Revision 9dc896c9
Added by Andreas Müller almost 7 years ago
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/ipni/IpniService.java | ||
|---|---|---|
| 51 | 51 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
| 52 | 52 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
| 53 | 53 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 54 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 54 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 55 | 55 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
| 56 | 56 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType; |
| 57 | 57 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 449 | 449 |
} |
| 450 | 450 |
|
| 451 | 451 |
|
| 452 |
private List<TaxonNameBase<?,?>> 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<TaxonNameBase<?,?>> 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(); |
| ... | ... | |
| 461 | 461 |
String line = reader.readLine(); |
| 462 | 462 |
while (isNotBlank(line)){
|
| 463 | 463 |
// System.out.println(line); |
| 464 |
TaxonNameBase<?,?> name = (TaxonNameBase<?,?>)getNameFromLine(line,parameterMap, repository, config);
|
|
| 464 |
TaxonName name = (TaxonName)getNameFromLine(line,parameterMap, repository, config);
|
|
| 465 | 465 |
result.add(name); |
| 466 | 466 |
line = reader.readLine(); |
| 467 | 467 |
} |
| ... | ... | |
| 578 | 578 |
|
| 579 | 579 |
//basionym |
| 580 | 580 |
if (config.isDoBasionyms() && valueMap.get(BASIONYM)!= null){
|
| 581 |
TaxonNameBase<?,?> basionym = TaxonNameFactory.NewBotanicalInstance(null);
|
|
| 581 |
TaxonName basionym = TaxonNameFactory.NewBotanicalInstance(null); |
|
| 582 | 582 |
basionym.setTitleCache(valueMap.get(BASIONYM), true); |
| 583 | 583 |
name.addBasionym(basionym); |
| 584 | 584 |
} |
| 585 | 585 |
|
| 586 | 586 |
//replaced synonym |
| 587 | 587 |
if (config.isDoBasionyms() && valueMap.get(REPLACED_SYNONYM)!= null){
|
| 588 |
TaxonNameBase<?,?> replacedSynoynm = TaxonNameFactory.NewBotanicalInstance(null);
|
|
| 588 |
TaxonName replacedSynoynm = TaxonNameFactory.NewBotanicalInstance(null); |
|
| 589 | 589 |
replacedSynoynm.setTitleCache(valueMap.get(REPLACED_SYNONYM), true); |
| 590 | 590 |
name.addReplacedSynonym(replacedSynoynm, null, null, null); |
| 591 | 591 |
} |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/occurrence/gbif/GbifJsonOccurrenceParser.java | ||
|---|---|---|
| 38 | 38 |
import eu.etaxonomy.cdm.model.media.MediaRepresentation; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 40 | 40 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 41 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 41 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 42 | 42 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
| 43 | 43 |
import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent; |
| 44 | 44 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType; |
| ... | ... | |
| 210 | 210 |
String dataSetKey = null; |
| 211 | 211 |
GbifDataSetProtocol dataSetProtocol = null; |
| 212 | 212 |
DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(SpecimenOrObservationType.PreservedSpecimen); |
| 213 |
TaxonNameBase name = null;
|
|
| 213 |
TaxonName name = null; |
|
| 214 | 214 |
JSONObject record = (JSONObject)o; |
| 215 | 215 |
|
| 216 | 216 |
if(record.has(DATASET_PROTOCOL)){
|
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/occurrence/gbif/GbifResponse.java | ||
|---|---|---|
| 12 | 12 |
|
| 13 | 13 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
| 14 | 14 |
import eu.etaxonomy.cdm.ext.occurrence.DataResponse; |
| 15 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 15 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 16 | 16 |
|
| 17 | 17 |
/** |
| 18 | 18 |
* Wrapper class which holds a {@link DerivedUnitFacade} which was parsed from a GBIF JSON response.
|
| ... | ... | |
| 28 | 28 |
|
| 29 | 29 |
private final GbifDataSetProtocol dataSetProtocol; |
| 30 | 30 |
|
| 31 |
private final TaxonNameBase scientificName;
|
|
| 31 |
private final TaxonName scientificName; |
|
| 32 | 32 |
/** |
| 33 | 33 |
* @param derivedUnitFacade |
| 34 | 34 |
* @param dataSetUrl |
| 35 | 35 |
*/ |
| 36 |
public GbifResponse(DerivedUnitFacade derivedUnitFacade, URI dataSetUrl, GbifDataSetProtocol dataSetProtocol, String [] tripleID, TaxonNameBase scientificName) {
|
|
| 36 |
public GbifResponse(DerivedUnitFacade derivedUnitFacade, URI dataSetUrl, GbifDataSetProtocol dataSetProtocol, String [] tripleID, TaxonName scientificName) {
|
|
| 37 | 37 |
super(derivedUnitFacade,dataSetUrl, tripleID); |
| 38 | 38 |
this.dataSetProtocol = dataSetProtocol; |
| 39 | 39 |
|
| ... | ... | |
| 63 | 63 |
/** |
| 64 | 64 |
* @return the scientificName |
| 65 | 65 |
*/ |
| 66 |
public TaxonNameBase getScientificName() {
|
|
| 66 |
public TaxonName getScientificName() {
|
|
| 67 | 67 |
return scientificName; |
| 68 | 68 |
} |
| 69 | 69 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/CacheUpdater.java | ||
|---|---|---|
| 16 | 16 |
import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity; |
| 17 | 17 |
import eu.etaxonomy.cdm.model.media.Media; |
| 18 | 18 |
import eu.etaxonomy.cdm.model.molecular.Sequence; |
| 19 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 19 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 20 | 20 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
| 21 | 21 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
| 22 | 22 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 65 | 65 |
List list = Arrays.asList(new Class[]{
|
| 66 | 66 |
DescriptionBase.class, IdentifiableMediaEntity.class, |
| 67 | 67 |
Media.class, Sequence.class, |
| 68 |
TaxonBase.class, TaxonNameBase.class,
|
|
| 68 |
TaxonBase.class, TaxonName.class, |
|
| 69 | 69 |
Classification.class, TermBase.class |
| 70 | 70 |
}); |
| 71 | 71 |
handleClassList(list); |
| ... | ... | |
| 118 | 118 |
//TODO misuse TaxonServic for sequence update, use sequence service when it exists |
| 119 | 119 |
getTaxonService().updateTitleCache((Class) clazz, null, null, null); |
| 120 | 120 |
} |
| 121 |
//TaxonNameBase
|
|
| 122 |
else if (TaxonNameBase.class.isAssignableFrom(clazz)){
|
|
| 121 |
//TaxonName |
|
| 122 |
else if (TaxonName.class.isAssignableFrom(clazz)){
|
|
| 123 | 123 |
getNameService().updateTitleCache((Class) clazz, null, null, null); |
| 124 | 124 |
} |
| 125 | 125 |
//Classification |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/CacheUpdaterWithNewCacheStrategy.java | ||
|---|---|---|
| 13 | 13 |
import eu.etaxonomy.cdm.model.description.FeatureTree; |
| 14 | 14 |
import eu.etaxonomy.cdm.model.media.Media; |
| 15 | 15 |
import eu.etaxonomy.cdm.model.molecular.Sequence; |
| 16 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 16 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 17 | 17 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
| 18 | 18 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
| 19 | 19 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 85 | 85 |
//TODO misuse TaxonServic for sequence update, use sequence service when it exists |
| 86 | 86 |
getTaxonService().updateTitleCache((Class) clazz, null, null, null); |
| 87 | 87 |
} |
| 88 |
//TaxonNameBase
|
|
| 89 |
else if (TaxonNameBase.class.isAssignableFrom(clazz)){
|
|
| 88 |
//TaxonName |
|
| 89 |
else if (TaxonName.class.isAssignableFrom(clazz)){
|
|
| 90 | 90 |
getNameService().updateTitleCache((Class) clazz, null, null, null); |
| 91 | 91 |
} |
| 92 | 92 |
//Classification |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/CdmApplicationAwareDefaultExport.java | ||
|---|---|---|
| 20 | 20 |
|
| 21 | 21 |
import eu.etaxonomy.cdm.api.service.IService; |
| 22 | 22 |
import eu.etaxonomy.cdm.io.common.events.IIoObserver; |
| 23 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
|
| 24 | 23 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 25 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
|
| 26 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
|
| 27 |
import eu.etaxonomy.cdm.model.reference.Reference; |
|
| 28 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
| 29 | 24 |
|
| 30 | 25 |
/** |
| 31 | 26 |
* This class is an default exporter class that is a spring bean and therefore it knows all other IO classes that are beans |
| ... | ... | |
| 60 | 55 |
Map<String, MapWrapper<? extends CdmBase>> stores = new HashMap<String, MapWrapper<? extends CdmBase>>(); |
| 61 | 56 |
|
| 62 | 57 |
public CdmApplicationAwareDefaultExport(){
|
| 63 |
stores.put(ICdmIO.TEAM_STORE, new MapWrapper<TeamOrPersonBase>(service));
|
|
| 64 |
stores.put(ICdmIO.REFERENCE_STORE, new MapWrapper<Reference>(service));
|
|
| 65 |
stores.put(ICdmIO.NOMREF_STORE, new MapWrapper<Reference>(service));
|
|
| 66 |
stores.put(ICdmIO.TAXONNAME_STORE, new MapWrapper<TaxonNameBase>(service));
|
|
| 67 |
stores.put(ICdmIO.TAXON_STORE, new MapWrapper<TaxonBase>(service));
|
|
| 68 |
stores.put(ICdmIO.SPECIMEN_STORE, new MapWrapper<DerivedUnit>(service));
|
|
| 58 |
stores.put(ICdmIO.TEAM_STORE, new MapWrapper<>(service)); |
|
| 59 |
stores.put(ICdmIO.REFERENCE_STORE, new MapWrapper<>(service)); |
|
| 60 |
stores.put(ICdmIO.NOMREF_STORE, new MapWrapper<>(service)); |
|
| 61 |
stores.put(ICdmIO.TAXONNAME_STORE, new MapWrapper<>(service)); |
|
| 62 |
stores.put(ICdmIO.TAXON_STORE, new MapWrapper<>(service)); |
|
| 63 |
stores.put(ICdmIO.SPECIMEN_STORE, new MapWrapper<>(service)); |
|
| 69 | 64 |
} |
| 70 | 65 |
|
| 71 | 66 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/CdmImportBase.java | ||
|---|---|---|
| 71 | 71 |
import eu.etaxonomy.cdm.model.name.INonViralName; |
| 72 | 72 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 73 | 73 |
import eu.etaxonomy.cdm.model.name.RankClass; |
| 74 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 74 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 75 | 75 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
| 76 | 76 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 77 | 77 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| ... | ... | |
| 1026 | 1026 |
* If false only taxon description being no image galleries are considered. |
| 1027 | 1027 |
* @return |
| 1028 | 1028 |
*/ |
| 1029 |
public TaxonNameDescription getTaxonNameDescription(TaxonNameBase name, boolean isImageGallery, boolean createNewIfNotExists) {
|
|
| 1029 |
public TaxonNameDescription getTaxonNameDescription(TaxonName name, boolean isImageGallery, boolean createNewIfNotExists) {
|
|
| 1030 | 1030 |
Reference ref = null; |
| 1031 | 1031 |
return getTaxonNameDescription(name, ref, isImageGallery, createNewIfNotExists); |
| 1032 | 1032 |
} |
| ... | ... | |
| 1038 | 1038 |
* |
| 1039 | 1039 |
* @see #getTaxonDescription(Taxon, boolean, boolean) |
| 1040 | 1040 |
*/ |
| 1041 |
public TaxonNameDescription getTaxonNameDescription(TaxonNameBase<?,?> name, Reference ref, boolean isImageGallery, boolean createNewIfNotExists) {
|
|
| 1041 |
public TaxonNameDescription getTaxonNameDescription(TaxonName<?,?> name, Reference ref, boolean isImageGallery, boolean createNewIfNotExists) {
|
|
| 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/ImportHelper.java | ||
|---|---|---|
| 34 | 34 |
import eu.etaxonomy.cdm.model.common.TimePeriod; |
| 35 | 35 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
| 36 | 36 |
import eu.etaxonomy.cdm.model.description.DescriptionElementSource; |
| 37 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 37 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 38 | 38 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 39 | 39 |
import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser; |
| 40 | 40 |
/** |
| ... | ... | |
| 318 | 318 |
T result; |
| 319 | 319 |
try {
|
| 320 | 320 |
methodName = getGetterMethodName(cdmAttrName, isBoolean); |
| 321 |
if (cdmBase.isInstanceOf(TaxonNameBase.class)){
|
|
| 321 |
if (cdmBase.isInstanceOf(TaxonName.class)){
|
|
| 322 | 322 |
cdmBase = CdmBase.deproxy(cdmBase); |
| 323 | 323 |
} |
| 324 | 324 |
Method cdmMethod = cdmBase.getClass().getMethod(methodName); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/ImportStateBase.java | ||
|---|---|---|
| 17 | 17 |
|
| 18 | 18 |
import eu.etaxonomy.cdm.api.service.IService; |
| 19 | 19 |
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
| 20 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
|
| 21 | 20 |
import eu.etaxonomy.cdm.model.common.AnnotationType; |
| 22 | 21 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 23 | 22 |
import eu.etaxonomy.cdm.model.common.DefinedTerm; |
| ... | ... | |
| 34 | 33 |
import eu.etaxonomy.cdm.model.location.NamedAreaLevel; |
| 35 | 34 |
import eu.etaxonomy.cdm.model.location.ReferenceSystem; |
| 36 | 35 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 37 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
|
| 38 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
|
| 39 | 36 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 40 | 37 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 41 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
| 42 | 38 |
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; |
| 43 | 39 |
|
| 44 | 40 |
/** |
| ... | ... | |
| 96 | 92 |
|
| 97 | 93 |
protected ImportStateBase(CONFIG config){
|
| 98 | 94 |
this.config = config; |
| 99 |
stores.put(ICdmIO.TEAM_STORE, new MapWrapper<TeamOrPersonBase<?>>(service));
|
|
| 100 |
stores.put(ICdmIO.REFERENCE_STORE, new MapWrapper<Reference>(service));
|
|
| 101 |
stores.put(ICdmIO.NOMREF_STORE, new MapWrapper<Reference>(service));
|
|
| 102 |
stores.put(ICdmIO.TAXONNAME_STORE, new MapWrapper<TaxonNameBase<?,?>>(service));
|
|
| 103 |
stores.put(ICdmIO.TAXON_STORE, new MapWrapper<TaxonBase>(service));
|
|
| 104 |
stores.put(ICdmIO.SPECIMEN_STORE, new MapWrapper<DerivedUnit>(service));
|
|
| 95 |
stores.put(ICdmIO.TEAM_STORE, new MapWrapper<>(service)); |
|
| 96 |
stores.put(ICdmIO.REFERENCE_STORE, new MapWrapper<>(service)); |
|
| 97 |
stores.put(ICdmIO.NOMREF_STORE, new MapWrapper<>(service)); |
|
| 98 |
stores.put(ICdmIO.TAXONNAME_STORE, new MapWrapper<>(service)); |
|
| 99 |
stores.put(ICdmIO.TAXON_STORE, new MapWrapper<>(service)); |
|
| 100 |
stores.put(ICdmIO.SPECIMEN_STORE, new MapWrapper<>(service)); |
|
| 105 | 101 |
|
| 106 | 102 |
if (getTransformer() == null){
|
| 107 | 103 |
IInputTransformer newTransformer = config.getTransformer(); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/DbImportNameTypeDesignationMapper.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2007 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
|
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 | 4 |
* http://www.e-taxonomy.eu |
| 5 |
*
|
|
| 5 |
* |
|
| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
| 18 | 18 |
import eu.etaxonomy.cdm.io.common.DbImportStateBase; |
| 19 | 19 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 20 | 20 |
import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus; |
| 21 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 21 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 22 | 22 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 23 | 23 |
|
| 24 | 24 |
/** |
| ... | ... | |
| 35 | 35 |
*/ |
| 36 | 36 |
public class DbImportNameTypeDesignationMapper<STATE extends DbImportStateBase<?,?>, T extends IDbImportTransformed> extends DbImportMultiAttributeMapperBase<CdmBase, STATE> {
|
| 37 | 37 |
private static final Logger logger = Logger.getLogger(DbImportNameTypeDesignationMapper.class); |
| 38 |
|
|
| 38 |
|
|
| 39 | 39 |
//******************************** FACTORY METHOD ***************************************************/ |
| 40 |
|
|
| 40 |
|
|
| 41 | 41 |
public static DbImportNameTypeDesignationMapper<?,?> NewInstance(String dbFromAttribute, String dbToAttribute, String relatedObjectNamespace, String desigStatusAttribute){
|
| 42 | 42 |
return new DbImportNameTypeDesignationMapper(dbFromAttribute, dbToAttribute, null, relatedObjectNamespace, desigStatusAttribute); |
| 43 | 43 |
} |
| 44 |
|
|
| 44 |
|
|
| 45 | 45 |
//******************************* ATTRIBUTES ***************************************/ |
| 46 | 46 |
private String fromAttribute; |
| 47 | 47 |
private String toAttribute; |
| ... | ... | |
| 50 | 50 |
private String citationAttribute; |
| 51 | 51 |
private String microCitationAttribute; |
| 52 | 52 |
private String designationStatusAttribute; |
| 53 |
|
|
| 54 |
|
|
| 53 |
|
|
| 54 |
|
|
| 55 | 55 |
//********************************* CONSTRUCTOR ****************************************/ |
| 56 | 56 |
/** |
| 57 |
* @param relatedObjectNamespace
|
|
| 57 |
* @param relatedObjectNamespace |
|
| 58 | 58 |
* @param mappingImport |
| 59 | 59 |
*/ |
| 60 | 60 |
protected DbImportNameTypeDesignationMapper(String fromAttribute, String toAttribute, NameTypeDesignationStatus designationStatus, String relatedObjectNamespace, String desigStatusAttribute) {
|
| ... | ... | |
| 68 | 68 |
} |
| 69 | 69 |
|
| 70 | 70 |
//************************************ METHODS *******************************************/ |
| 71 |
|
|
| 71 |
|
|
| 72 | 72 |
/* (non-Javadoc) |
| 73 | 73 |
* @see eu.etaxonomy.cdm.io.common.mapping.IDbImportMapper#invoke(java.sql.ResultSet, eu.etaxonomy.cdm.model.common.CdmBase) |
| 74 | 74 |
*/ |
| 75 |
public CdmBase invoke(ResultSet rs, CdmBase cdmBase) throws SQLException {
|
|
| 75 |
@Override |
|
| 76 |
public CdmBase invoke(ResultSet rs, CdmBase cdmBase) throws SQLException {
|
|
| 76 | 77 |
STATE state = importMapperHelper.getState(); |
| 77 | 78 |
CdmImportBase currentImport = state.getCurrentIO(); |
| 78 | 79 |
if (currentImport instanceof ICheckIgnoreMapper){
|
| ... | ... | |
| 81 | 82 |
return cdmBase; |
| 82 | 83 |
} |
| 83 | 84 |
} |
| 84 |
|
|
| 85 |
|
|
| 85 | 86 |
CdmBase fromObject = getRelatedObject(rs, fromAttribute); |
| 86 | 87 |
CdmBase toObject = getRelatedObject(rs, toAttribute); |
| 87 | 88 |
//TODO cast |
| ... | ... | |
| 90 | 91 |
if (citationAttribute != null){
|
| 91 | 92 |
microCitation = rs.getString(microCitationAttribute); |
| 92 | 93 |
} |
| 93 |
|
|
| 94 |
|
|
| 94 | 95 |
Object designationStatusValue = null; |
| 95 | 96 |
if (citationAttribute != null){
|
| 96 | 97 |
designationStatusValue = rs.getObject(designationStatusAttribute); |
| ... | ... | |
| 102 | 103 |
logger.warn(warning); |
| 103 | 104 |
return cdmBase; |
| 104 | 105 |
} |
| 105 |
TaxonNameBase typifiedName = checkTaxonNameBaseType(fromObject);
|
|
| 106 |
|
|
| 106 |
TaxonName typifiedName = checkTaxonNameType(fromObject);
|
|
| 107 |
|
|
| 107 | 108 |
if (toObject == null){
|
| 108 | 109 |
String warning = "Species name could not be found. Name type not added to higher rank name"; |
| 109 | 110 |
logger.warn(warning); |
| 110 | 111 |
return cdmBase; |
| 111 | 112 |
} |
| 112 |
TaxonNameBase typeName = checkTaxonNameBaseType(toObject);
|
|
| 113 |
|
|
| 113 |
TaxonName typeName = checkTaxonNameType(toObject);
|
|
| 114 |
|
|
| 114 | 115 |
boolean addToAllHomotypicNames = false; //TODO check if this is correct |
| 115 | 116 |
String originalNameString = null; //TODO what is this |
| 116 |
|
|
| 117 |
|
|
| 117 | 118 |
NameTypeDesignationStatus status = this.designationStatus; |
| 118 | 119 |
if (designationStatusValue != null){
|
| 119 | 120 |
//FIXME this needs work in generics to remove casts. Or find an other solution |
| ... | ... | |
| 123 | 124 |
} |
| 124 | 125 |
} |
| 125 | 126 |
typifiedName.addNameTypeDesignation(typeName, citation, microCitation, originalNameString, status, addToAllHomotypicNames); |
| 126 |
|
|
| 127 |
|
|
| 127 | 128 |
return typifiedName; |
| 128 | 129 |
} |
| 129 |
|
|
| 130 |
|
|
| 130 | 131 |
/** |
| 131 | 132 |
* //TODO copied from DbImportObjectMapper. Maybe these can be merged again in future |
| 132 | 133 |
* @param rs |
| ... | ... | |
| 144 | 145 |
} |
| 145 | 146 |
return result; |
| 146 | 147 |
} |
| 147 |
|
|
| 148 |
|
|
| 148 | 149 |
/** |
| 149 |
* Checks if cdmBase is of type Taxon
|
|
| 150 |
* Checks if cdmBase is of type Taxon |
|
| 150 | 151 |
* @param fromObject |
| 151 | 152 |
*/ |
| 152 |
private TaxonNameBase checkTaxonNameBaseType(CdmBase cdmBase) {
|
|
| 153 |
if (! cdmBase.isInstanceOf(TaxonNameBase.class)){
|
|
| 154 |
String warning = "Type name or typifier name is not of type TaxonNameBase but " + cdmBase.getClass().getName();
|
|
| 153 |
private TaxonName checkTaxonNameType(CdmBase cdmBase) {
|
|
| 154 |
if (! cdmBase.isInstanceOf(TaxonName.class)){
|
|
| 155 |
String warning = "Type name or typifier name is not of type TaxonName but " + cdmBase.getClass().getName(); |
|
| 155 | 156 |
logger.warn(warning); |
| 156 | 157 |
throw new IllegalArgumentException(warning); |
| 157 | 158 |
} |
| 158 |
return (cdmBase.deproxy(cdmBase, TaxonNameBase.class));
|
|
| 159 |
return (cdmBase.deproxy(cdmBase, TaxonName.class)); |
|
| 159 | 160 |
} |
| 160 | 161 |
|
| 161 | 162 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/out/DbDescriptionElementTaxonMapper.java | ||
|---|---|---|
| 19 | 19 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
| 20 | 20 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 21 | 21 |
import eu.etaxonomy.cdm.model.description.TaxonNameDescription; |
| 22 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 22 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 23 | 23 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 24 | 24 |
|
| 25 | 25 |
/** |
| ... | ... | |
| 76 | 76 |
} |
| 77 | 77 |
}else if (inDescription.isInstanceOf(TaxonNameDescription.class)){
|
| 78 | 78 |
TaxonNameDescription nameDescription = CdmBase.deproxy(inDescription, TaxonNameDescription.class); |
| 79 |
TaxonNameBase<?,?> 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 | ||
|---|---|---|
| 17 | 17 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 18 | 18 |
import eu.etaxonomy.cdm.model.common.OriginalSourceBase; |
| 19 | 19 |
import eu.etaxonomy.cdm.model.description.DescriptionElementSource; |
| 20 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 20 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 21 | 21 |
|
| 22 | 22 |
/** |
| 23 | 23 |
* @author a.mueller |
| ... | ... | |
| 52 | 52 |
if (cdmBase.isInstanceOf(OriginalSourceBase.class)){
|
| 53 | 53 |
OriginalSourceBase<?> source = CdmBase.deproxy(cdmBase, OriginalSourceBase.class); |
| 54 | 54 |
String nameString = source.getOriginalNameString(); |
| 55 |
TaxonNameBase<?,?> 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 | ||
|---|---|---|
| 31 | 31 |
import eu.etaxonomy.cdm.model.media.RightsType; |
| 32 | 32 |
import eu.etaxonomy.cdm.model.name.HybridRelationship; |
| 33 | 33 |
import eu.etaxonomy.cdm.model.name.INonViralName; |
| 34 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 34 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 35 | 35 |
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference; |
| 36 | 36 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 37 | 37 |
import eu.etaxonomy.cdm.strategy.match.DefaultMatchStrategy; |
| ... | ... | |
| 65 | 65 |
|
| 66 | 66 |
|
| 67 | 67 |
private IMatchStrategy referenceMatcher = DefaultMatchStrategy.NewInstance(Reference.class); |
| 68 |
private IMatchStrategy nameMatcher = DefaultMatchStrategy.NewInstance(TaxonNameBase.class);
|
|
| 68 |
private IMatchStrategy nameMatcher = DefaultMatchStrategy.NewInstance(TaxonName.class); |
|
| 69 | 69 |
|
| 70 | 70 |
|
| 71 | 71 |
// ************************** FACTORY *******************************/ |
| ... | ... | |
| 364 | 364 |
private void initNameMap(STATE state) {
|
| 365 | 365 |
if (!nameMapIsInitialized && repository != null){
|
| 366 | 366 |
List<String> propertyPaths = Arrays.asList("");
|
| 367 |
List<TaxonNameBase<?,?>> existingNames = repository.getNameService().list(null, null, null, null, propertyPaths);
|
|
| 368 |
for (TaxonNameBase<?,?> 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/csv/caryophyllales/out/CsvNameExport.java | ||
|---|---|---|
| 43 | 43 |
import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus; |
| 44 | 44 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
| 45 | 45 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 46 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 46 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 47 | 47 |
import eu.etaxonomy.cdm.model.name.TypeDesignationBase; |
| 48 | 48 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 49 | 49 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| ... | ... | |
| 184 | 184 |
Set<UUID> parentsNodesUUID = new HashSet<UUID>(childrenUuids); |
| 185 | 185 |
childrenUuids.clear(); |
| 186 | 186 |
List<TaxonNode> childrenNodes = new ArrayList<TaxonNode>(); |
| 187 |
TaxonNameBase name;
|
|
| 187 |
TaxonName name; |
|
| 188 | 188 |
|
| 189 | 189 |
|
| 190 | 190 |
findChildren(state, childrenUuids, parentsNodesUUID); |
| ... | ... | |
| 213 | 213 |
* @param familyNode |
| 214 | 214 |
*/ |
| 215 | 215 |
private void findChildren(CsvNameExportState state, Set<UUID> childrenUuids, Set<UUID> parentsNodesUUID) {
|
| 216 |
TaxonNameBase name;
|
|
| 216 |
TaxonName name; |
|
| 217 | 217 |
List<TaxonNode> familyNodes = getTaxonNodeService().find(parentsNodesUUID); |
| 218 | 218 |
parentsNodesUUID =new HashSet<UUID>(); |
| 219 | 219 |
for (TaxonNode familyNode: familyNodes){
|
| ... | ... | |
| 223 | 223 |
child = HibernateProxyHelper.deproxy(child, TaxonNode.class); |
| 224 | 224 |
Taxon taxon = HibernateProxyHelper.deproxy(child.getTaxon()); |
| 225 | 225 |
if (taxon != null){
|
| 226 |
name = HibernateProxyHelper.deproxy(taxon.getName(), TaxonNameBase.class);
|
|
| 226 |
name = HibernateProxyHelper.deproxy(taxon.getName(), TaxonName.class); |
|
| 227 | 227 |
if (child.getTaxon().getName().getRank().isLower(state.getConfig().getRank()) ) {
|
| 228 | 228 |
childrenUuids.add(child.getUuid()); |
| 229 | 229 |
if (child.hasChildNodes()){
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/in/DatabaseMapping.java | ||
|---|---|---|
| 25 | 25 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 26 | 26 |
import eu.etaxonomy.cdm.model.agent.Team; |
| 27 | 27 |
import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
| 28 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 28 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 29 | 29 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 30 | 30 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 31 | 31 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| ... | ... | |
| 268 | 268 |
|
| 269 | 269 |
private void initDatasource(String file) {
|
| 270 | 270 |
getDatabase(file); |
| 271 |
shortCuts.put("TaxonNameBase", TaxonNameBase.class);
|
|
| 271 |
shortCuts.put("TaxonName", TaxonName.class);
|
|
| 272 | 272 |
shortCuts.put("Taxon", Taxon.class);
|
| 273 | 273 |
shortCuts.put("Synonym", Synonym.class);
|
| 274 | 274 |
shortCuts.put("Reference", Reference.class);
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/in/DwcTaxonStreamItem2CdmTaxonConverter.java | ||
|---|---|---|
| 40 | 40 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 41 | 41 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 42 | 42 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 43 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 43 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 44 | 44 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 45 | 45 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 46 | 46 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| ... | ... | |
| 133 | 133 |
Rank rank = getRank(csvTaxonRecord, nomCode); |
| 134 | 134 |
|
| 135 | 135 |
//name && name published in |
| 136 |
TaxonNameBase<?,?> 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 TaxonNameBase<?,?> getScientificName(StreamItem item, NomenclaturalCode nomCode, Rank rank, List<MappedCdmBase> resultList, Reference sourceReference) {
|
|
| 504 |
TaxonNameBase<?,?> name = null;
|
|
| 503 |
private TaxonName<?,?> getScientificName(StreamItem item, NomenclaturalCode nomCode, Rank rank, List<MappedCdmBase> resultList, Reference sourceReference) {
|
|
| 504 |
TaxonName<?,?> name = null; |
|
| 505 | 505 |
String strScientificName = getValue(item, TermUri.DWC_SCIENTIFIC_NAME); |
| 506 | 506 |
//Name |
| 507 | 507 |
if (strScientificName != null){
|
| 508 |
name = (TaxonNameBase<?,?>)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(TaxonNameBase<?,?> nameBase, StreamItem item) {
|
|
| 610 |
private void checkAuthorship(TaxonName<?,?> nameBase, StreamItem item) {
|
|
| 611 | 611 |
if (!nameBase.isNonViral()){
|
| 612 | 612 |
return; |
| 613 | 613 |
} |
| ... | ... | |
| 677 | 677 |
* @return |
| 678 | 678 |
*/ |
| 679 | 679 |
private TaxonBase<?> getTaxonBase(StreamItem item) {
|
| 680 |
TaxonNameBase<?,?> 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/in/GbifReferenceCsv2CdmConverter.java | ||
|---|---|---|
| 33 | 33 |
import eu.etaxonomy.cdm.model.description.TextData; |
| 34 | 34 |
import eu.etaxonomy.cdm.model.name.INonViralName; |
| 35 | 35 |
import eu.etaxonomy.cdm.model.name.IZoologicalName; |
| 36 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 36 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 37 | 37 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 38 | 38 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| ... | ... | |
| 185 | 185 |
|
| 186 | 186 |
} |
| 187 | 187 |
|
| 188 |
private void createCitation(TaxonDescription desc, Reference ref, TaxonNameBase nameUsedInSource) {
|
|
| 188 |
private void createCitation(TaxonDescription desc, Reference ref, TaxonName nameUsedInSource) {
|
|
| 189 | 189 |
Feature feature = Feature.CITATION(); |
| 190 | 190 |
TextData textData = TextData.NewInstance(feature); |
| 191 | 191 |
DescriptionElementSource source = DescriptionElementSource.NewPrimarySourceInstance(ref, null, nameUsedInSource, null); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/in/GbifTypesAndSpecimen2CdmConverter.java | ||
|---|---|---|
| 23 | 23 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 24 | 24 |
import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus; |
| 25 | 25 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| 26 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 26 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 27 | 27 |
import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase; |
| 28 | 28 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
| 29 | 29 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
| ... | ... | |
| 87 | 87 |
DerivedUnit specimen = facade.innerDerivedUnit(); |
| 88 | 88 |
|
| 89 | 89 |
if (isType){
|
| 90 |
TaxonNameBase<?,?> name = taxon.getName();
|
|
| 90 |
TaxonName name = taxon.getName(); |
|
| 91 | 91 |
if (typeStatus.isInstanceOf(SpecimenTypeDesignationStatus.class)){
|
| 92 | 92 |
SpecimenTypeDesignationStatus status = CdmBase.deproxy(typeStatus, SpecimenTypeDesignationStatus.class); |
| 93 | 93 |
name.addSpecimenTypeDesignation(specimen, status, null, null, null, false, true); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaResourceRelationExport.java | ||
|---|---|---|
| 35 | 35 |
import eu.etaxonomy.cdm.model.description.TaxonInteraction; |
| 36 | 36 |
import eu.etaxonomy.cdm.model.name.INonViralName; |
| 37 | 37 |
import eu.etaxonomy.cdm.model.name.NameRelationship; |
| 38 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 38 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 39 | 39 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 40 | 40 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 41 | 41 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| ... | ... | |
| 150 | 150 |
Set<NameRelationship> rels = name.getNameRelations(); |
| 151 | 151 |
for (NameRelationship rel : rels){
|
| 152 | 152 |
DwcaResourceRelationRecord record = new DwcaResourceRelationRecord(metaRecord, config); |
| 153 |
IdentifiableEntity<?> subject = CdmBase.deproxy(rel.getFromName(), TaxonNameBase.class);
|
|
| 154 |
IdentifiableEntity<?> object = CdmBase.deproxy(rel.getToName(), TaxonNameBase.class);
|
|
| 153 |
IdentifiableEntity<?> subject = CdmBase.deproxy(rel.getFromName(), TaxonName.class); |
|
| 154 |
IdentifiableEntity<?> object = CdmBase.deproxy(rel.getToName(), TaxonName.class); |
|
| 155 | 155 |
boolean isInverse = false; |
| 156 | 156 |
if(subject == name){
|
| 157 | 157 |
subject = taxon; |
| ... | ... | |
| 218 | 218 |
//TODO missing |
| 219 | 219 |
record.setRelatioshipEstablishedDate(null); |
| 220 | 220 |
record.setRelationshipRemarks(rel.getAnnotations()); |
| 221 |
if (object.isInstanceOf(TaxonNameBase.class)){
|
|
| 221 |
if (object.isInstanceOf(TaxonName.class)){
|
|
| 222 | 222 |
record.setScientificName(object.getTitleCache()); |
| 223 | 223 |
} |
| 224 | 224 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTaxExport.java | ||
|---|---|---|
| 32 | 32 |
import eu.etaxonomy.cdm.model.name.INonViralName; |
| 33 | 33 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
| 34 | 34 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 35 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 35 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 36 | 36 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 37 | 37 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 38 | 38 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| ... | ... | |
| 109 | 109 |
|
| 110 | 110 |
INonViralName name = taxon.getName(); |
| 111 | 111 |
Taxon parent = node.getParent() == null ? null : node.getParent().getTaxon(); |
| 112 |
TaxonNameBase<?, ?> basionym = name.getBasionym();
|
|
| 112 |
TaxonName basionym = name.getBasionym(); |
|
| 113 | 113 |
Classification classification = node.getClassification(); |
| 114 | 114 |
if (! this.recordExists(taxon)){
|
| 115 | 115 |
handleTaxonBase(record, taxon, name, taxon, parent, basionym, classification, null, false, false, config); |
| ... | ... | |
| 157 | 157 |
INonViralName name = synonym.getName(); |
| 158 | 158 |
//???? |
| 159 | 159 |
Taxon parent = null; |
| 160 |
TaxonNameBase<?, ?> basionym = name.getBasionym();
|
|
| 160 |
TaxonName basionym = name.getBasionym(); |
|
| 161 | 161 |
|
| 162 | 162 |
if (! this.recordExists(synonym)){
|
| 163 | 163 |
handleTaxonBase(record, synonym, name, taxon, parent, basionym, classification, type, isProParte, isPartial, config); |
| ... | ... | |
| 175 | 175 |
INonViralName name = misappliedName.getName(); |
| 176 | 176 |
//???? |
| 177 | 177 |
Taxon parent = null; |
| 178 |
TaxonNameBase<?, ?> basionym = name.getBasionym();
|
|
| 178 |
TaxonName basionym = name.getBasionym(); |
|
| 179 | 179 |
|
| 180 | 180 |
if (! this.recordExists(misappliedName)){
|
| 181 | 181 |
handleTaxonBase(record, misappliedName, name, taxon, parent, basionym, classification, relType, false, false, config); |
| ... | ... | |
| 198 | 198 |
* @param type |
| 199 | 199 |
*/ |
| 200 | 200 |
private void handleTaxonBase(DwcaTaxRecord record, TaxonBase<?> taxonBase, INonViralName name, |
| 201 |
Taxon acceptedTaxon, Taxon parent, TaxonNameBase<?, ?> basionym, Classification classification,
|
|
| 201 |
Taxon acceptedTaxon, Taxon parent, TaxonName basionym, Classification classification, |
|
| 202 | 202 |
RelationshipTermBase<?> relType, boolean isProParte, boolean isPartial, DwcaTaxExportConfigurator config) {
|
| 203 | 203 |
record.setId(taxonBase.getId()); |
| 204 | 204 |
record.setUuid(taxonBase.getUuid()); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTypesExport.java | ||
|---|---|---|
| 31 | 31 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 32 | 32 |
import eu.etaxonomy.cdm.model.name.INonViralName; |
| 33 | 33 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 34 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 34 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 35 | 35 |
import eu.etaxonomy.cdm.model.name.TypeDesignationBase; |
| 36 | 36 |
import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase; |
| 37 | 37 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
| ... | ... | |
| 191 | 191 |
record.setTypeStatus(status); |
| 192 | 192 |
record.setTypeDesignatedBy( (designation == null || designation.getCitation()==null)? null: designation.getCitation().getTitleCache()); |
| 193 | 193 |
|
| 194 |
TaxonNameBase<?,?> scientificName = getScientificName(facade);
|
|
| 194 |
TaxonName scientificName = getScientificName(facade); |
|
| 195 | 195 |
if (scientificName != null){
|
| 196 | 196 |
record.setScientificName(scientificName.getTitleCache()); |
| 197 | 197 |
record.setTaxonRank(scientificName.getRank()); |
| ... | ... | |
| 241 | 241 |
return true; |
| 242 | 242 |
} |
| 243 | 243 |
|
| 244 |
private TaxonNameBase<?,?> getScientificName(DerivedUnitFacade facade) {
|
|
| 244 |
private TaxonName<?,?> getScientificName(DerivedUnitFacade facade) {
|
|
| 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/common/ExcelRowBase.java | ||
|---|---|---|
| 24 | 24 |
import eu.etaxonomy.cdm.model.common.OriginalSourceType; |
| 25 | 25 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 26 | 26 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| 27 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 27 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 28 | 28 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 29 | 29 |
|
| 30 | 30 |
/** |
| ... | ... | |
| 181 | 181 |
SpecimenTypeDesignation designation = getOrMakeTypeDesignation(key); |
| 182 | 182 |
designation.setTypeStatus(status); |
| 183 | 183 |
} |
| 184 |
public void putTypifiedName(int key, TaxonNameBase<?,?> name){
|
|
| 184 |
public void putTypifiedName(int key, TaxonName name){
|
|
| 185 | 185 |
if (name != null){
|
| 186 | 186 |
SpecimenTypeDesignation designation = getOrMakeTypeDesignation(key); |
| 187 | 187 |
name.addTypeDesignation(designation, false); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/distribution/DistributionImport.java | ||
|---|---|---|
| 34 | 34 |
import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm; |
| 35 | 35 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 36 | 36 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 37 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 37 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 38 | 38 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 39 | 39 |
import eu.etaxonomy.cdm.persistence.query.MatchMode; |
| 40 | 40 |
|
| ... | ... | |
| 171 | 171 |
private void saveRecord(String taxonName, ArrayList<String> distributionList, |
| 172 | 172 |
String status, String literatureNumber, String literature) {
|
| 173 | 173 |
|
| 174 |
IdentifiableServiceConfiguratorImpl<TaxonNameBase> config = IdentifiableServiceConfiguratorFactory.getConfigurator(TaxonNameBase.class);
|
|
| 174 |
IdentifiableServiceConfiguratorImpl<TaxonName> config = IdentifiableServiceConfiguratorFactory.getConfigurator(TaxonName.class);
|
|
| 175 | 175 |
config.setTitleSearchString(taxonName); |
| 176 | 176 |
config.setMatchMode(MatchMode.BEGINNING); |
| 177 | 177 |
|
| 178 | 178 |
try {
|
| 179 | 179 |
// get the matching names from the DB |
| 180 |
//List<TaxonNameBase> taxonNameBases = getNameService().findByTitle(config);
|
|
| 181 |
List<TaxonNameBase> taxonNameBases = getNameService().findByName(null, taxonName, null, null, null, null,null,null).getRecords();
|
|
| 182 |
if (taxonNameBases.isEmpty()) {
|
|
| 180 |
//List<TaxonName> taxonNames = getNameService().findByTitle(config);
|
|
| 181 |
List<TaxonName> taxonNames = getNameService().findByName(null, taxonName, null, null, null, null,null,null).getRecords();
|
|
| 182 |
if (taxonNames.isEmpty()) {
|
|
| 183 | 183 |
logger.error("Taxon name '" + taxonName + "' not found in DB");
|
| 184 | 184 |
} else {
|
| 185 | 185 |
if (logger.isDebugEnabled()) { logger.debug("Taxon found"); }
|
| 186 | 186 |
} |
| 187 | 187 |
|
| 188 | 188 |
// get the taxa for the matching names |
| 189 |
for(TaxonNameBase<?,?> dbTaxonName: taxonNameBases) {
|
|
| 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 | ||
|---|---|---|
| 52 | 52 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 53 | 53 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
| 54 | 54 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 55 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 55 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 56 | 56 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
| 57 | 57 |
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference; |
| 58 | 58 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 327 | 327 |
String childId = taxonDataHolder.getId(); |
| 328 | 328 |
UUID cdmUuid = taxonDataHolder.getCdmUuid(); |
| 329 | 329 |
Taxon acceptedTaxon = null; |
| 330 |
TaxonNameBase<?,?> nameUsedInSource = null;
|
|
| 330 |
TaxonName nameUsedInSource = null; |
|
| 331 | 331 |
TaxonBase<?> taxonBase = null; |
| 332 | 332 |
Taxon parentTaxon = null; |
| 333 | 333 |
|
| ... | ... | |
| 522 | 522 |
* @param taxonDataHolder |
| 523 | 523 |
* @param acceptedTaxon |
| 524 | 524 |
*/ |
| 525 |
private void handleFeatures(TaxonExcelImportState state, NormalExplicitRow taxonDataHolder, Taxon acceptedTaxon, TaxonNameBase nameUsedInSource) {
|
|
| 525 |
private void handleFeatures(TaxonExcelImportState state, NormalExplicitRow taxonDataHolder, Taxon acceptedTaxon, TaxonName nameUsedInSource) {
|
|
| 526 | 526 |
//feature |
| 527 | 527 |
for (UUID featureUuid : taxonDataHolder.getFeatures()){
|
| 528 | 528 |
Feature feature = getFeature(state, featureUuid); |
| ... | ... | |
| 761 | 761 |
private TaxonBase<?> createTaxon(TaxonExcelImportState state, Rank rank, String taxonNameStr, |
| 762 | 762 |
String authorStr, String publishingAutorStr, String basionymAuthor, String reference, String date, String nameStatus, NomenclaturalCode nc) {
|
| 763 | 763 |
TaxonBase<?> taxonBase; |
| 764 |
INonViralName taxonNameBase = null;
|
|
| 764 |
INonViralName taxonName = null; |
|
| 765 | 765 |
if (nc == NomenclaturalCode.ICVCN){
|
| 766 | 766 |
logger.warn("ICVCN not yet supported");
|
| 767 | 767 |
|
| 768 | 768 |
}else{
|
| 769 | 769 |
//String taxonNameStr = titleCache.substring(0, titleCache.indexOf(authorStr)); |
| 770 |
taxonNameBase = nc.getNewTaxonNameInstance(rank);
|
|
| 770 |
taxonName = nc.getNewTaxonNameInstance(rank); |
|
| 771 | 771 |
NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance(); |
| 772 |
taxonNameBase = parser.parseFullName(taxonNameStr, nc, rank);
|
|
| 772 |
taxonName = parser.parseFullName(taxonNameStr, nc, rank); |
|
| 773 | 773 |
|
| 774 |
if (! taxonNameBase.getNameCache().equals(taxonNameStr)){
|
|
| 775 |
taxonNameBase.setNameCache(taxonNameStr, true);
|
|
| 774 |
if (! taxonName.getNameCache().equals(taxonNameStr)){
|
|
| 775 |
taxonName.setNameCache(taxonNameStr, true); |
|
| 776 | 776 |
} |
| 777 | 777 |
|
| 778 | 778 |
// Create the author |
| 779 | 779 |
if (StringUtils.isNotBlank(authorStr)) {
|
| 780 | 780 |
try {
|
| 781 |
parser.parseAuthors(taxonNameBase, authorStr);
|
|
| 781 |
parser.parseAuthors(taxonName, authorStr); |
|
| 782 | 782 |
} catch (StringNotParsableException e) {
|
| 783 |
taxonNameBase.setAuthorshipCache(authorStr);
|
|
| 783 |
taxonName.setAuthorshipCache(authorStr); |
|
| 784 | 784 |
} |
| 785 | 785 |
} |
| 786 | 786 |
if (StringUtils.isNotBlank(reference)) {
|
| 787 | 787 |
|
| 788 | 788 |
INomenclaturalReference ref = parser.parseReferenceTitle(reference, date, true); |
| 789 | 789 |
if (ref.getAuthorship() == null){
|
| 790 |
ref.setAuthorship(taxonNameBase.getCombinationAuthorship());
|
|
| 790 |
ref.setAuthorship(taxonName.getCombinationAuthorship()); |
|
| 791 | 791 |
} |
| 792 | 792 |
|
| 793 | 793 |
if (ref.getAbbrevTitle() == null && !ref.isOfType(ReferenceType.Article)) {
|
| ... | ... | |
| 797 | 797 |
|
| 798 | 798 |
ref.setProtectedTitleCache(false); |
| 799 | 799 |
|
| 800 |
taxonNameBase.setNomenclaturalReference(ref);
|
|
| 801 |
taxonNameBase.setNomenclaturalMicroReference(state.getCurrentRow().getCollation());
|
|
| 800 |
taxonName.setNomenclaturalReference(ref); |
|
| 801 |
taxonName.setNomenclaturalMicroReference(state.getCurrentRow().getCollation()); |
|
| 802 | 802 |
} |
| 803 | 803 |
} |
| 804 | 804 |
|
| ... | ... | |
| 807 | 807 |
// Create the status |
| 808 | 808 |
nameStatus = CdmUtils.Nz(nameStatus).trim().toLowerCase(); |
| 809 | 809 |
if (validMarkers.contains(nameStatus)){
|
| 810 |
taxonBase = Taxon.NewInstance(taxonNameBase, sec);
|
|
| 810 |
taxonBase = Taxon.NewInstance(taxonName, sec); |
|
| 811 | 811 |
}else if (synonymMarkers.contains(nameStatus)){
|
| 812 |
taxonBase = Synonym.NewInstance(taxonNameBase, sec);
|
|
| 812 |
taxonBase = Synonym.NewInstance(taxonName, sec); |
|
| 813 | 813 |
}else {
|
| 814 |
Taxon taxon = Taxon.NewInstance(taxonNameBase, sec);
|
|
| 814 |
Taxon taxon = Taxon.NewInstance(taxonName, sec); |
|
| 815 | 815 |
if (nameStatusMarkers.contains(nameStatus)){
|
| 816 | 816 |
if (nameStatus.equals(NOM_ILLEG)){
|
| 817 |
taxonNameBase.addStatus(NomenclaturalStatusType.ILLEGITIMATE(), null, null);
|
|
| 817 |
taxonName.addStatus(NomenclaturalStatusType.ILLEGITIMATE(), null, null); |
|
| 818 | 818 |
} else if (nameStatus.equals(NOM_REJ)){
|
| 819 |
taxonNameBase.addStatus(NomenclaturalStatusType.REJECTED(), null, null);
|
|
| 819 |
taxonName.addStatus(NomenclaturalStatusType.REJECTED(), null, null); |
|
| 820 | 820 |
} else if (nameStatus.equals(NOM_CONS)){
|
| 821 |
taxonNameBase.addStatus(NomenclaturalStatusType.CONSERVED(), null, null);
|
|
| 821 |
taxonName.addStatus(NomenclaturalStatusType.CONSERVED(), null, null); |
|
| 822 | 822 |
} |
| 823 | 823 |
}else{
|
| 824 | 824 |
taxon.setTaxonStatusUnknown(true); |
| ... | ... | |
| 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(TaxonNameBase<?,?> 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/jaxb/CdmIDResolver.java | ||
|---|---|---|
| 35 | 35 |
import eu.etaxonomy.cdm.model.description.FeatureTree; |
| 36 | 36 |
import eu.etaxonomy.cdm.model.media.Media; |
| 37 | 37 |
import eu.etaxonomy.cdm.model.name.HomotypicalGroup; |
| 38 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 38 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 39 | 39 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
| 40 | 40 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
| 41 | 41 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 43 | 43 |
|
| 44 | 44 |
public class CdmIDResolver extends IDResolver {
|
| 45 | 45 |
private static final Logger logger = Logger.getLogger(CdmIDResolver.class); |
| 46 |
|
|
| 46 |
|
|
| 47 | 47 |
IUserService userService; |
| 48 |
|
|
| 49 |
IAgentService agentService;
|
|
| 50 |
|
|
| 48 |
|
|
| 49 |
IAgentService agentService; |
|
| 50 |
|
|
| 51 | 51 |
ITermService termService; |
| 52 |
|
|
| 52 |
|
|
| 53 | 53 |
IVocabularyService vocabularyService; |
| 54 |
|
|
| 54 |
|
|
| 55 | 55 |
IDescriptionService descriptionService; |
| 56 |
|
|
| 56 |
|
|
| 57 | 57 |
IFeatureTreeService featureTreeService; |
| 58 |
|
|
| 58 |
|
|
| 59 | 59 |
IMediaService mediaService; |
| 60 |
|
|
| 60 |
|
|
| 61 | 61 |
INameService nameService; |
| 62 |
|
|
| 62 |
|
|
| 63 | 63 |
IOccurrenceService occurrenceService; |
| 64 |
|
|
| 64 |
|
|
| 65 | 65 |
ICollectionService collectionService; |
| 66 |
|
|
| 66 |
|
|
| 67 | 67 |
IReferenceService referenceService; |
| 68 |
|
|
| 68 |
|
|
| 69 | 69 |
ITaxonService taxonService; |
| 70 |
|
|
| 70 |
|
|
| 71 | 71 |
@Autowired |
| 72 | 72 |
public void setUserService(IUserService userService) {
|
| 73 | 73 |
this.userService = userService; |
| ... | ... | |
| 127 | 127 |
public void setTaxonService(ITaxonService taxonService) {
|
| 128 | 128 |
this.taxonService = taxonService; |
| 129 | 129 |
} |
| 130 |
|
|
| 130 |
|
|
| 131 | 131 |
private HashMap<String,Object> idmap = null; |
| 132 |
|
|
| 132 |
|
|
| 133 | 133 |
@Override |
| 134 | 134 |
public void startDocument(ValidationEventHandler eventHandler) throws SAXException {
|
| 135 | 135 |
if(idmap!=null) {
|
| ... | ... | |
| 144 | 144 |
} |
| 145 | 145 |
idmap.put(id,obj); |
| 146 | 146 |
} |
| 147 |
|
|
| 147 |
|
|
| 148 | 148 |
|
| 149 | 149 |
@Override |
| 150 | 150 |
public Callable<?> resolve(final String id, final Class targetType) throws SAXException {
|
| 151 | 151 |
return new Callable() {
|
| 152 |
public Object call() throws Exception {
|
|
| 152 |
@Override |
|
| 153 |
public Object call() throws Exception {
|
|
| 153 | 154 |
logger.info("Resolving " + id + " for class " + targetType);
|
| 154 |
|
|
| 155 |
|
|
| 155 | 156 |
if(idmap==null || !idmap.containsKey(id)) {
|
| 156 |
|
|
| 157 |
|
|
| 157 | 158 |
String uuidPart = id.substring(UUIDAdapter.UUID_URN_PREFIX.length()); |
| 158 | 159 |
UUID uuid = UUID.fromString(uuidPart); |
| 159 | 160 |
logger.info(uuid + " not in idmap, looking in database"); |
| ... | ... | |
| 171 | 172 |
return resolveObject(uuid, targetType, featureTreeService); |
| 172 | 173 |
} else if(Media.class.isAssignableFrom(targetType)) {
|
| 173 | 174 |
return resolveObject(uuid, targetType, mediaService); |
| 174 |
} else if(TaxonNameBase.class.isAssignableFrom(targetType)) {
|
|
| 175 |
} else if(TaxonName.class.isAssignableFrom(targetType)) {
|
|
| 175 | 176 |
return resolveObject(uuid, targetType, nameService); |
| 176 | 177 |
} else if(SpecimenOrObservationBase.class.isAssignableFrom(targetType)) {
|
| 177 | 178 |
return resolveObject(uuid, targetType, occurrenceService); |
| ... | ... | |
| 191 | 192 |
/** |
| 192 | 193 |
* Collections of IDREFS do not have a type at runtime |
| 193 | 194 |
* https://jaxb.dev.java.net/issues/show_bug.cgi?id=546 |
| 194 |
*
|
|
| 195 |
* |
|
| 195 | 196 |
* Maybe in the future we'll be able to add targetType to IDREF |
| 196 | 197 |
* but the spec has to be changed first so no fix is likely at the moment |
| 197 |
*
|
|
| 198 |
* |
|
| 198 | 199 |
*/ |
| 199 |
|
|
| 200 |
|
|
| 200 | 201 |
AgentBase agent = agentService.find(uuid); |
| 201 |
if(agent != null) {
|
|
| 202 |
if(agent != null) {
|
|
| 202 | 203 |
return agent; |
| 203 | 204 |
} |
| 204 | 205 |
DefinedTermBase term = termService.find(uuid); |
| 205 |
if(term != null) {
|
|
| 206 |
if(term != null) {
|
|
| 206 | 207 |
return term; |
| 207 | 208 |
} |
| 208 | 209 |
Media media = mediaService.find(uuid); |
| 209 |
if(media != null) {
|
|
| 210 |
if(media != null) {
|
|
| 210 | 211 |
return media; |
| 211 | 212 |
} |
| 212 | 213 |
throw new SAXException(targetType.getSimpleName() + " with " + uuid + " not found"); |
| 213 | 214 |
} |
| 214 | 215 |
} else {
|
| 215 | 216 |
return idmap.get(id); |
| 216 |
}
|
|
| 217 |
} |
|
| 217 | 218 |
} |
| 218 | 219 |
}; |
| 219 | 220 |
} |
| 220 |
|
|
| 221 |
|
|
| 221 | 222 |
private Object resolveObject(UUID uuid, Class targetType, IService service) throws SAXException {
|
| 222 | 223 |
Object object = service.find(uuid); |
| 223 | 224 |
if(object == null) {
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/jaxb/DataSet.java | ||
|---|---|---|
| 69 | 69 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 70 | 70 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 71 | 71 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| 72 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 72 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 73 | 73 |
import eu.etaxonomy.cdm.model.name.TypeDesignationBase; |
| 74 | 74 |
import eu.etaxonomy.cdm.model.occurrence.DerivationEvent; |
| 75 | 75 |
import eu.etaxonomy.cdm.model.occurrence.DerivationEventType; |
| ... | ... | |
| 235 | 235 |
|
| 236 | 236 |
@XmlElementWrapper(name = "TaxonomicNames") |
| 237 | 237 |
@XmlElements({
|
| 238 |
@XmlElement(name = "TaxonNameBase", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = TaxonNameBase.class),
|
|
| 238 |
@XmlElement(name = "TaxonName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = TaxonName.class),
|
|
| 239 | 239 |
}) |
| 240 |
protected List<TaxonNameBase> taxonomicNames = new ArrayList<>();
|
|
| 240 |
protected List<TaxonName> taxonomicNames = new ArrayList<>(); |
|
| 241 | 241 |
|
| 242 | 242 |
@XmlElementWrapper(name = "TaxonBases") |
| 243 | 243 |
@XmlElements({
|
| ... | ... | |
| 377 | 377 |
* {@link List<axonNameBase> }
|
| 378 | 378 |
* |
| 379 | 379 |
*/ |
| 380 |
public List<TaxonNameBase> getTaxonomicNames() {
|
|
| 380 |
public List<TaxonName> getTaxonomicNames() {
|
|
| 381 | 381 |
return taxonomicNames; |
| 382 | 382 |
} |
| 383 | 383 |
|
| ... | ... | |
| 386 | 386 |
* |
| 387 | 387 |
* @param value |
| 388 | 388 |
* allowed object is |
| 389 |
* {@link List<TaxonNameBase> }
|
|
| 389 |
* {@link List<TaxonName> }
|
|
| 390 | 390 |
* |
| 391 | 391 |
*/ |
| 392 |
public void setTaxonomicNames(List<TaxonNameBase> value) {
|
|
| 392 |
public void setTaxonomicNames(List<TaxonName> value) {
|
|
| 393 | 393 |
this.taxonomicNames = value; |
| 394 | 394 |
} |
| 395 | 395 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/jaxb/JaxbExport.java | ||
|---|---|---|
| 37 | 37 |
import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
| 38 | 38 |
import eu.etaxonomy.cdm.model.common.User; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.description.FeatureTree; |
| 40 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 40 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 41 | 41 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
| 42 | 42 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 43 | 43 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| ... | ... | |
| 159 | 159 |
int agentRows = numberOfRows; |
| 160 | 160 |
int definedTermBaseRows = numberOfRows; |
| 161 | 161 |
int referenceBaseRows = numberOfRows; |
| 162 |
int taxonNameBaseRows = numberOfRows;
|
|
| 162 |
int taxonNameRows = numberOfRows; |
|
| 163 | 163 |
int taxonBaseRows = numberOfRows; |
| 164 | 164 |
int taxonNodeRows = numberOfRows; |
| 165 | 165 |
int relationshipRows = numberOfRows; |
| ... | ... | |
| 228 | 228 |
} |
| 229 | 229 |
|
| 230 | 230 |
if (jaxbExpConfig.isDoTaxonNames() == true) {
|
| 231 |
if (taxonNameBaseRows == 0) { taxonNameBaseRows = getNameService().count(TaxonNameBase.class); }
|
|
| 232 |
logger.info("# TaxonNameBase: " + taxonNameBaseRows);
|
|
| 231 |
if (taxonNameRows == 0) { taxonNameRows = getNameService().count(TaxonName.class); }
|
|
| 232 |
logger.info("# TaxonName: " + taxonNameRows);
|
|
| 233 | 233 |
//logger.info(" # Taxon: " + getNameService().count(BotanicalName.class));
|
| 234 |
dataSet.setTaxonomicNames(getNameService().list(null,taxonNameBaseRows, 0,null,null));
|
|
| 234 |
dataSet.setTaxonomicNames(getNameService().list(null,taxonNameRows, 0,null,null)); |
|
| 235 | 235 |
} |
| 236 | 236 |
|
| 237 | 237 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/jaxb/JaxbImport.java | ||
|---|---|---|
| 33 | 33 |
import eu.etaxonomy.cdm.model.description.FeatureTree; |
| 34 | 34 |
import eu.etaxonomy.cdm.model.media.Media; |
| 35 | 35 |
import eu.etaxonomy.cdm.model.name.HomotypicalGroup; |
| 36 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 36 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 37 | 37 |
import eu.etaxonomy.cdm.model.name.TypeDesignationBase; |
| 38 | 38 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 113 | 113 |
List<DefinedTermBase> terms; |
| 114 | 114 |
List<User> users; |
| 115 | 115 |
List<Reference> references; |
| 116 |
List<TaxonNameBase> taxonomicNames;
|
|
| 116 |
List<TaxonName> taxonomicNames; |
|
| 117 | 117 |
List<DescriptionBase> descriptions; |
| 118 | 118 |
List<TypeDesignationBase> typeDesignations; |
| 119 | 119 |
List<SpecimenOrObservationBase> occurrences; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/markup/MarkupNomenclatureImport.java | ||
|---|---|---|
| 33 | 33 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
| 34 | 34 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
| 35 | 35 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 36 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 36 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 37 | 37 |
import eu.etaxonomy.cdm.model.reference.IArticle; |
| 38 | 38 |
import eu.etaxonomy.cdm.model.reference.IBook; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.reference.IJournal; |
| ... | ... | |
| 162 | 162 |
if (isStartingElement(next, NOM)) {
|
| 163 | 163 |
// TODO should we check if the type is always a species, is |
| 164 | 164 |
// this a rule? |
| 165 |
TaxonNameBase<?,?> speciesName = TaxonNameBase.castAndDeproxy(
|
|
| 165 |
TaxonName speciesName = TaxonName.castAndDeproxy(
|
|
| 166 | 166 |
handleNom(state, reader, next, null)); |
| 167 |
for (TaxonNameBase<?, ?> 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); |
| ... | ... | |
| 622 | 622 |
if (taxon.getHomotypicGroup().equals(homotypicalGroup)) {
|
| 623 | 623 |
synonymType = SynonymType.HOMOTYPIC_SYNONYM_OF(); |
| 624 | 624 |
} |
| 625 |
taxon.addSynonymName(TaxonNameBase.castAndDeproxy(name), synonymType);
|
|
| 625 |
taxon.addSynonymName(TaxonName.castAndDeproxy(name), synonymType); |
|
| 626 | 626 |
} else {
|
| 627 | 627 |
name = taxon.getName(); |
| 628 | 628 |
} |
| ... | ... | |
| 633 | 633 |
XMLEvent parentEvent, INonViralName nvn, TaxonRelationship misappliedRel) throws XMLStreamException {
|
| 634 | 634 |
String classValue = getClassOnlyAttribute(parentEvent); |
| 635 | 635 |
|
| 636 |
TaxonNameBase<?,?> name = TaxonNameBase.castAndDeproxy(nvn);
|
|
| 636 |
TaxonName name = TaxonName.castAndDeproxy(nvn);
|
|
| 637 | 637 |
state.setCitation(true); |
| 638 | 638 |
boolean hasRefPart = false; |
| 639 | 639 |
Map<String, String> refMap = new HashMap<>(); |
| ... | ... | |
| 659 | 659 |
} |
| 660 | 660 |
|
| 661 | 661 |
|
| 662 |
private void doCitation(MarkupImportState state, TaxonNameBase<?,?> name,
|
|
| 662 |
private void doCitation(MarkupImportState state, TaxonName name, |
|
| 663 | 663 |
String classValue, TaxonRelationship misappliedRel, |
| 664 | 664 |
Reference reference, String microCitation, |
| 665 | 665 |
XMLEvent parentEvent) {
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/markup/MarkupSpecimenImport.java | ||
|---|---|---|
| 50 | 50 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 51 | 51 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 52 | 52 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| 53 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 53 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 54 | 54 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
| 55 | 55 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
| 56 | 56 |
import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent; |
| ... | ... | |
| 137 | 137 |
} |
| 138 | 138 |
|
| 139 | 139 |
INonViralName firstName = null; |
| 140 |
Set<TaxonNameBase> names = homotypicalGroup.getTypifiedNames();
|
|
| 140 |
Set<TaxonName> names = homotypicalGroup.getTypifiedNames(); |
|
| 141 | 141 |
if (names.isEmpty()) {
|
| 142 | 142 |
String message = "There is no name in a homotypical group. Can't create the specimen type"; |
| 143 | 143 |
fireWarningEvent(message, parentEvent, 8); |
| ... | ... | |
| 629 | 629 |
Rank defaultRank = Rank.SPECIES(); // can be any |
| 630 | 630 |
INonViralName nvn = createNameByCode(state, defaultRank); |
| 631 | 631 |
handleFullName(state, reader, nvn, next); |
| 632 |
TaxonNameBase<?,?> name = TaxonNameBase.castAndDeproxy(nvn);
|
|
| 632 |
TaxonName name = TaxonName.castAndDeproxy(nvn);
|
|
| 633 | 633 |
DeterminationEvent.NewInstance(name, facade.innerDerivedUnit() != null ? facade.innerDerivedUnit() : facade.innerFieldUnit()); |
| 634 | 634 |
} else if (isStartingElement(next, DATES)) {
|
| 635 | 635 |
TimePeriod timePeriod = handleDates(state, reader, next); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/outputmodel/OutputModelClassificationExport.java | ||
|---|---|---|
| 55 | 55 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
| 56 | 56 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 57 | 57 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 58 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 58 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 59 | 59 |
import eu.etaxonomy.cdm.model.name.TypeComparator; |
| 60 | 60 |
import eu.etaxonomy.cdm.model.name.TypeDesignationBase; |
| 61 | 61 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
| ... | ... | |
| 141 | 141 |
|
| 142 | 142 |
}else{
|
| 143 | 143 |
try{
|
| 144 |
TaxonNameBase name = taxon.getName();
|
|
| 144 |
TaxonName name = taxon.getName(); |
|
| 145 | 145 |
handleName(state, name); |
| 146 | 146 |
for (Synonym syn : taxon.getSynonyms()){
|
| 147 | 147 |
handleSynonym(state, syn); |
| ... | ... | |
| 427 | 427 |
* @param syn |
| 428 | 428 |
*/ |
| 429 | 429 |
private void handleSynonym(OutputModelExportState state, Synonym syn) {
|
| 430 |
TaxonNameBase name = syn.getName();
|
|
| 430 |
TaxonName name = syn.getName(); |
|
| 431 | 431 |
handleName(state, name); |
| 432 | 432 |
|
| 433 | 433 |
OutputModelTable table = OutputModelTable.SYNONYM; |
| ... | ... | |
| 446 | 446 |
* @param state |
| 447 | 447 |
* @param name |
| 448 | 448 |
*/ |
| 449 |
private void handleName(OutputModelExportState state, TaxonNameBase name) {
|
|
| 449 |
private void handleName(OutputModelExportState state, TaxonName name) {
|
|
| 450 | 450 |
Rank rank = name.getRank(); |
| 451 | 451 |
OutputModelTable table = OutputModelTable.SCIENTIFIC_NAME; |
| 452 | 452 |
name = HibernateProxyHelper.deproxy(name); |
| ... | ... | |
| 645 | 645 |
* @param state |
| 646 | 646 |
* @param name |
| 647 | 647 |
*/ |
| 648 |
private void handleIdentifier(OutputModelExportState state, TaxonNameBase name, String[] csvLine, OutputModelTable table) {
|
|
| 648 |
private void handleIdentifier(OutputModelExportState state, TaxonName name, String[] csvLine, OutputModelTable table) {
|
|
| 649 | 649 |
Set<String> IPNIidentifiers = name.getIdentifiers(DefinedTerm.IPNI_NAME_IDENTIFIER()); |
| 650 | 650 |
Set<String> tropicosIdentifiers = name.getIdentifiers(DefinedTerm.TROPICOS_NAME_IDENTIFIER()); |
| 651 | 651 |
Set<String> WFOIdentifiers = name.getIdentifiers(DefinedTerm.uuidWfoNameIdentifier); |
| ... | ... | |
| 775 | 775 |
* @param statusString |
| 776 | 776 |
* @return |
| 777 | 777 |
*/ |
| 778 |
private String extractStatusString(TaxonNameBase name, boolean abbrev) {
|
|
| 778 |
private String extractStatusString(TaxonName name, boolean abbrev) {
|
|
| 779 | 779 |
Set<NomenclaturalStatus> status = name.getStatus(); |
| 780 | 780 |
if (status.isEmpty()){
|
| 781 | 781 |
return ""; |
| ... | ... | |
| 819 | 819 |
String[] csvLine = new String[table.getSize()]; |
| 820 | 820 |
|
| 821 | 821 |
csvLine[table.getIndex(OutputModelTable.HOMOTYPIC_GROUP_ID)] = getId(state, group); |
| 822 |
List<TaxonNameBase> typifiedNames = new ArrayList<>();
|
|
| 822 |
List<TaxonName> typifiedNames = new ArrayList<>(); |
|
| 823 | 823 |
typifiedNames.addAll(group.getTypifiedNames()); |
| 824 | 824 |
Collections.sort(typifiedNames, new HomotypicalGroupNameComparator(null, true)); |
| 825 | 825 |
String typifiedNamesString = ""; |
| 826 |
for (TaxonNameBase name: typifiedNames){
|
|
| 826 |
for (TaxonName name: typifiedNames){
|
|
| 827 | 827 |
//Concatenated output string for homotypic group (names and citations) + status + some name relations (e.g. “non”) |
| 828 | 828 |
//TODO: nameRelations, which and how to display |
| 829 | 829 |
|
| ... | ... | |
| 885 | 885 |
* @param name |
| 886 | 886 |
* @return |
| 887 | 887 |
*/ |
| 888 |
private String getTropicosTitleCache(TaxonNameBase name) {
|
|
| 888 |
private String getTropicosTitleCache(TaxonName name) {
|
|
| 889 | 889 |
String basionymStart = "(";
|
| 890 | 890 |
String basionymEnd = ") "; |
| 891 | 891 |
String exAuthorSeperator = " ex "; |
| ... | ... | |
| 1074 | 1074 |
* TypeDesignatedByRef_Fk |
| 1075 | 1075 |
*/ |
| 1076 | 1076 |
|
| 1077 |
private void handleTypeDesignations(OutputModelExportState state, TaxonNameBase name){
|
|
| 1077 |
private void handleTypeDesignations(OutputModelExportState state, TaxonName name){
|
|
| 1078 | 1078 |
Set<SpecimenTypeDesignation> typeDesignations = name.getTypeDesignations(); |
| 1079 | 1079 |
OutputModelTable table = OutputModelTable.TYPE_DESIGNATION; |
| 1080 | 1080 |
String nameId = getId(state, name); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/pilotOutputHtml/PilotOutputDescriptionExporter.java | ||
|---|---|---|
| 26 | 26 |
import eu.etaxonomy.cdm.io.sdd.out.SDDDataSet; |
| 27 | 27 |
import eu.etaxonomy.cdm.model.agent.AgentBase; |
| 28 | 28 |
import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
| 29 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 29 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 30 | 30 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
| 31 | 31 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 32 | 32 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| ... | ... | |
| 130 | 130 |
int agentRows = numberOfRows; |
| 131 | 131 |
int definedTermBaseRows = numberOfRows; |
| 132 | 132 |
int referenceBaseRows = numberOfRows; |
| 133 |
int taxonNameBaseRows = numberOfRows;
|
|
| 133 |
int taxonNameRows = numberOfRows; |
|
| 134 | 134 |
int taxonBaseRows = numberOfRows; |
| 135 | 135 |
int relationshipRows = numberOfRows; |
| 136 | 136 |
int occurrencesRows = numberOfRows; |
| ... | ... | |
| 173 | 173 |
} |
| 174 | 174 |
|
| 175 | 175 |
if (sddExpConfig.isDoTaxonNames() == true) {
|
| 176 |
if (taxonNameBaseRows == 0) { taxonNameBaseRows = getNameService().count(TaxonNameBase.class); }
|
|
| 177 |
logger.info("# TaxonNameBase: " + taxonNameBaseRows);
|
|
| 176 |
if (taxonNameRows == 0) { taxonNameRows = getNameService().count(TaxonName.class); }
|
|
| 177 |
logger.info("# TaxonName: " + taxonNameRows);
|
|
| 178 | 178 |
//logger.info(" # Taxon: " + getNameService().count(BotanicalName.class));
|
| 179 |
sddDataSet.setTaxonomicNames(getNameService().list(null,taxonNameBaseRows, 0,null,null));
|
|
| 179 |
sddDataSet.setTaxonomicNames(getNameService().list(null,taxonNameRows, 0,null,null)); |
|
| 180 | 180 |
} |
| 181 | 181 |
|
| 182 | 182 |
if (sddExpConfig.isDoHomotypicalGroups() == true) {
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/pilotOutputHtml/PilotOutputDocumentBuilder.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2007 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
|
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 | 4 |
* http://www.e-taxonomy.eu |
| 5 |
*
|
|
| 5 |
* |
|
| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
| 20 | 20 |
|
| 21 | 21 |
import eu.etaxonomy.cdm.io.jaxb.CdmMarshallerListener; |
| 22 | 22 |
import eu.etaxonomy.cdm.io.sdd.out.SDDDataSet; |
| 23 |
import eu.etaxonomy.cdm.model.common.Language; |
|
| 24 |
import eu.etaxonomy.cdm.model.common.LanguageString; |
|
| 25 | 23 |
import eu.etaxonomy.cdm.model.common.Representation; |
| 26 | 24 |
import eu.etaxonomy.cdm.model.description.CategoricalData; |
| 27 | 25 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
| ... | ... | |
| 32 | 30 |
import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue; |
| 33 | 31 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 34 | 32 |
import eu.etaxonomy.cdm.model.description.TextData; |
| 35 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
| 33 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 36 | 34 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 37 | 35 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 38 | 36 |
|
| 39 | 37 |
/** |
| 40 |
* Writes the SDD XML file.
|
|
| 41 |
*
|
|
| 38 |
* Writes the SDD XML file. |
|
| 39 |
* |
|
| 42 | 40 |
* @author h.fradin |
| 43 | 41 |
* @created 10.12.2008 |
| 44 | 42 |
* @version 1.0 |
| ... | ... | |
| 59 | 57 |
public void marshal(SDDDataSet cdmSource, String sddDestination) throws IOException {
|
| 60 | 58 |
|
| 61 | 59 |
this.cdmSource = cdmSource; |
| 62 |
Marshaller marshaller;
|
|
| 60 |
Marshaller marshaller; |
|
| 63 | 61 |
CdmMarshallerListener marshallerListener = new CdmMarshallerListener(); |
| 64 | 62 |
logger.info("Start marshalling");
|
| 65 | 63 |
writeCDMtoHTML(sddDestination); |
| ... | ... | |
| 104 | 102 |
*/ |
| 105 | 103 |
public String writeTaxonDescriptionsToHTML(Taxon taxon, String texte) throws IOException {
|
| 106 | 104 |
|
Also available in: Unified diff
fix #6368 rename table and class TaxonNameBase