore(ICdmIO.TAXON_STORE); |
| 125 |
MapWrapper<TaxonName<?,?>> taxonNameMap = (MapWrapper<TaxonName<?,?>>)state.getStore(ICdmIO.TAXONNAME_STORE);
|
|
| 125 |
MapWrapper<TaxonName> taxonNameMap = (MapWrapper<TaxonName>)state.getStore(ICdmIO.TAXONNAME_STORE);
|
|
| 126 | 126 |
MapWrapper<Reference> referenceMap = (MapWrapper<Reference>)state.getStore(ICdmIO.REFERENCE_STORE); |
| 127 | 127 |
Map<String, CommonTaxonName> commonNameMap = new HashMap<String, CommonTaxonName>(); |
| 128 | 128 |
|
| ... | ... | |
| 311 | 311 |
* @param elTaxonRelationships |
| 312 | 312 |
* @param success |
| 313 | 313 |
*/ |
| 314 |
private TaxonName<?, ?> makeScientificName(Element elName, NomenclaturalCode code, MapWrapper<? extends TaxonName<?,?>> objectMap, ResultWrapper<Boolean> success){
|
|
| 315 |
TaxonName<?,?> result = null;
|
|
| 314 |
private TaxonName makeScientificName(Element elName, NomenclaturalCode code, MapWrapper<? extends TaxonName> objectMap, ResultWrapper<Boolean> success){
|
|
| 315 |
TaxonName result = null; |
|
| 316 | 316 |
if (elName != null){
|
| 317 | 317 |
String language = elName.getAttributeValue("language");
|
| 318 | 318 |
//Language |
| ... | ... | |
| 320 | 320 |
logger.warn("language for name not yet implemented. Language for scientific name should always be Latin");
|
| 321 | 321 |
} |
| 322 | 322 |
Class<? extends IdentifiableEntity> clazz = TaxonName.class; |
| 323 |
result = (TaxonName<?,?>)makeReferenceType (elName, clazz , objectMap, success);
|
|
| 323 |
result = (TaxonName)makeReferenceType (elName, clazz , objectMap, success); |
|
| 324 | 324 |
if(result == null){
|
| 325 | 325 |
logger.warn("Name not found");
|
| 326 | 326 |
success.setValue(false); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsxml/in/TcsXmlTaxonNameRelationsImport.java | ||
|---|---|---|
| 59 | 59 |
|
| 60 | 60 |
|
| 61 | 61 |
logger.info("start make taxon name relations ...");
|
| 62 |
MapWrapper<TaxonName<?,?>> taxonNameMap = (MapWrapper<TaxonName<?,?>>)state.getStore(ICdmIO.TAXONNAME_STORE);
|
|
| 62 |
MapWrapper<TaxonName> taxonNameMap = (MapWrapper<TaxonName>)state.getStore(ICdmIO.TAXONNAME_STORE);
|
|
| 63 | 63 |
MapWrapper<Reference> referenceMap = (MapWrapper<Reference>)state.getStore(ICdmIO.REFERENCE_STORE); |
| 64 | 64 |
|
| 65 | 65 |
Set<TaxonName> nameStore = new HashSet<TaxonName>(); |
| ... | ... | |
| 309 | 309 |
} |
| 310 | 310 |
|
| 311 | 311 |
|
| 312 |
private boolean makeNomenclaturalNoteType(TcsXmlImportConfigurator tcsConfig, Element elRelation, NameRelationshipType relType, MapWrapper<TaxonName<?,?>> taxonNameMap, Set<TaxonName> nameStore, String id, boolean inverse){
|
|
| 312 |
private boolean makeNomenclaturalNoteType(TcsXmlImportConfigurator tcsConfig, Element elRelation, NameRelationshipType relType, MapWrapper<TaxonName> taxonNameMap, Set<TaxonName> nameStore, String id, boolean inverse){
|
|
| 313 | 313 |
if (elRelation == null){
|
| 314 | 314 |
return false; |
| 315 | 315 |
} |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsxml/in/TcsXmlTaxonRelationsImport.java | ||
|---|---|---|
| 574 | 574 |
TaxonName aboutName = aboutTaxon.getName(); |
| 575 | 575 |
if (aboutName != null){
|
| 576 | 576 |
Set<TaxonName> typifiedNames = aboutName.getHomotypicalGroup().getTypifiedNames(); |
| 577 |
for (TaxonName<?,?> typifiedName : typifiedNames){
|
|
| 577 |
for (TaxonName typifiedName : typifiedNames){
|
|
| 578 | 578 |
//TODO check if name is part of this tcs file |
| 579 | 579 |
if (typifiedName.equals(aboutName)){
|
| 580 | 580 |
continue; |
| cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/dwca/in/DatabaseMappingTest.java | ||
|---|---|---|
| 77 | 77 |
ICdmDataSource datasource = mapping.getDatabase(); |
| 78 | 78 |
Assert.assertNotNull("Datasource should not be null", datasource);
|
| 79 | 79 |
|
| 80 |
TaxonName<?,?> botName1 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
| 80 |
TaxonName botName1 = TaxonNameFactory.NewBotanicalInstance(null); |
|
| 81 | 81 |
int id = 23; |
| 82 | 82 |
botName1.setId(id); |
| 83 | 83 |
String sourceNS = "sourceNS"; |
| cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/SpecimenImportConfiguratorTest.java | ||
|---|---|---|
| 250 | 250 |
assertEquals(3, nameService.count(TaxonName.class)); |
| 251 | 251 |
assertEquals(1, occurrenceService.count(DerivedUnit.class)); |
| 252 | 252 |
boolean varietyFound = false; |
| 253 |
for(TaxonName<?, ?> name:nameService.list(TaxonName.class, null, null, null, null)){
|
|
| 253 |
for(TaxonName name:nameService.list(TaxonName.class, null, null, null, null)){
|
|
| 254 | 254 |
if(name.getRank().equals(Rank.VARIETY())){
|
| 255 | 255 |
varietyFound = true; |
| 256 | 256 |
} |
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IntextReference.java | ||
|---|---|---|
| 276 | 276 |
private void setTarget(IIntextReferenceTarget target) {
|
| 277 | 277 |
target = CdmBase.deproxy(target); |
| 278 | 278 |
if (target instanceof TaxonName){
|
| 279 |
this.taxonName = (TaxonName<?,?>)target;
|
|
| 279 |
this.taxonName = (TaxonName)target; |
|
| 280 | 280 |
}else if (target instanceof TaxonBase){
|
| 281 | 281 |
this.taxon = (TaxonBase<?>)target; |
| 282 | 282 |
}else if (target instanceof SpecimenOrObservationBase){
|
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/DescriptionElementSource.java | ||
|---|---|---|
| 122 | 122 |
@XmlSchemaType(name = "IDREF") |
| 123 | 123 |
@ManyToOne(fetch = FetchType.LAZY) |
| 124 | 124 |
@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
|
| 125 |
private TaxonName<?,?> nameUsedInSource;
|
|
| 125 |
private TaxonName nameUsedInSource; |
|
| 126 | 126 |
|
| 127 | 127 |
//*********************** CONSTRUCTOR ******************************/ |
| 128 | 128 |
|
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/TaxonNameDescription.java | ||
|---|---|---|
| 62 | 62 |
@ManyToOne(fetch = FetchType.LAZY) |
| 63 | 63 |
@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
|
| 64 | 64 |
@FieldBridge(impl=NotNullAwareIdBridge.class) |
| 65 |
private TaxonName<?,?> taxonName;
|
|
| 65 |
private TaxonName taxonName; |
|
| 66 | 66 |
|
| 67 | 67 |
//******************* FACTORY ********************************************/ |
| 68 | 68 |
|
| ... | ... | |
| 103 | 103 |
* Returns the {@link TaxonName taxon name} to which <i>this</i> taxon name description
|
| 104 | 104 |
* provides additional information not ruled by a {@link NomenclaturalCode nomenclatural code}.
|
| 105 | 105 |
*/ |
| 106 |
public TaxonName<?,?> getTaxonName() {
|
|
| 106 |
public TaxonName getTaxonName() {
|
|
| 107 | 107 |
return taxonName; |
| 108 | 108 |
} |
| 109 | 109 |
|
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/HomotypicalGroup.java | ||
|---|---|---|
| 309 | 309 |
// */ |
| 310 | 310 |
// public void guessAndSetBasionym(){
|
| 311 | 311 |
// Map<String, INonViralName> candidates = new HashMap<>(); |
| 312 |
// for (TaxonName<?,?> typifiedName : this.typifiedNames){
|
|
| 312 |
// for (TaxonName typifiedName : this.typifiedNames){
|
|
| 313 | 313 |
// if (! typifiedName.protectedAuthorshipCache && nvn.getBasionymAuthorship() == null){
|
| 314 | 314 |
// candidates.add(typifiedName); |
| 315 | 315 |
// } |
| 316 | 316 |
// } |
| 317 | 317 |
// if (candidates.size() == 1){
|
| 318 |
// for (TaxonName<?,?> typifiedName : this.typifiedNames){
|
|
| 318 |
// for (TaxonName typifiedName : this.typifiedNames){
|
|
| 319 | 319 |
// removeGroupBasionym(typifiedName); |
| 320 | 320 |
// } |
| 321 | 321 |
// this.setGroupBasionym(candidates.iterator().next()); |
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/HomotypicalGroupComparator.java | ||
|---|---|---|
| 33 | 33 |
TaxonComparator taxComparator = new HomotypicGroupTaxonComparator(null); |
| 34 | 34 |
Set<TaxonName> typifiedNames1 = group1.getTypifiedNames(); |
| 35 | 35 |
List<TaxonBase> taxonBasesOfTypifiedNames = new ArrayList<>(); |
| 36 |
for (TaxonName<?,?> typifiedName:typifiedNames1){
|
|
| 36 |
for (TaxonName typifiedName:typifiedNames1){
|
|
| 37 | 37 |
if (!typifiedName.getTaxonBases().isEmpty()){
|
| 38 | 38 |
taxonBasesOfTypifiedNames.add(typifiedName.getTaxonBases().iterator().next()); |
| 39 | 39 |
} |
| ... | ... | |
| 43 | 43 |
|
| 44 | 44 |
Set<TaxonName> typifiedNames2 = group2.getTypifiedNames(); |
| 45 | 45 |
taxonBasesOfTypifiedNames = new ArrayList<TaxonBase>(); |
| 46 |
for (TaxonName<?,?> typifiedName:typifiedNames2){
|
|
| 46 |
for (TaxonName typifiedName:typifiedNames2){
|
|
| 47 | 47 |
if (!typifiedName.getTaxonBases().isEmpty()){
|
| 48 | 48 |
taxonBasesOfTypifiedNames.add(typifiedName.getTaxonBases().iterator().next()); |
| 49 | 49 |
} |
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/HomotypicalGroupNameComparator.java | ||
|---|---|---|
| 130 | 130 |
* @param name2 second name to compare |
| 131 | 131 |
* @return compare value according to the {@link Comparator#compare(Object, Object)} contract.
|
| 132 | 132 |
*/ |
| 133 |
private int handleSameBasionym(TaxonName<?, ?> basionym,
|
|
| 134 |
TaxonName<?, ?> name1,
|
|
| 135 |
TaxonName<?, ?> name2) {
|
|
| 133 |
private int handleSameBasionym(TaxonName basionym, |
|
| 134 |
TaxonName name1, |
|
| 135 |
TaxonName name2) {
|
|
| 136 | 136 |
|
| 137 | 137 |
if (basionym.equals(name1)){
|
| 138 | 138 |
return -1; |
| ... | ... | |
| 149 | 149 |
* @param basionym2 |
| 150 | 150 |
* @return |
| 151 | 151 |
*/ |
| 152 |
private int compareBasionyms(TaxonName<?,?> basionym1Orig, TaxonName basionym2Orig) {
|
|
| 152 |
private int compareBasionyms(TaxonName basionym1Orig, TaxonName basionym2Orig) {
|
|
| 153 | 153 |
//one taxon is first in group |
| 154 | 154 |
TaxonName basionym1 = getFirstNameInGroup(basionym1Orig); |
| 155 | 155 |
TaxonName basionym2 = getFirstNameInGroup(basionym2Orig); |
| ... | ... | |
| 180 | 180 |
* @param basionym |
| 181 | 181 |
* @return |
| 182 | 182 |
*/ |
| 183 |
private TaxonName<?, ?> getFirstNameInGroup(TaxonName<?, ?> basionym) {
|
|
| 183 |
private TaxonName getFirstNameInGroup(TaxonName basionym) {
|
|
| 184 | 184 |
for (NameRelationship nameRel : basionym.getRelationsFromThisName()){
|
| 185 | 185 |
if (nameRel.getType() != null && nameRel.getType().equals(NameRelationshipType.BASIONYM())){
|
| 186 | 186 |
if (nameRel.getToName().equals(firstNameInGroup)){
|
| ... | ... | |
| 196 | 196 |
* @return |
| 197 | 197 |
*/ |
| 198 | 198 |
@SuppressWarnings("rawtypes")
|
| 199 |
private Set<TaxonName> getReplacedSynonymClosure(TaxonName<?, ?> name) {
|
|
| 199 |
private Set<TaxonName> getReplacedSynonymClosure(TaxonName name) {
|
|
| 200 | 200 |
Set<TaxonName> set = name.getReplacedSynonyms(); |
| 201 | 201 |
if (set.isEmpty()){
|
| 202 | 202 |
return set; |
| 203 | 203 |
} |
| 204 | 204 |
Set<TaxonName> result = new HashSet<TaxonName>(); |
| 205 |
for (TaxonName<?,?> replSyn : set){
|
|
| 205 |
for (TaxonName replSyn : set){
|
|
| 206 | 206 |
boolean notYetContained = result.add(replSyn); |
| 207 | 207 |
if (notYetContained){
|
| 208 | 208 |
result.addAll(replSyn.getReplacedSynonyms()); |
| ... | ... | |
| 215 | 215 |
* @param name |
| 216 | 216 |
* @return |
| 217 | 217 |
*/ |
| 218 |
private TaxonName getPreferredInBasionymGroup(TaxonName<?,?> name) {
|
|
| 218 |
private TaxonName getPreferredInBasionymGroup(TaxonName name) {
|
|
| 219 | 219 |
Set<TaxonName> candidates = new HashSet<>(); |
| 220 | 220 |
//get all final basionyms, except for those being part of a basionym circle |
| 221 |
for (TaxonName<?,?> candidate : name.getBasionyms()){
|
|
| 221 |
for (TaxonName candidate : name.getBasionyms()){
|
|
| 222 | 222 |
if (candidate != null |
| 223 | 223 |
&& candidate.getHomotypicalGroup().equals(name.getHomotypicalGroup()) |
| 224 | 224 |
&& !hasBasionymCircle(candidate, null)){
|
| ... | ... | |
| 234 | 234 |
}else{
|
| 235 | 235 |
TaxonName result = candidates.iterator().next(); |
| 236 | 236 |
candidates.remove(result); |
| 237 |
for(TaxonName<?,?> candidate : candidates){
|
|
| 237 |
for(TaxonName candidate : candidates){
|
|
| 238 | 238 |
if (this.compare(result, candidate) > 0){
|
| 239 | 239 |
result = candidate; |
| 240 | 240 |
} |
| ... | ... | |
| 247 | 247 |
* @param candidate |
| 248 | 248 |
* @return |
| 249 | 249 |
*/ |
| 250 |
private boolean hasBasionymCircle(TaxonName<?, ?> name, Set<TaxonName<?,?>> existing) {
|
|
| 250 |
private boolean hasBasionymCircle(TaxonName name, Set<TaxonName> existing) {
|
|
| 251 | 251 |
if (existing == null){
|
| 252 | 252 |
existing = new HashSet<>(); |
| 253 | 253 |
} |
| ... | ... | |
| 336 | 336 |
* without status nom. illeg. |
| 337 | 337 |
* @return |
| 338 | 338 |
*/ |
| 339 |
protected int compare(TaxonName<?,?> name1, TaxonName name2, boolean includeNomIlleg) {
|
|
| 339 |
protected int compare(TaxonName name1, TaxonName name2, boolean includeNomIlleg) {
|
|
| 340 | 340 |
int result; |
| 341 | 341 |
|
| 342 | 342 |
//dates |
| ... | ... | |
| 386 | 386 |
return result; |
| 387 | 387 |
} |
| 388 | 388 |
|
| 389 |
private Integer getIntegerDate(TaxonName<?,?> name){
|
|
| 389 |
private Integer getIntegerDate(TaxonName name){
|
|
| 390 | 390 |
Integer result; |
| 391 | 391 |
|
| 392 | 392 |
if (name == null){
|
| ... | ... | |
| 420 | 420 |
return result; |
| 421 | 421 |
} |
| 422 | 422 |
|
| 423 |
protected int compareNomIlleg(TaxonName<?,?> taxonName1, TaxonName taxonName2) {
|
|
| 423 |
protected int compareNomIlleg(TaxonName taxonName1, TaxonName taxonName2) {
|
|
| 424 | 424 |
int isNomIlleg1 = isNomIlleg(taxonName1); |
| 425 | 425 |
int isNomIlleg2 = isNomIlleg(taxonName2); |
| 426 | 426 |
return isNomIlleg1 - isNomIlleg2; |
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/HybridRelationship.java | ||
|---|---|---|
| 68 | 68 |
@XmlSchemaType(name = "IDREF") |
| 69 | 69 |
@ManyToOne(fetch=FetchType.LAZY) |
| 70 | 70 |
@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
|
| 71 |
private TaxonName<?,?> relatedFrom;
|
|
| 71 |
private TaxonName relatedFrom; |
|
| 72 | 72 |
|
| 73 | 73 |
@XmlElement(name = "RelatedTo") |
| 74 | 74 |
@XmlIDREF |
| 75 | 75 |
@XmlSchemaType(name = "IDREF") |
| 76 | 76 |
@ManyToOne(fetch=FetchType.LAZY) |
| 77 | 77 |
@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
|
| 78 |
private TaxonName<?,?> relatedTo;
|
|
| 78 |
private TaxonName relatedTo; |
|
| 79 | 79 |
|
| 80 | 80 |
@XmlElement(name = "Type") |
| 81 | 81 |
@XmlIDREF |
| ... | ... | |
| 222 | 222 |
if (compareType != 0){
|
| 223 | 223 |
return compareType; |
| 224 | 224 |
}else{
|
| 225 |
TaxonName<?,?> related1 = this.getRelatedFrom();
|
|
| 226 |
TaxonName<?,?> related2 = rel2.getRelatedFrom();
|
|
| 225 |
TaxonName related1 = this.getRelatedFrom(); |
|
| 226 |
TaxonName related2 = rel2.getRelatedFrom(); |
|
| 227 | 227 |
if (related1 != related2){
|
| 228 | 228 |
related1 = this.getRelatedTo(); |
| 229 | 229 |
related2 = rel2.getRelatedTo(); |
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/ITaxonNameBase.java | ||
|---|---|---|
| 828 | 828 |
* @return the compareTo result similar to {@link Comparable#compareTo(Object)}
|
| 829 | 829 |
* @throws NullPointerException if otherTaxon is <code>null</code> |
| 830 | 830 |
*/ |
| 831 |
public int compareToName(TaxonName<?,?> otherName);
|
|
| 831 |
public int compareToName(TaxonName otherName); |
|
| 832 | 832 |
|
| 833 | 833 |
/** |
| 834 | 834 |
* This method returns als {@link Registration registrations} for the given name.
|
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/TaxonName.java | ||
|---|---|---|
| 182 | 182 |
@NameMustHaveAuthority(groups = Level2.class) |
| 183 | 183 |
@NoDuplicateNames(groups = Level3.class) |
| 184 | 184 |
@Indexed(index = "eu.etaxonomy.cdm.model.name.TaxonName") |
| 185 |
public class TaxonName<T extends TaxonName<?,?>, S extends INameCacheStrategy>
|
|
| 186 |
extends IdentifiableEntity<S>
|
|
| 185 |
public class TaxonName |
|
| 186 |
extends IdentifiableEntity<INameCacheStrategy>
|
|
| 187 | 187 |
implements ITaxonNameBase, INonViralName, IViralName, IBacterialName, IZoologicalName, |
| 188 | 188 |
IBotanicalName, ICultivarPlantName, IFungusName, |
| 189 | 189 |
IParsable, IRelated, IMatchable, IIntextReferenceTarget, Cloneable {
|
| ... | ... | |
| 561 | 561 |
*/ |
| 562 | 562 |
protected static TaxonName NewInstance(NomenclaturalCode code, Rank rank, |
| 563 | 563 |
HomotypicalGroup homotypicalGroup) {
|
| 564 |
TaxonName<?,?> result = new TaxonName<>(code, rank, homotypicalGroup);
|
|
| 564 |
TaxonName result = new TaxonName(code, rank, homotypicalGroup);
|
|
| 565 | 565 |
return result; |
| 566 | 566 |
} |
| 567 | 567 |
|
| ... | ... | |
| 583 | 583 |
String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, |
| 584 | 584 |
TeamOrPersonBase combinationAuthorship, Reference nomenclaturalReference, |
| 585 | 585 |
String nomenclMicroRef, HomotypicalGroup homotypicalGroup) {
|
| 586 |
TaxonName result = new TaxonName<>(code, rank, genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet, combinationAuthorship, nomenclaturalReference, nomenclMicroRef, homotypicalGroup);
|
|
| 586 |
TaxonName result = new TaxonName(code, rank, genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet, combinationAuthorship, nomenclaturalReference, nomenclMicroRef, homotypicalGroup); |
|
| 587 | 587 |
return result; |
| 588 | 588 |
} |
| 589 | 589 |
|
| ... | ... | |
| 679 | 679 |
}else if (this.cacheStrategy != null){
|
| 680 | 680 |
// |
| 681 | 681 |
}else if (getNameType() == NomenclaturalCode.NonViral){
|
| 682 |
this.cacheStrategy = (S)NonViralNameDefaultCacheStrategy.NewInstance();
|
|
| 682 |
this.cacheStrategy = NonViralNameDefaultCacheStrategy.NewInstance(); |
|
| 683 | 683 |
}else if (getNameType().isBotanical()){
|
| 684 |
this.cacheStrategy = (S)NonViralNameDefaultCacheStrategy.NewInstance();
|
|
| 684 |
this.cacheStrategy = NonViralNameDefaultCacheStrategy.NewInstance(); |
|
| 685 | 685 |
}else if (getNameType() == NomenclaturalCode.ICZN){
|
| 686 |
this.cacheStrategy = (S)NonViralNameDefaultCacheStrategy.NewInstance();
|
|
| 686 |
this.cacheStrategy = NonViralNameDefaultCacheStrategy.NewInstance(); |
|
| 687 | 687 |
}else if (getNameType() == NomenclaturalCode.ICNB){
|
| 688 |
this.cacheStrategy = (S)NonViralNameDefaultCacheStrategy.NewInstance();;
|
|
| 688 |
this.cacheStrategy = NonViralNameDefaultCacheStrategy.NewInstance();; |
|
| 689 | 689 |
}else if (getNameType() == NomenclaturalCode.ICVCN){
|
| 690 |
this.cacheStrategy = (S) ViralNameDefaultCacheStrategy.NewInstance();
|
|
| 690 |
this.cacheStrategy = ViralNameDefaultCacheStrategy.NewInstance(); |
|
| 691 | 691 |
} |
| 692 | 692 |
} |
| 693 | 693 |
|
| ... | ... | |
| 1354 | 1354 |
return; |
| 1355 | 1355 |
} |
| 1356 | 1356 |
|
| 1357 |
TaxonName<?,?> parent = hybridRelation.getParentName();
|
|
| 1358 |
TaxonName<?,?> child = hybridRelation.getHybridName();
|
|
| 1357 |
TaxonName parent = hybridRelation.getParentName(); |
|
| 1358 |
TaxonName child = hybridRelation.getHybridName(); |
|
| 1359 | 1359 |
if (this.equals(parent)){
|
| 1360 | 1360 |
this.hybridParentRelations.remove(hybridRelation); |
| 1361 | 1361 |
child.hybridChildRelations.remove(hybridRelation); |
| ... | ... | |
| 1373 | 1373 |
//********* METHODS **************************************/ |
| 1374 | 1374 |
|
| 1375 | 1375 |
@Override |
| 1376 |
public S getCacheStrategy() {
|
|
| 1376 |
public INameCacheStrategy getCacheStrategy() {
|
|
| 1377 | 1377 |
rectifyNameCacheStrategy(); |
| 1378 | 1378 |
return this.cacheStrategy; |
| 1379 | 1379 |
} |
| ... | ... | |
| 1430 | 1430 |
@Override |
| 1431 | 1431 |
@Transient |
| 1432 | 1432 |
public List<TaggedText> getTaggedName(){
|
| 1433 |
S strat = getCacheStrategy();
|
|
| 1433 |
INameCacheStrategy strat = getCacheStrategy();
|
|
| 1434 | 1434 |
return strat.getTaggedTitle(this); |
| 1435 | 1435 |
} |
| 1436 | 1436 |
|
| ... | ... | |
| 2046 | 2046 |
Set<NameRelationship> rels = this.getRelationsToThisName(); |
| 2047 | 2047 |
for (NameRelationship rel : rels){
|
| 2048 | 2048 |
if (rel.getType()!= null && rel.getType().isBasionymRelation()){
|
| 2049 |
TaxonName<?,?> basionym = rel.getFromName();
|
|
| 2049 |
TaxonName basionym = rel.getFromName(); |
|
| 2050 | 2050 |
result.add(basionym); |
| 2051 | 2051 |
} |
| 2052 | 2052 |
} |
| ... | ... | |
| 2934 | 2934 |
return false; |
| 2935 | 2935 |
} |
| 2936 | 2936 |
|
| 2937 |
for (TaxonName<?,?> taxonName : typifiedNames) {
|
|
| 2937 |
for (TaxonName taxonName : typifiedNames) {
|
|
| 2938 | 2938 |
if (!taxonName.equals(this)) {
|
| 2939 | 2939 |
if (! isBasionymFor(taxonName)) {
|
| 2940 | 2940 |
return false; |
| ... | ... | |
| 3175 | 3175 |
Set<NameRelationship> relations = new HashSet<NameRelationship>(); |
| 3176 | 3176 |
Set<NameRelationship> removeRelations = new HashSet<NameRelationship>(); |
| 3177 | 3177 |
|
| 3178 |
for(TaxonName<?, ?> typifiedName : homotypicalGroup.getTypifiedNames()){
|
|
| 3178 |
for(TaxonName typifiedName : homotypicalGroup.getTypifiedNames()){
|
|
| 3179 | 3179 |
|
| 3180 | 3180 |
Set<NameRelationship> nameRelations = typifiedName.getRelationsFromThisName(); |
| 3181 | 3181 |
|
| ... | ... | |
| 3201 | 3201 |
this.removeNameRelationship(relation); |
| 3202 | 3202 |
} |
| 3203 | 3203 |
|
| 3204 |
for (TaxonName<?, ?> name : homotypicalGroup.getTypifiedNames()) {
|
|
| 3204 |
for (TaxonName name : homotypicalGroup.getTypifiedNames()) {
|
|
| 3205 | 3205 |
if (!name.equals(this)) {
|
| 3206 | 3206 |
|
| 3207 | 3207 |
// First check whether the relationship already exists |
| ... | ... | |
| 3234 | 3234 |
Set<NameRelationship> relations = new HashSet<NameRelationship>(); |
| 3235 | 3235 |
Set<NameRelationship> removeRelations = new HashSet<NameRelationship>(); |
| 3236 | 3236 |
|
| 3237 |
for(TaxonName<?, ?> typifiedName : homotypicalGroup.getTypifiedNames()){
|
|
| 3237 |
for(TaxonName typifiedName : homotypicalGroup.getTypifiedNames()){
|
|
| 3238 | 3238 |
|
| 3239 | 3239 |
Set<NameRelationship> nameRelations = typifiedName.getRelationsFromThisName(); |
| 3240 | 3240 |
|
| ... | ... | |
| 3305 | 3305 |
// ***************** COMPARE ********************************/ |
| 3306 | 3306 |
|
| 3307 | 3307 |
@Override |
| 3308 |
public int compareToName(TaxonName<?,?> otherName){
|
|
| 3308 |
public int compareToName(TaxonName otherName){
|
|
| 3309 | 3309 |
|
| 3310 | 3310 |
int result = 0; |
| 3311 | 3311 |
|
| ... | ... | |
| 3425 | 3425 |
*/ |
| 3426 | 3426 |
@Override |
| 3427 | 3427 |
public Object clone() {
|
| 3428 |
TaxonName<?,?> result;
|
|
| 3428 |
TaxonName result; |
|
| 3429 | 3429 |
try {
|
| 3430 | 3430 |
result = (TaxonName)super.clone(); |
| 3431 | 3431 |
|
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/TaxonNameFactory.java | ||
|---|---|---|
| 425 | 425 |
* @param rank |
| 426 | 426 |
* @return |
| 427 | 427 |
*/ |
| 428 |
public static TaxonName<?, ?> NewFungusInstance(Rank rank) {
|
|
| 428 |
public static TaxonName NewFungusInstance(Rank rank) {
|
|
| 429 | 429 |
return TaxonName.NewInstance(NomenclaturalCode.Fungi, rank, null); |
| 430 | 430 |
} |
| 431 | 431 |
|
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/DeterminationEvent.java | ||
|---|---|---|
| 89 | 89 |
@ManyToOne(fetch = FetchType.LAZY) |
| 90 | 90 |
@IndexedEmbedded(includeEmbeddedObjectId=true) |
| 91 | 91 |
@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
|
| 92 |
private TaxonName<?,?> taxonName;
|
|
| 92 |
private TaxonName taxonName; |
|
| 93 | 93 |
|
| 94 | 94 |
@XmlElement(name = "Modifier") |
| 95 | 95 |
@XmlIDREF |
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/HomotypicGroupTaxonComparator.java | ||
|---|---|---|
| 201 | 201 |
* @param basionym |
| 202 | 202 |
* @return |
| 203 | 203 |
*/ |
| 204 |
private TaxonName getFirstNameInGroup(TaxonName<?,?> basionym) {
|
|
| 204 |
private TaxonName getFirstNameInGroup(TaxonName basionym) {
|
|
| 205 | 205 |
for (NameRelationship nameRel : basionym.getRelationsFromThisName()){
|
| 206 | 206 |
if (nameRel.getType() != null && nameRel.getType().equals(NameRelationshipType.BASIONYM())){
|
| 207 | 207 |
if (nameRel.getToName().equals(firstNameInGroup)){
|
| ... | ... | |
| 217 | 217 |
* @return |
| 218 | 218 |
*/ |
| 219 | 219 |
@SuppressWarnings("rawtypes")
|
| 220 |
private Set<TaxonName> getReplacedSynonymClosure(TaxonName<?, ?> name) {
|
|
| 220 |
private Set<TaxonName> getReplacedSynonymClosure(TaxonName name) {
|
|
| 221 | 221 |
Set<TaxonName> set = name.getReplacedSynonyms(); |
| 222 | 222 |
if (set.isEmpty()){
|
| 223 | 223 |
return set; |
| 224 | 224 |
} |
| 225 | 225 |
Set<TaxonName> result = new HashSet<>(); |
| 226 |
for (TaxonName<?,?> replSyn : set){
|
|
| 226 |
for (TaxonName replSyn : set){
|
|
| 227 | 227 |
boolean notYetContained = result.add(replSyn); |
| 228 | 228 |
if (notYetContained){
|
| 229 | 229 |
result.addAll(replSyn.getReplacedSynonyms()); |
| ... | ... | |
| 236 | 236 |
* @param name |
| 237 | 237 |
* @return |
| 238 | 238 |
*/ |
| 239 |
private TaxonName getPreferredInBasionymGroup(TaxonName<?,?> name) {
|
|
| 240 |
Set<TaxonName<?,?>> candidates = new HashSet<>();
|
|
| 239 |
private TaxonName getPreferredInBasionymGroup(TaxonName name) {
|
|
| 240 |
Set<TaxonName> candidates = new HashSet<>(); |
|
| 241 | 241 |
//get all final basionyms, except for those being part of a basionym circle |
| 242 |
for (TaxonName<?,?> candidate : name.getBasionyms()){
|
|
| 242 |
for (TaxonName candidate : name.getBasionyms()){
|
|
| 243 | 243 |
if (candidate != null |
| 244 | 244 |
&& candidate.getHomotypicalGroup().equals(name.getHomotypicalGroup()) |
| 245 | 245 |
&& !hasBasionymCircle(candidate, null)){
|
| ... | ... | |
| 255 | 255 |
}else{
|
| 256 | 256 |
TaxonName result = candidates.iterator().next(); |
| 257 | 257 |
candidates.remove(result); |
| 258 |
for (TaxonName<?,?> candidate : candidates){
|
|
| 258 |
for (TaxonName candidate : candidates){
|
|
| 259 | 259 |
if (super.compare(result, candidate, false) > 0){
|
| 260 | 260 |
result = candidate; |
| 261 | 261 |
} |
| ... | ... | |
| 268 | 268 |
* @param candidate |
| 269 | 269 |
* @return |
| 270 | 270 |
*/ |
| 271 |
private boolean hasBasionymCircle(TaxonName<?, ?> name, Set<TaxonName> existing) {
|
|
| 271 |
private boolean hasBasionymCircle(TaxonName name, Set<TaxonName> existing) {
|
|
| 272 | 272 |
if (existing == null){
|
| 273 | 273 |
existing = new HashSet<>(); |
| 274 | 274 |
} |
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonBase.java | ||
|---|---|---|
| 128 | 128 |
@IndexedEmbedded(includeEmbeddedObjectId=true) |
| 129 | 129 |
@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
|
| 130 | 130 |
@NotNull(groups = Level2.class) |
| 131 |
private TaxonName<?,?> name;
|
|
| 131 |
private TaxonName name; |
|
| 132 | 132 |
|
| 133 | 133 |
// The concept reference |
| 134 | 134 |
@XmlElement(name = "Sec") |
| ... | ... | |
| 404 | 404 |
|
| 405 | 405 |
otherTaxon = deproxy(otherTaxon); |
| 406 | 406 |
|
| 407 |
TaxonName<?,?> otherName = deproxy(otherTaxon.getName());
|
|
| 407 |
TaxonName otherName = deproxy(otherTaxon.getName()); |
|
| 408 | 408 |
ITaxonNameBase thisName = this.getName(); |
| 409 | 409 |
if ((otherName == null || thisName == null)){
|
| 410 | 410 |
if (otherName != thisName){
|
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/taxon/TaxonBaseDefaultCacheStrategy.java | ||
|---|---|---|
| 93 | 93 |
|
| 94 | 94 |
private <X extends ITaxonNameBase> List<TaggedText> getNameTags(T taxonBase) {
|
| 95 | 95 |
List<TaggedText> tags = new ArrayList<>(); |
| 96 |
TaxonName<?, INameCacheStrategy> name = CdmBase.deproxy(taxonBase.getName());
|
|
| 96 |
TaxonName name = CdmBase.deproxy(taxonBase.getName()); |
|
| 97 | 97 |
|
| 98 | 98 |
if (name != null){
|
| 99 | 99 |
INameCacheStrategy nameCacheStrategy = name.getCacheStrategy(); |
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/homotypicgroup/BasionymRelationCreator.java | ||
|---|---|---|
| 62 | 62 |
|
| 63 | 63 |
//compare accepted against synonyms |
| 64 | 64 |
for (Synonym synonym: synonyms){
|
| 65 |
TaxonName<?, ?> basionym = compareHomotypic(taxon.getName(), synonym.getName());
|
|
| 65 |
TaxonName basionym = compareHomotypic(taxon.getName(), synonym.getName()); |
|
| 66 | 66 |
if (basionym != null){
|
| 67 | 67 |
synonym.setType(SynonymType.HOMOTYPIC_SYNONYM_OF()); |
| 68 | 68 |
adaptHomotypicGroup(basionym, taxon.getName(), synonym.getName()); |
| ... | ... | |
| 75 | 75 |
for (int j = i + 1; j < synonymList.size(); j++){
|
| 76 | 76 |
Synonym syn1 = synonymList.get(i); |
| 77 | 77 |
Synonym syn2 = synonymList.get(j); |
| 78 |
TaxonName<?, ?> basionym = compareHomotypic(syn1.getName(), syn2.getName());
|
|
| 78 |
TaxonName basionym = compareHomotypic(syn1.getName(), syn2.getName()); |
|
| 79 | 79 |
if (basionym != null){
|
| 80 | 80 |
adaptHomotypicGroup(basionym, syn1.getName(), syn2.getName()); |
| 81 | 81 |
if (taxon.getName().getBasionyms().contains(basionym)){
|
| ... | ... | |
| 92 | 92 |
* @param name |
| 93 | 93 |
* @param name2 |
| 94 | 94 |
*/ |
| 95 |
private void adaptHomotypicGroup(TaxonName<?, ?> basionym,
|
|
| 96 |
TaxonName<?,?> name1, TaxonName<?,?> name2) {
|
|
| 95 |
private void adaptHomotypicGroup(TaxonName basionym, |
|
| 96 |
TaxonName name1, TaxonName name2) {
|
|
| 97 | 97 |
if (basionym.equals(name1)){
|
| 98 | 98 |
if (!name2.getBasionyms().contains(name1)){
|
| 99 | 99 |
name2.addBasionym(name1); |
| ... | ... | |
| 109 | 109 |
* @param name |
| 110 | 110 |
* @param name2 |
| 111 | 111 |
*/ |
| 112 |
private TaxonName<?,?> compareHomotypic(TaxonName<?,?> name1, TaxonName<?,?> name2) {
|
|
| 112 |
private TaxonName compareHomotypic(TaxonName name1, TaxonName name2) {
|
|
| 113 | 113 |
if (name1 == null || name2 == null){
|
| 114 | 114 |
return null; |
| 115 | 115 |
} |
| 116 |
TaxonName<?,?> basionymCandidate = checkAuthors(name1, name2);
|
|
| 116 |
TaxonName basionymCandidate = checkAuthors(name1, name2); |
|
| 117 | 117 |
if (basionymCandidate == null){
|
| 118 | 118 |
return null; |
| 119 | 119 |
}else{
|
| 120 |
TaxonName<?,?> newCombinationCandidate
|
|
| 120 |
TaxonName newCombinationCandidate |
|
| 121 | 121 |
= basionymCandidate == name1? name2: name1; |
| 122 | 122 |
boolean isBasionym = compareNameParts(basionymCandidate, newCombinationCandidate); |
| 123 | 123 |
if (isBasionym){
|
| ... | ... | |
| 132 | 132 |
* @param basionymCandiate |
| 133 | 133 |
* @param newCombinationCandidate |
| 134 | 134 |
*/ |
| 135 |
private boolean compareNameParts(TaxonName<?, ?> basionymCandidate,
|
|
| 136 |
TaxonName<?, ?> newCombinationCandidate) {
|
|
| 135 |
private boolean compareNameParts(TaxonName basionymCandidate, |
|
| 136 |
TaxonName newCombinationCandidate) {
|
|
| 137 | 137 |
if (basionymCandidate.isGenusOrSupraGeneric() || newCombinationCandidate.isGenusOrSupraGeneric()){
|
| 138 | 138 |
return false; |
| 139 | 139 |
}else if (matchLastNamePart(basionymCandidate, newCombinationCandidate)){
|
| ... | ... | |
| 147 | 147 |
* @param name2 |
| 148 | 148 |
* @return |
| 149 | 149 |
*/ |
| 150 |
private TaxonName<?,?> checkAuthors(TaxonName<?, ?> name1, TaxonName<?, ?> name2) {
|
|
| 150 |
private TaxonName checkAuthors(TaxonName name1, TaxonName name2) {
|
|
| 151 | 151 |
if (hasBasionymAuthorOf(name1, name2)){
|
| 152 | 152 |
return name1; |
| 153 | 153 |
}else if (hasBasionymAuthorOf(name2, name1)){
|
| ... | ... | |
| 162 | 162 |
* @param name2 |
| 163 | 163 |
* @return |
| 164 | 164 |
*/ |
| 165 |
private boolean hasBasionymAuthorOf(TaxonName<?,?> name1, TaxonName<?,?> name2) {
|
|
| 165 |
private boolean hasBasionymAuthorOf(TaxonName name1, TaxonName name2) {
|
|
| 166 | 166 |
TeamOrPersonBase<?> basAuthor2 = name2.getBasionymAuthorship(); |
| 167 | 167 |
TeamOrPersonBase<?> combinationAuthor = name1.getCombinationAuthorship(); |
| 168 | 168 |
TeamOrPersonBase<?> basAuthor1 = name1.getBasionymAuthorship(); |
| ... | ... | |
| 198 | 198 |
* @param newCombination |
| 199 | 199 |
* @return |
| 200 | 200 |
*/ |
| 201 |
public static boolean matchLastNamePart(TaxonName<?,?> name1, TaxonName<?,?> name2) {
|
|
| 201 |
public static boolean matchLastNamePart(TaxonName name1, TaxonName name2) {
|
|
| 202 | 202 |
String lastNamePart1 = name1.getLastNamePart(); |
| 203 | 203 |
String lastNamePart2 = name2.getLastNamePart(); |
| 204 | 204 |
if (lastNamePart1 != null && lastNamePart2 != null){
|
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/validation/constraint/BasionymsMustShareEpithetsAndAuthorsValidator.java | ||
|---|---|---|
| 30 | 30 |
public boolean isValid(NameRelationship nameRelationship, ConstraintValidatorContext constraintContext) {
|
| 31 | 31 |
boolean valid = true; |
| 32 | 32 |
if(nameRelationship.getType() != null && nameRelationship.getType().equals(NameRelationshipType.BASIONYM())) {
|
| 33 |
TaxonName<?,?> from = CdmBase.deproxy(nameRelationship.getFromName(), TaxonName.class);
|
|
| 34 |
TaxonName<?,?> to = CdmBase.deproxy(nameRelationship.getToName(), TaxonName.class);
|
|
| 33 |
TaxonName from = CdmBase.deproxy(nameRelationship.getFromName(), TaxonName.class); |
|
| 34 |
TaxonName to = CdmBase.deproxy(nameRelationship.getToName(), TaxonName.class); |
|
| 35 | 35 |
|
| 36 | 36 |
if(from.isNonViral() && to.isNonViral()) {
|
| 37 | 37 |
INonViralName fromName = from; |
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/validation/constraint/ChildTaxaMustDeriveNameFromParentValidator.java | ||
|---|---|---|
| 35 | 35 |
Taxon child = taxonNode.getTaxon(); |
| 36 | 36 |
|
| 37 | 37 |
if (parent != null && child != null && parent.getName() != null && child.getName() != null){
|
| 38 |
TaxonName<?,?> parentNameBase = CdmBase.deproxy(parent.getName(), TaxonName.class);
|
|
| 39 |
TaxonName<?,?> childNameBase = CdmBase.deproxy(child.getName(), TaxonName.class);
|
|
| 38 |
TaxonName parentNameBase = CdmBase.deproxy(parent.getName(), TaxonName.class); |
|
| 39 |
TaxonName childNameBase = CdmBase.deproxy(child.getName(), TaxonName.class); |
|
| 40 | 40 |
if(parentNameBase.isNonViral() && childNameBase.isNonViral()) {
|
| 41 | 41 |
INonViralName parentName = parentNameBase; |
| 42 | 42 |
INonViralName childName = childNameBase; |
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/validation/constraint/NameMustFollowCodeValidator.java | ||
|---|---|---|
| 31 | 31 |
* |
| 32 | 32 |
*/ |
| 33 | 33 |
public class NameMustFollowCodeValidator implements |
| 34 |
ConstraintValidator<NameMustFollowCode, TaxonName<?,?>> {
|
|
| 34 |
ConstraintValidator<NameMustFollowCode, TaxonName> {
|
|
| 35 | 35 |
|
| 36 | 36 |
@Override |
| 37 | 37 |
public void initialize(NameMustFollowCode nameMustFollowTheirCode) { }
|
| 38 | 38 |
|
| 39 | 39 |
@Override |
| 40 |
public boolean isValid(TaxonName<?,?> name, ConstraintValidatorContext constraintContext) {
|
|
| 40 |
public boolean isValid(TaxonName name, ConstraintValidatorContext constraintContext) {
|
|
| 41 | 41 |
name = CdmBase.deproxy(name); |
| 42 | 42 |
boolean valid = true; |
| 43 | 43 |
|
| cdmlib-model/src/test/java/eu/etaxonomy/cdm/aspectj/PropertyChangeTest.java | ||
|---|---|---|
| 39 | 39 |
@Test |
| 40 | 40 |
public void testPropertyChange() {
|
| 41 | 41 |
INonViralName b = TaxonNameFactory.NewNonViralInstance(Rank.SPECIES()); |
| 42 |
((TaxonName<?,?>)b).addPropertyChangeListener(this);
|
|
| 42 |
((TaxonName)b).addPropertyChangeListener(this); |
|
| 43 | 43 |
b.setGenusOrUninomial("Abies");
|
| 44 | 44 |
assertEquals(b.getGenusOrUninomial(), lastPropValue); |
| 45 | 45 |
b.setGenusOrUninomial("Picea");
|
| cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/name/TaxonNameTest.java | ||
|---|---|---|
| 61 | 61 |
} |
| 62 | 62 |
|
| 63 | 63 |
|
| 64 |
private class TaxonNameTestClass extends TaxonName<TaxonNameTestClass, INameCacheStrategy>{
|
|
| 64 |
private class TaxonNameTestClass extends TaxonName{
|
|
| 65 | 65 |
public TaxonNameTestClass(Rank rank, HomotypicalGroup hg){super(null, rank, hg);}
|
| 66 | 66 |
@Override |
| 67 | 67 |
public void setCacheStrategy(INameCacheStrategy strategy){}
|
| ... | ... | |
| 822 | 822 |
description.addElement(textData); |
| 823 | 823 |
|
| 824 | 824 |
//CLONE |
| 825 |
TaxonName<?,?> clone = (TaxonName)taxonName1.clone();
|
|
| 825 |
TaxonName clone = (TaxonName)taxonName1.clone(); |
|
| 826 | 826 |
TaxonName genusClone = (TaxonName)genusName.clone(); |
| 827 | 827 |
assertSame("Rank should be same", taxonName1.getRank(), clone.getRank());
|
| 828 | 828 |
assertTrue("TaxonBases should not be cloned", clone.getTaxonBases().isEmpty());
|
| cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/taxon/ClassificationTest.java | ||
|---|---|---|
| 64 | 64 |
private static Taxon taxon3; |
| 65 | 65 |
private static Taxon taxon12; |
| 66 | 66 |
private static Taxon taxon121; |
| 67 |
private static TaxonName<?,?> taxonName1;
|
|
| 68 |
private static TaxonName<?,?> taxonName2;
|
|
| 69 |
private static TaxonName<?,?> taxonName3;
|
|
| 70 |
private static TaxonName<?,?> taxonName12;
|
|
| 71 |
private static TaxonName<?,?> taxonName121;
|
|
| 67 |
private static TaxonName taxonName1; |
|
| 68 |
private static TaxonName taxonName2; |
|
| 69 |
private static TaxonName taxonName3; |
|
| 70 |
private static TaxonName taxonName12; |
|
| 71 |
private static TaxonName taxonName121; |
|
| 72 | 72 |
private static Reference ref1; |
| 73 | 73 |
private static Reference ref2; |
| 74 | 74 |
private static Reference ref3; |
| ... | ... | |
| 129 | 129 |
*/ |
| 130 | 130 |
@Test |
| 131 | 131 |
public void testAddRoot() {
|
| 132 |
TaxonName<?,?> synonymName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 132 |
TaxonName synonymName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()); |
|
| 133 | 133 |
Synonym synonym = Synonym.NewInstance(synonymName, ref1); |
| 134 | 134 |
TaxonNode taxonNode1 = classification1.addChildTaxon(taxon1, null, null); |
| 135 | 135 |
taxonNode1.setSynonymToBeUsed(synonym); |
| ... | ... | |
| 230 | 230 |
@Test |
| 231 | 231 |
public void testAddParentChild() {
|
| 232 | 232 |
|
| 233 |
TaxonName<?,?> synonymName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 233 |
TaxonName synonymName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()); |
|
| 234 | 234 |
Synonym synonym = Synonym.NewInstance(synonymName, ref1); |
| 235 | 235 |
TaxonNode rootNode = classification1.addChildTaxon(taxon1, null, null); |
| 236 | 236 |
rootNode.setSynonymToBeUsed(synonym); |
| ... | ... | |
| 346 | 346 |
//genericDao.getCdmBasesByFieldAndClass(clazz, field.getName(), value); |
| 347 | 347 |
|
| 348 | 348 |
|
| 349 |
TaxonName<?,?> name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
|
|
| 349 |
TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS()); |
|
| 350 | 350 |
name.setTitleCache("A dummy name", true);
|
| 351 | 351 |
result.add(name); |
| 352 | 352 |
Reference ref = ReferenceFactory.newBook(); |
| cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/taxon/TaxonBaseTest.java | ||
|---|---|---|
| 166 | 166 |
@Test |
| 167 | 167 |
public void testCompareTo() {
|
| 168 | 168 |
|
| 169 |
TaxonName<?,?> abies = TaxonNameFactory.NewNonViralInstance(Rank.GENUS(), null);
|
|
| 169 |
TaxonName abies = TaxonNameFactory.NewNonViralInstance(Rank.GENUS(), null); |
|
| 170 | 170 |
abies.setNameCache("Abies");
|
| 171 | 171 |
abies.setTitleCache("Abies", true);
|
| 172 | 172 |
Reference sec = ReferenceFactory.newArticle(); |
| cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/cache/name/NonViralNameDefaultCacheStrategyTest.java | ||
|---|---|---|
| 312 | 312 |
@Test |
| 313 | 313 |
public void testOriginalSpelling() {
|
| 314 | 314 |
NameRelationshipType origSpellingType = NameRelationshipType.ORIGINAL_SPELLING(); |
| 315 |
TaxonName originalName = (TaxonName<?,?>)speciesName.clone();
|
|
| 315 |
TaxonName originalName = (TaxonName)speciesName.clone(); |
|
| 316 | 316 |
originalName.setSpecificEpithet("alpa");
|
| 317 | 317 |
Assert.assertEquals("Preconditions are wrong", "Abies alpa", originalName.getTitleCache());
|
| 318 | 318 |
Assert.assertEquals("Name cache should not show original spelling", "Abies alpa", originalName.getNameCache());
|
| ... | ... | |
| 331 | 331 |
|
| 332 | 332 |
//#3665 |
| 333 | 333 |
INonViralName correctName = NonViralNameParserImpl.NewInstance().parseFullName("Nepenthes glabrata J.R.Turnbull & A.T.Middleton");
|
| 334 |
TaxonName originalSpelling = (TaxonName<?,?>)NonViralNameParserImpl.NewInstance().parseFullName("Nepenthes glabratus");
|
|
| 334 |
TaxonName originalSpelling = (TaxonName)NonViralNameParserImpl.NewInstance().parseFullName("Nepenthes glabratus");
|
|
| 335 | 335 |
correctName.addRelationshipFromName(originalSpelling, origSpellingType, null); |
| 336 | 336 |
Assert.assertEquals("Nepenthes glabrata", correctName.getNameCache());
|
| 337 | 337 |
Assert.assertEquals("Nepenthes glabrata J.R.Turnbull & A.T.Middleton", correctName.getTitleCache());
|
| cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/homotypicgroup/BasionymRelationCreatorTest.java | ||
|---|---|---|
| 40 | 40 |
private Synonym synonym1; |
| 41 | 41 |
private Synonym synonym2; |
| 42 | 42 |
private Synonym synonym3; |
| 43 |
private TaxonName<?,?> accName1;
|
|
| 44 |
private TaxonName<?,?> synName1;
|
|
| 45 |
private TaxonName<?,?> synName2;
|
|
| 46 |
private TaxonName<?,?> synName3;
|
|
| 43 |
private TaxonName accName1; |
|
| 44 |
private TaxonName synName1; |
|
| 45 |
private TaxonName synName2; |
|
| 46 |
private TaxonName synName3; |
|
| 47 | 47 |
private Person person1; |
| 48 | 48 |
private Person person2; |
| 49 | 49 |
private Person person3; |
| cdmlib-model/src/test/java/eu/etaxonomy/cdm/validation/NameMustFollowCodeTest.java | ||
|---|---|---|
| 62 | 62 |
|
| 63 | 63 |
@Test |
| 64 | 64 |
public void testValidEmptyNames() {
|
| 65 |
Set<ConstraintViolation<TaxonName<?,?>>> constraintViolations
|
|
| 65 |
Set<ConstraintViolation<TaxonName>> constraintViolations |
|
| 66 | 66 |
= validator.validate(cultivarName); |
| 67 | 67 |
assertTrue("There should be no constraint violations as this name has data set and therefore no unvalid attributes set", constraintViolations.isEmpty());
|
| 68 | 68 |
|
| ... | ... | |
| 82 | 82 |
@Test |
| 83 | 83 |
public void testMessage() {
|
| 84 | 84 |
nonViralName.setAcronym("acronym");
|
| 85 |
Set<ConstraintViolation<TaxonName<?,?>>> constraintViolations = validator.validate(nonViralName);
|
|
| 85 |
Set<ConstraintViolation<TaxonName>> constraintViolations = validator.validate(nonViralName); |
|
| 86 | 86 |
assertFalse("There should be a constraint violation as a nonViralName must not have an acronym", constraintViolations.isEmpty());
|
| 87 | 87 |
String message = constraintViolations.iterator().next().getMessage(); |
| 88 | 88 |
String expected = "Taxon name must only have attributes set that are available according to their code. E.g. 'acronym name' should only be available for viral names."; |
| ... | ... | |
| 92 | 92 |
@Test |
| 93 | 93 |
public void testValidNonViralName() {
|
| 94 | 94 |
nonViralName.setAcronym("acronym");
|
| 95 |
Set<ConstraintViolation<TaxonName<?,?>>> constraintViolations = validator.validate(nonViralName);
|
|
| 95 |
Set<ConstraintViolation<TaxonName>> constraintViolations = validator.validate(nonViralName); |
|
| 96 | 96 |
assertFalse("There should be a constraint violation as a nonViralName must not have an acronym", constraintViolations.isEmpty());
|
| 97 | 97 |
|
| 98 | 98 |
nonViralName = TaxonNameFactory.NewNonViralInstance(Rank.SPECIES()); |
| ... | ... | |
| 148 | 148 |
@Test |
| 149 | 149 |
public void testValidViralName() {
|
| 150 | 150 |
viralName.setAcronym("acronym");
|
| 151 |
Set<ConstraintViolation<TaxonName<?,?>>> constraintViolations = validator.validate(viralName);
|
|
| 151 |
Set<ConstraintViolation<TaxonName>> constraintViolations = validator.validate(viralName); |
|
| 152 | 152 |
assertTrue("There should be no constraint violation as a viral name may have acronym set", constraintViolations.isEmpty());
|
| 153 | 153 |
|
| 154 | 154 |
//Invalid |
| ... | ... | |
| 183 | 183 |
zoologicalName.setOriginalPublicationYear(1987); |
| 184 | 184 |
zoologicalName.setPublicationYear(2001); |
| 185 | 185 |
|
| 186 |
Set<ConstraintViolation<TaxonName<?,?>>> constraintViolations = validator.validate(zoologicalName);
|
|
| 186 |
Set<ConstraintViolation<TaxonName>> constraintViolations = validator.validate(zoologicalName); |
|
| 187 | 187 |
assertTrue("There should be no constraint violation as a zoological name may have breed and years set", constraintViolations.isEmpty());
|
| 188 | 188 |
} |
| 189 | 189 |
|
| ... | ... | |
| 192 | 192 |
bacterialName.setSubGenusAuthorship("Subgenus author");
|
| 193 | 193 |
bacterialName.setNameApprobation("Name approbation");
|
| 194 | 194 |
|
| 195 |
Set<ConstraintViolation<TaxonName<?,?>>> constraintViolations = validator.validate(bacterialName);
|
|
| 195 |
Set<ConstraintViolation<TaxonName>> constraintViolations = validator.validate(bacterialName); |
|
| 196 | 196 |
assertTrue("There should be no constraint violation as a bacterial name may have subgenus authorship or name approbation set", constraintViolations.isEmpty());
|
| 197 | 197 |
} |
| 198 | 198 |
|
| cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/DeduplicationHelper.java | ||
|---|---|---|
| 265 | 265 |
//TODO cast |
| 266 | 266 |
getCollectionRoles(clazz, sessionFactory); |
| 267 | 267 |
|
| 268 |
TaxonName<?,?> name1 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
| 268 |
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(null); |
|
| 269 | 269 |
name1.getTaxonBases(); |
| 270 | 270 |
|
| 271 | 271 |
Type propType = sessionFactory.getReferencedPropertyType(TaxonName.class.getCanonicalName(), "taxonBases"); |
| cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/name/TaxonNameDaoHibernateImpl.java | ||
|---|---|---|
| 395 | 395 |
} |
| 396 | 396 |
|
| 397 | 397 |
|
| 398 |
public List<TaxonName<?,?>> searchNames(String queryString, MatchMode matchMode, Integer pageSize, Integer pageNumber) {
|
|
| 398 |
public List<TaxonName> searchNames(String queryString, MatchMode matchMode, Integer pageSize, Integer pageNumber) {
|
|
| 399 | 399 |
checkNotInPriorView("TaxonNameDaoHibernateImpl.searchNames(String queryString, Integer pageSize, Integer pageNumber)");
|
| 400 | 400 |
Criteria criteria = getSession().createCriteria(TaxonName.class); |
| 401 | 401 |
|
| ... | ... | |
| 410 | 410 |
criteria.setFirstResult(0); |
| 411 | 411 |
} |
| 412 | 412 |
} |
| 413 |
List<TaxonName<?,?>> results = criteria.list();
|
|
| 413 |
List<TaxonName> results = criteria.list(); |
|
| 414 | 414 |
return results; |
| 415 | 415 |
} |
| 416 | 416 |
|
| 417 | 417 |
|
| 418 | 418 |
@Override |
| 419 |
public List<TaxonName<?,?>> searchNames(String queryString, Integer pageSize, Integer pageNumber) {
|
|
| 419 |
public List<TaxonName> searchNames(String queryString, Integer pageSize, Integer pageNumber) {
|
|
| 420 | 420 |
return searchNames(queryString, MatchMode.BEGINNING, pageSize, pageNumber); |
| 421 | 421 |
} |
| 422 | 422 |
|
| ... | ... | |
| 521 | 521 |
} |
| 522 | 522 |
|
| 523 | 523 |
@Override |
| 524 |
public List<? extends TaxonName<?,?>> findByName(boolean doIncludeAuthors,
|
|
| 524 |
public List<? extends TaxonName> findByName(boolean doIncludeAuthors, |
|
| 525 | 525 |
String queryString, MatchMode matchmode, Integer pageSize, |
| 526 | 526 |
Integer pageNumber, List<Criterion> criteria, List<String> propertyPaths) {
|
| 527 | 527 |
|
| ... | ... | |
| 564 | 564 |
} |
| 565 | 565 |
|
| 566 | 566 |
@SuppressWarnings("unchecked")
|
| 567 |
List<? extends TaxonName<?,?>> results = crit.list();
|
|
| 567 |
List<? extends TaxonName> results = crit.list(); |
|
| 568 | 568 |
defaultBeanInitializer.initializeAll(results, propertyPaths); |
| 569 | 569 |
|
| 570 | 570 |
return results; |
| 571 | 571 |
} |
| 572 | 572 |
|
| 573 | 573 |
@Override |
| 574 |
public List<? extends TaxonName<?,?>> findByTitle(String queryString,
|
|
| 574 |
public List<? extends TaxonName> findByTitle(String queryString, |
|
| 575 | 575 |
MatchMode matchmode, Integer pageSize, Integer pageNumber, List<Criterion> criteria, List<String> propertyPaths) {
|
| 576 | 576 |
|
| 577 | 577 |
Criteria crit = getSession().createCriteria(type); |
| ... | ... | |
| 594 | 594 |
} |
| 595 | 595 |
} |
| 596 | 596 |
|
| 597 |
List<? extends TaxonName<?,?>> results = crit.list();
|
|
| 597 |
List<? extends TaxonName> results = crit.list(); |
|
| 598 | 598 |
defaultBeanInitializer.initializeAll(results, propertyPaths); |
| 599 | 599 |
|
| 600 | 600 |
return results; |
| ... | ... | |
| 619 | 619 |
} |
| 620 | 620 |
crit.addOrder(Order.asc("uuid"));
|
| 621 | 621 |
|
| 622 |
List<? extends TaxonName<?,?>> results = crit.list();
|
|
| 622 |
List<? extends TaxonName> results = crit.list(); |
|
| 623 | 623 |
if (results.size() == 1) {
|
| 624 | 624 |
defaultBeanInitializer.initializeAll(results, propertyPaths); |
| 625 |
TaxonName<?, ?> taxonName = results.iterator().next();
|
|
| 625 |
TaxonName taxonName = results.iterator().next(); |
|
| 626 | 626 |
return taxonName; |
| 627 | 627 |
} else if (results.size() > 1) {
|
| 628 | 628 |
logger.error("Multiple results for UUID: " + uuid);
|
| ... | ... | |
| 701 | 701 |
public Integer countByName(String queryString, MatchMode matchmode, List<Criterion> criteria) {
|
| 702 | 702 |
//TODO improve performance |
| 703 | 703 |
boolean includeAuthors = false; |
| 704 |
List<? extends TaxonName<?,?>> results = findByName(
|
|
| 704 |
List<? extends TaxonName> results = findByName( |
|
| 705 | 705 |
includeAuthors,queryString, matchmode, null, null, criteria, null); |
| 706 | 706 |
return results.size(); |
| 707 | 707 |
|
| ... | ... | |
| 791 | 791 |
} |
| 792 | 792 |
|
| 793 | 793 |
@SuppressWarnings("unchecked")
|
| 794 |
List<? extends TaxonName<?,?>> results = criteria.list();
|
|
| 794 |
List<? extends TaxonName> results = criteria.list(); |
|
| 795 | 795 |
if (results.size() == 1) {
|
| 796 | 796 |
defaultBeanInitializer.initializeAll(results, null); |
| 797 |
TaxonName<?, ?> taxonName = results.iterator().next();
|
|
| 797 |
TaxonName taxonName = results.iterator().next(); |
|
| 798 | 798 |
if (taxonName.isZoological()) {
|
| 799 | 799 |
IZoologicalName zoologicalName = taxonName; |
| 800 | 800 |
return zoologicalName; |
| cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImpl.java | ||
|---|---|---|
| 42 | 42 |
|
| 43 | 43 |
import eu.etaxonomy.cdm.model.common.DefinedTerm; |
| 44 | 44 |
import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
| 45 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
|
| 45 | 46 |
import eu.etaxonomy.cdm.model.common.LSID; |
| 46 | 47 |
import eu.etaxonomy.cdm.model.common.MarkerType; |
| 47 |
import eu.etaxonomy.cdm.model.common.OriginalSourceBase; |
|
| 48 | 48 |
import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction; |
| 49 | 49 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 50 | 50 |
import eu.etaxonomy.cdm.model.name.Rank; |
| ... | ... | |
| 192 | 192 |
boolean includeAuthors = false; |
| 193 | 193 |
List<UuidAndTitleCache<IdentifiableEntity>> resultObjects = new ArrayList<UuidAndTitleCache<IdentifiableEntity>>(); |
| 194 | 194 |
if (doNamesWithoutTaxa){
|
| 195 |
List<? extends TaxonName<?,?>> nameResult = taxonNameDao.findByName(
|
|
| 195 |
List<? extends TaxonName> nameResult = taxonNameDao.findByName( |
|
| 196 | 196 |
includeAuthors, queryString, matchMode, null, null, null, null); |
| 197 | 197 |
|
| 198 | 198 |
for (TaxonName name: nameResult){
|
| ... | ... | |
| 1357 | 1357 |
query = getSession().createQuery("from ZoologicalName zn where zn.nameCache IN (:identicalNames)");
|
| 1358 | 1358 |
query.setParameterList("identicalNames", identicalNames);
|
| 1359 | 1359 |
List<TaxonName> result = query.list(); |
| 1360 |
TaxonName temp = result.get(0); |
|
| 1360 |
TaxonName tempName = result.get(0);
|
|
| 1361 | 1361 |
|
| 1362 |
Iterator<OriginalSourceBase> sources = temp.getSources().iterator();
|
|
| 1362 |
Iterator<IdentifiableSource> sources = tempName.getSources().iterator();
|
|
| 1363 | 1363 |
|
| 1364 | 1364 |
TaxonNameComparator taxComp = new TaxonNameComparator(); |
| 1365 | 1365 |
Collections.sort(result, taxComp); |
| cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/initializer/TitleAndNameCacheAutoInitializer.java | ||
|---|---|---|
| 72 | 72 |
} |
| 73 | 73 |
} else if(bean instanceof TaxonName) {
|
| 74 | 74 |
// ---> TaxonName |
| 75 |
TaxonName n = (TaxonName<?,?>)bean;
|
|
| 75 |
TaxonName n = (TaxonName)bean; |
|
| 76 | 76 |
if(!n.isProtectedFullTitleCache()) {
|
| 77 | 77 |
n.getFullTitleCache(); |
| 78 | 78 |
} else if(!bean.isProtectedTitleCache()){
|
| cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/name/ITaxonNameDao.java | ||
|---|---|---|
| 229 | 229 |
* set (0 - based) |
| 230 | 230 |
* @return a List of TaxonName instances |
| 231 | 231 |
*/ |
| 232 |
public List<TaxonName<?, ?>> searchNames(String queryString,
|
|
| 232 |
public List<TaxonName> searchNames(String queryString, |
|
| 233 | 233 |
Integer pageSize, Integer pageNumber); |
| 234 | 234 |
|
| 235 | 235 |
|
| ... | ... | |
| 252 | 252 |
* @param propertyPaths TODO |
| 253 | 253 |
* @return |
| 254 | 254 |
*/ |
| 255 |
public List<? extends TaxonName<?, ?>> findByName(boolean doIncludeAuthors,
|
|
| 255 |
public List<? extends TaxonName> findByName(boolean doIncludeAuthors, |
|
| 256 | 256 |
String queryString, |
| 257 | 257 |
MatchMode matchmode, Integer pageSize, Integer pageNumber, |
| 258 | 258 |
List<Criterion> criteria, List<String> propertyPaths); |
| ... | ... | |
| 266 | 266 |
* @param propertyPaths TODO |
| 267 | 267 |
* @return |
| 268 | 268 |
*/ |
| 269 |
public List<? extends TaxonName<?, ?>> findByTitle(String queryString,
|
|
| 269 |
public List<? extends TaxonName> findByTitle(String queryString, |
|
| 270 | 270 |
MatchMode matchmode, Integer pageSize, Integer pageNumber, |
| 271 | 271 |
List<Criterion> criteria, List<String> propertyPaths); |
| 272 | 272 |
|
| ... | ... | |
| 281 | 281 |
* |
| 282 | 282 |
* @return |
| 283 | 283 |
*/ |
| 284 |
public TaxonName<?, ?> findByUuid(UUID uuid, List<Criterion> criteria, List<String> propertyPaths);
|
|
| 284 |
public TaxonName findByUuid(UUID uuid, List<Criterion> criteria, List<String> propertyPaths); |
|
| 285 | 285 |
|
| 286 | 286 |
/** |
| 287 | 287 |
* @param queryString |
| cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/BeanInitializerIntegration.java | ||
|---|---|---|
| 98 | 98 |
propertyPaths.add("combinationAuthorship");
|
| 99 | 99 |
propertyPaths.add("hybridRelationships");
|
| 100 | 100 |
|
| 101 |
TaxonName<?,?> sphingidae = taxonNameDao.load(sphingidaeUuid, propertyPaths);
|
|
| 101 |
TaxonName sphingidae = taxonNameDao.load(sphingidaeUuid, propertyPaths); |
|
| 102 | 102 |
setComplete(); |
| 103 | 103 |
endTransaction(); |
| 104 | 104 |
|
| cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/CdmGenericDaoImplTest.java | ||
|---|---|---|
| 492 | 492 |
// @Ignore |
| 493 | 493 |
public void testMergeCdmBaseReferenceAndIdentifiable() throws MergeException {
|
| 494 | 494 |
|
| 495 |
TaxonName<?,?> name1 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 495 |
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()); |
|
| 496 | 496 |
name1.setTitleCache("BotanicalName1", true);
|
| 497 | 497 |
|
| 498 |
TaxonName<?,?> name2 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 498 |
TaxonName name2 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()); |
|
| 499 | 499 |
name2.setTitleCache("BotanicalName2", true);
|
| 500 | 500 |
|
| 501 | 501 |
TaxonName zooName1 = TaxonNameFactory.NewZoologicalInstance(Rank.SPECIES()); |
| ... | ... | |
| 622 | 622 |
@Test |
| 623 | 623 |
// @Ignore |
| 624 | 624 |
public void testMergeTaxonNameAndTaxon() throws MergeException {
|
| 625 |
TaxonName<?,?> name1 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 625 |
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()); |
|
| 626 | 626 |
name1.setTitleCache("BotanicalName1", true);
|
| 627 | 627 |
|
| 628 |
TaxonName<?,?> name2 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 628 |
TaxonName name2 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()); |
|
| 629 | 629 |
name2.setTitleCache("BotanicalName2", true);
|
| 630 | 630 |
|
| 631 | 631 |
IBotanicalName name3 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()); |
| ... | ... | |
| 869 | 869 |
UUID uuidAbiesAlba = UUID.fromString("6ed56b43-7cca-4c3b-bb90-7576da81c072");
|
| 870 | 870 |
|
| 871 | 871 |
// CREATE DATA |
| 872 |
TaxonName<?,?> pinusAlba = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 872 |
TaxonName pinusAlba = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()); |
|
| 873 | 873 |
pinusAlba.setTitleCache("BotanicalName1", true);
|
| 874 | 874 |
pinusAlba.setUuid(uuidPinusAlba); |
| 875 | 875 |
|
| 876 |
TaxonName<?,?> abiesAlba = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 876 |
TaxonName abiesAlba = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()); |
|
| 877 | 877 |
abiesAlba.setTitleCache("Abies alba", true);
|
| 878 | 878 |
abiesAlba.setUuid(uuidAbiesAlba); |
| 879 | 879 |
|
| ... | ... | |
| 912 | 912 |
@Test |
| 913 | 913 |
public void testReallocatePersonTeam() throws MergeException {
|
| 914 | 914 |
|
| 915 |
TaxonName<?,?> name1 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 915 |
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()); |
|
| 916 | 916 |
name1.setTitleCache("BotanicalName1", true);
|
| 917 | 917 |
|
| 918 | 918 |
IBook book1 = ReferenceFactory.newBook(); |
| cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/hibernate/CacheStrategyGeneratorTest.java | ||
|---|---|---|
| 101 | 101 |
@ExpectedDataSet |
| 102 | 102 |
public void testOnSaveOrUpdateNames() {
|
| 103 | 103 |
//names |
| 104 |
TaxonName<?,?> name = cdmEntityDaoBase.findByUuid(UUID.fromString("a49a3963-c4ea-4047-8588-2f8f15352730"));
|
|
| 104 |
TaxonName name = cdmEntityDaoBase.findByUuid(UUID.fromString("a49a3963-c4ea-4047-8588-2f8f15352730"));
|
|
| 105 | 105 |
name.setTitleCache(null, false); |
| 106 | 106 |
name.setNameCache(null, false); |
| 107 | 107 |
name.setGenusOrUninomial("Abies");
|
| 108 | 108 |
name.setAuthorshipCache("Mill.", true);
|
| 109 | 109 |
cdmEntityDaoBase.saveOrUpdate(name); |
| 110 |
TaxonName<?,?> name2 = cdmEntityDaoBase.findByUuid(UUID.fromString("05a438d6-065f-49ef-84db-c7dc2c259975"));
|
|
| 110 |
TaxonName name2 = cdmEntityDaoBase.findByUuid(UUID.fromString("05a438d6-065f-49ef-84db-c7dc2c259975"));
|
|
| 111 | 111 |
name2.setProtectedFullTitleCache(false); |
| 112 | 112 |
name2.setProtectedTitleCache(false); |
| 113 | 113 |
name2.setProtectedNameCache(false); |
Also available in: Unified diff
ref #6630 and ref #6368 remove generics from TaxonName