Revision ded3de15
Added by Andreas Müller about 7 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/util/TestDatabase.java | ||
|---|---|---|
| 41 | 41 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 42 | 42 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 43 | 43 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 44 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 44 | 45 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
| 45 | 46 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
| 46 | 47 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 194 | 195 |
|
| 195 | 196 |
// taxonomic names |
| 196 | 197 |
|
| 197 |
nameRoot1 = BotanicalName.NewInstance(rankGenus,"Calendula",null,null,null,linne,null,"p.100", null);
|
|
| 198 |
nameRoot1 = TaxonNameFactory.NewBotanicalInstance(rankGenus,"Calendula",null,null,null,linne,null,"p.100", null);
|
|
| 198 | 199 |
nameRoot1.addDescription(taxNameDescription); |
| 199 | 200 |
nameRoot1.addDescription(newTaxNameDesc); |
| 200 |
name1 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"arvensis",null,linne,null,"p.1", null);
|
|
| 201 |
synName11 = BotanicalName.NewInstance(rankSpecies,"Caltha",null,"arvensis",null,linne,null,"p.11", null);
|
|
| 202 |
synName12 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"sancta",null,linne,null,"p.12", null);
|
|
| 201 |
name1 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Calendula",null,"arvensis",null,linne,null,"p.1", null);
|
|
| 202 |
synName11 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Caltha",null,"arvensis",null,linne,null,"p.11", null);
|
|
| 203 |
synName12 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Calendula",null,"sancta",null,linne,null,"p.12", null);
|
|
| 203 | 204 |
|
| 204 |
name2 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzae",null,linne,null,"p.2", null);
|
|
| 205 |
synName2 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"echinata",null,linne,null,"p.2", null);
|
|
| 205 |
name2 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Calendula",null,"lanzae",null,linne,null,"p.2", null);
|
|
| 206 |
synName2 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Calendula",null,"echinata",null,linne,null,"p.2", null);
|
|
| 206 | 207 |
|
| 207 |
name21 = BotanicalName.NewInstance(rankSubspecies,"Calendula",null,"lanzea","something",linne,null,"p.1", null);
|
|
| 208 |
//name211 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null);
|
|
| 209 |
//name212 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null);
|
|
| 208 |
name21 = TaxonNameFactory.NewBotanicalInstance(rankSubspecies,"Calendula",null,"lanzea","something",linne,null,"p.1", null);
|
|
| 209 |
//name211 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null);
|
|
| 210 |
//name212 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null);
|
|
| 210 | 211 |
|
| 211 | 212 |
nameRoot2 = |
| 212 |
BotanicalName.NewInstance(rankGenus,"Sonchus",null,null,null,linne,null,"p.200", null);
|
|
| 213 |
nameR2_1 = BotanicalName.NewInstance(rankSpecies,"Sonchus",null,"child1",null,linne,null,"p.1", null);
|
|
| 214 |
nameR2_2 = BotanicalName.NewInstance(rankSpecies,"Sonchus",null,"child2",null,linne,null,"p.2", null);
|
|
| 213 |
TaxonNameFactory.NewBotanicalInstance(rankGenus,"Sonchus",null,null,null,linne,null,"p.200", null);
|
|
| 214 |
nameR2_1 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Sonchus",null,"child1",null,linne,null,"p.1", null);
|
|
| 215 |
nameR2_2 = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Sonchus",null,"child2",null,linne,null,"p.2", null);
|
|
| 215 | 216 |
|
| 216 |
nameFree = BotanicalName.NewInstance(rankSpecies,"Cichorium",null,"intybus",null,linne,null,"p.200", null);
|
|
| 217 |
synNameFree = BotanicalName.NewInstance(rankSpecies,"Cichorium",null,"balearicum",null,linne,null,"p.2", null);
|
|
| 217 |
nameFree = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Cichorium",null,"intybus",null,linne,null,"p.200", null);
|
|
| 218 |
synNameFree = TaxonNameFactory.NewBotanicalInstance(rankSpecies,"Cichorium",null,"balearicum",null,linne,null,"p.2", null);
|
|
| 218 | 219 |
|
| 219 | 220 |
taxonomicNames.add(nameRoot1); |
| 220 | 221 |
taxonomicNames.add(name1); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraTypeImport.java | ||
|---|---|---|
| 43 | 43 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
| 44 | 44 |
import eu.etaxonomy.cdm.model.common.Language; |
| 45 | 45 |
import eu.etaxonomy.cdm.model.common.User; |
| 46 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
|
| 47 | 46 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 48 | 47 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 49 | 48 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| 50 | 49 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 50 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 51 | 51 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
| 52 | 52 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
| 53 | 53 |
import eu.etaxonomy.cdm.model.occurrence.FieldUnit; |
| ... | ... | |
| 340 | 340 |
result = taxonNameMap.get(String.valueOf(nameId)); |
| 341 | 341 |
}else{
|
| 342 | 342 |
//for testing |
| 343 |
result = BotanicalName.NewInstance(Rank.SPECIES());
|
|
| 343 |
result = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 344 | 344 |
} |
| 345 | 345 |
return result; |
| 346 | 346 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelImportBase.java | ||
|---|---|---|
| 34 | 34 |
import eu.etaxonomy.cdm.model.location.Country; |
| 35 | 35 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 36 | 36 |
import eu.etaxonomy.cdm.model.location.NamedAreaType; |
| 37 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
|
| 38 | 37 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 38 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 39 | 39 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 40 | 40 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 41 | 41 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| ... | ... | |
| 194 | 194 |
|
| 195 | 195 |
//TODO for testing |
| 196 | 196 |
if (taxonBase == null && ! state.getConfig().isDoTaxa()){
|
| 197 |
taxonBase = Taxon.NewInstance(BotanicalName.NewInstance(Rank.SPECIES()), null);
|
|
| 197 |
taxonBase = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null);
|
|
| 198 | 198 |
} |
| 199 | 199 |
|
| 200 | 200 |
Taxon taxon; |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelOccurrenceImport.java | ||
|---|---|---|
| 628 | 628 |
if (oldDescription == null || newTaxonId != oldTaxonId){
|
| 629 | 629 |
TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(newTaxonId)); |
| 630 | 630 |
//TODO for testing |
| 631 |
//TaxonBase taxonBase = Taxon.NewInstance(BotanicalName.NewInstance(Rank.SPECIES()), null);
|
|
| 631 |
//TaxonBase taxonBase = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null);
|
|
| 632 | 632 |
Taxon taxon; |
| 633 | 633 |
if ( taxonBase instanceof Taxon ) {
|
| 634 | 634 |
taxon = (Taxon) taxonBase; |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonNameImport.java | ||
|---|---|---|
| 43 | 43 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
| 44 | 44 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 45 | 45 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 46 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 46 | 47 |
import eu.etaxonomy.cdm.model.name.ZoologicalName; |
| 47 | 48 |
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference; |
| 48 | 49 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 191 | 192 |
//check cultivar |
| 192 | 193 |
if (taxonNameBase instanceof BotanicalName){
|
| 193 | 194 |
if (isNotBlank(strCultivarGroupName) && isNotBlank(strCultivarName)){
|
| 194 |
taxonNameBase = CultivarPlantName.NewInstance(rank);
|
|
| 195 |
taxonNameBase = TaxonNameFactory.NewCultivarInstance(rank);
|
|
| 195 | 196 |
} |
| 196 | 197 |
} |
| 197 | 198 |
}else{
|
| 198 |
taxonNameBase = NonViralName.NewInstance(rank);
|
|
| 199 |
taxonNameBase = TaxonNameFactory.NewNonViralInstance(rank);
|
|
| 199 | 200 |
} |
| 200 | 201 |
if (uuid != null){
|
| 201 | 202 |
taxonNameBase.setUuid(UUID.fromString(uuid)); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoTaxonImport.java | ||
|---|---|---|
| 36 | 36 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
| 37 | 37 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
| 38 | 38 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 39 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 39 | 40 |
import eu.etaxonomy.cdm.model.reference.IArticle; |
| 40 | 41 |
import eu.etaxonomy.cdm.model.reference.IBook; |
| 41 | 42 |
import eu.etaxonomy.cdm.model.reference.IBookSection; |
| ... | ... | |
| 159 | 160 |
// ,[OriginalCitation] |
| 160 | 161 |
|
| 161 | 162 |
|
| 162 |
BotanicalName name = BotanicalName.NewInstance(Rank.GENUS());
|
|
| 163 |
BotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
|
|
| 163 | 164 |
name.setGenusOrUninomial(genus); |
| 164 | 165 |
makeAuthors(name, autoren, id); |
| 165 | 166 |
INomenclaturalReference nomRef = makeNomRef(state, rs, id); |
| ... | ... | |
| 197 | 198 |
private void handleBasionym(CaryoImportState state, ResultSet rs, Taxon taxon, String basioStr, Integer id) {
|
| 198 | 199 |
if (StringUtils.isNotBlank(basioStr)){
|
| 199 | 200 |
BotanicalName name = (BotanicalName) taxon.getName(); |
| 200 |
BotanicalName basionym = BotanicalName.PARSED_REFERENCE(basioStr);
|
|
| 201 |
BotanicalName basionym = TaxonNameFactory.PARSED_BOTANICAL_REFERENCE(basioStr);
|
|
| 201 | 202 |
if (basionym.hasProblem()){
|
| 202 | 203 |
logger.warn("Problem when parsing basionym ("+id+"): " + basioStr);
|
| 203 | 204 |
} |
| ... | ... | |
| 219 | 220 |
return; |
| 220 | 221 |
}else{
|
| 221 | 222 |
BotanicalName name = (BotanicalName)taxon.getName(); |
| 222 |
BotanicalName typeName = BotanicalName.NewInstance(Rank.SPECIES());
|
|
| 223 |
BotanicalName typeName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 223 | 224 |
if ("not designated".equalsIgnoreCase(type)){
|
| 224 | 225 |
desig.setNotDesignated(true); |
| 225 | 226 |
}else{
|
| ... | ... | |
| 748 | 749 |
String family = rs.getString("family");
|
| 749 | 750 |
if (familyMap.get(family) == null ){
|
| 750 | 751 |
|
| 751 |
BotanicalName name = BotanicalName.NewInstance(Rank.FAMILY());
|
|
| 752 |
BotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());
|
|
| 752 | 753 |
name.setGenusOrUninomial(family); |
| 753 | 754 |
Taxon taxon = Taxon.NewInstance(name, state.getTransactionalSourceReference()); |
| 754 | 755 |
classification.addChildTaxon(taxon, null, null); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/cuba/CubaExcelImport.java | ||
|---|---|---|
| 54 | 54 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
| 55 | 55 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 56 | 56 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 57 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 57 | 58 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 58 | 59 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 59 | 60 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| ... | ... | |
| 918 | 919 |
if (genus != null){
|
| 919 | 920 |
higherNode = genus.getTaxonNodes().iterator().next(); |
| 920 | 921 |
}else{
|
| 921 |
BotanicalName name = BotanicalName.NewInstance(Rank.GENUS());
|
|
| 922 |
BotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
|
|
| 922 | 923 |
name.addSource(makeOriginalSource(state)); |
| 923 | 924 |
name.setGenusOrUninomial(genusStr); |
| 924 | 925 |
genus = Taxon.NewInstance(name, sec); |
| ... | ... | |
| 1223 | 1224 |
private BotanicalName makeFamilyName(CubaImportState state, String famStr) {
|
| 1224 | 1225 |
BotanicalName name = state.getFamilyName(famStr); |
| 1225 | 1226 |
if (name == null){
|
| 1226 |
name = BotanicalName.NewInstance(Rank.FAMILY());
|
|
| 1227 |
name = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());
|
|
| 1227 | 1228 |
name.setGenusOrUninomial(famStr); |
| 1228 | 1229 |
state.putFamilyName(famStr, name); |
| 1229 | 1230 |
name.addSource(makeOriginalSource(state)); |
| ... | ... | |
| 1257 | 1258 |
classification.getRootNode().setUuid(rootUuid); |
| 1258 | 1259 |
} |
| 1259 | 1260 |
|
| 1260 |
BotanicalName plantaeName = BotanicalName.NewInstance(Rank.KINGDOM());
|
|
| 1261 |
BotanicalName plantaeName = TaxonNameFactory.NewBotanicalInstance(Rank.KINGDOM());
|
|
| 1261 | 1262 |
plantaeName.setGenusOrUninomial("Plantae");
|
| 1262 | 1263 |
Taxon plantae = Taxon.NewInstance(plantaeName, sec); |
| 1263 | 1264 |
TaxonNode plantaeNode = classification.addChildTaxon(plantae, null, null); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/cyprus/CyprusDistributionImport.java | ||
|---|---|---|
| 271 | 271 |
result = taxonNameOnlyStore.get(taxonStr); |
| 272 | 272 |
}else {
|
| 273 | 273 |
// result = getTaxonService().findBestMatchingTaxon(taxonStr); |
| 274 |
// TaxonNameBase name = BotanicalName.NewInstance(Rank.SPECIES());
|
|
| 274 |
// TaxonNameBase name = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 275 | 275 |
// name.setTitleCache(taxonStr, true); |
| 276 | 276 |
// |
| 277 | 277 |
// result = Taxon.NewInstance(name, null); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/edaphobase/EdaphobaseTaxonImport.java | ||
|---|---|---|
| 32 | 32 |
import eu.etaxonomy.cdm.model.common.MarkerType; |
| 33 | 33 |
import eu.etaxonomy.cdm.model.common.Representation; |
| 34 | 34 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 35 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 35 | 36 |
import eu.etaxonomy.cdm.model.name.ZoologicalName; |
| 36 | 37 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 37 | 38 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| ... | ... | |
| 145 | 146 |
//Name etc. |
| 146 | 147 |
Rank rank = makeRank(state, rankStr); |
| 147 | 148 |
checkRankMarker(state, rank); |
| 148 |
ZoologicalName name = ZoologicalName.NewInstance(rank);
|
|
| 149 |
ZoologicalName name = TaxonNameFactory.NewZoologicalInstance(rank);
|
|
| 149 | 150 |
setNamePart(nameStr, rank, name); |
| 150 | 151 |
Rank parentRank = makeRank(state, parentRankStr); |
| 151 | 152 |
setNamePart(parentNameStr, parentRank, name); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisCurrentSpeciesImport.java | ||
|---|---|---|
| 32 | 32 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 33 | 33 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 34 | 34 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 35 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 35 | 36 |
import eu.etaxonomy.cdm.model.name.ZoologicalName; |
| 36 | 37 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 37 | 38 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| ... | ... | |
| 346 | 347 |
String key = keyEpithet + "@" + CdmUtils.Nz(author) + "@" + rank.getTitleCache(); |
| 347 | 348 |
Taxon taxon = taxonMap.get(key); |
| 348 | 349 |
if (taxon == null){
|
| 349 |
ZoologicalName name = ZoologicalName.NewInstance(rank);
|
|
| 350 |
ZoologicalName name = TaxonNameFactory.NewZoologicalInstance(rank);
|
|
| 350 | 351 |
name.setGenusOrUninomial(uninomial); |
| 351 | 352 |
if (isNotBlank(infraGenericEpi)){
|
| 352 | 353 |
name.setInfraGenericEpithet(infraGenericEpi); |
| ... | ... | |
| 388 | 389 |
String author = rs.getString("dtSpcAutor");
|
| 389 | 390 |
|
| 390 | 391 |
|
| 391 |
ZoologicalName zooName = ZoologicalName.NewInstance(Rank.SPECIES());
|
|
| 392 |
ZoologicalName zooName = TaxonNameFactory.NewZoologicalInstance(Rank.SPECIES());
|
|
| 392 | 393 |
zooName.setSpecificEpithet(speciesEpi); |
| 393 | 394 |
if (StringUtils.isNotBlank(subGenusEpi)){
|
| 394 | 395 |
zooName.setInfraGenericEpithet(subGenusEpi); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisSpecTaxImport.java | ||
|---|---|---|
| 46 | 46 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 47 | 47 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| 48 | 48 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 49 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 49 | 50 |
import eu.etaxonomy.cdm.model.name.ZoologicalName; |
| 50 | 51 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
| 51 | 52 |
import eu.etaxonomy.cdm.model.occurrence.DerivationEvent; |
| ... | ... | |
| 928 | 929 |
} |
| 929 | 930 |
|
| 930 | 931 |
//name |
| 931 |
ZoologicalName name = ZoologicalName.NewInstance(rank);
|
|
| 932 |
ZoologicalName name = TaxonNameFactory.NewZoologicalInstance(rank);
|
|
| 932 | 933 |
makeNamePartsAndCache(state, rs, rankStr, name); |
| 933 | 934 |
|
| 934 | 935 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaTaxonImport.java | ||
|---|---|---|
| 23 | 23 |
import eu.etaxonomy.cdm.model.common.Language; |
| 24 | 24 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 25 | 25 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 26 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 26 | 27 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 27 | 28 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 28 | 29 |
import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode; |
| ... | ... | |
| 163 | 164 |
*/ |
| 164 | 165 |
private TaxonNode makeGenusNode(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state, |
| 165 | 166 |
HashMap<String, String> record, String genusStr) {
|
| 166 |
BotanicalName name = BotanicalName.NewInstance(Rank.GENUS());
|
|
| 167 |
BotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
|
|
| 167 | 168 |
name.setGenusOrUninomial(genusStr); |
| 168 | 169 |
Taxon genus = Taxon.NewInstance(name, getSecReference(state)); |
| 169 | 170 |
TaxonNode family = getFamilyTaxon(record, state); |
| ... | ... | |
| 229 | 230 |
* @return |
| 230 | 231 |
*/ |
| 231 | 232 |
private BotanicalName makeFamilyName(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state, String famStr) {
|
| 232 |
BotanicalName name = BotanicalName.NewInstance(Rank.FAMILY());
|
|
| 233 |
BotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());
|
|
| 233 | 234 |
name.setGenusOrUninomial(famStr); |
| 234 | 235 |
name.addSource(makeOriginalSource(state)); |
| 235 | 236 |
return name; |
| ... | ... | |
| 247 | 248 |
classification.setUuid(state.getConfig().getClassificationUuid()); |
| 248 | 249 |
classification.getRootNode().setUuid(rootUuid); |
| 249 | 250 |
|
| 250 |
BotanicalName plantaeName = BotanicalName.NewInstance(Rank.KINGDOM());
|
|
| 251 |
BotanicalName plantaeName = TaxonNameFactory.NewBotanicalInstance(Rank.KINGDOM());
|
|
| 251 | 252 |
plantaeName.setGenusOrUninomial("Plantae");
|
| 252 | 253 |
Taxon plantae = Taxon.NewInstance(plantaeName, sec); |
| 253 | 254 |
TaxonNode plantaeNode = classification.addChildTaxon(plantae, null, null); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/iapt/IAPTExcelImport.java | ||
|---|---|---|
| 63 | 63 |
import eu.etaxonomy.cdm.model.name.RankClass; |
| 64 | 64 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| 65 | 65 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 66 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 66 | 67 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
| 67 | 68 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
| 68 | 69 |
import eu.etaxonomy.cdm.model.occurrence.FieldUnit; |
| ... | ... | |
| 1267 | 1268 |
|
| 1268 | 1269 |
Rank rank = guessRank(name); |
| 1269 | 1270 |
|
| 1270 |
BotanicalName taxonName = BotanicalName.NewInstance(rank);
|
|
| 1271 |
BotanicalName taxonName = TaxonNameFactory.NewBotanicalInstance(rank);
|
|
| 1271 | 1272 |
taxonName.addSource(makeOriginalSource(state)); |
| 1272 | 1273 |
taxonName.setGenusOrUninomial(StringUtils.capitalize(name)); |
| 1273 | 1274 |
return taxonName; |
| app-import/src/main/java/eu/etaxonomy/cdm/io/mexico/MexicoBorhidiExcelImport.java | ||
|---|---|---|
| 34 | 34 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 35 | 35 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 36 | 36 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 37 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 37 | 38 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 38 | 39 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 39 | 40 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| ... | ... | |
| 99 | 100 |
classification = Classification.NewInstance(state.getConfig().getClassificationName()); |
| 100 | 101 |
classification.setUuid(config.getClassificationUuid()); |
| 101 | 102 |
classification.setReference(config.getSecReference()); |
| 102 |
BotanicalName nameRubiaceae = BotanicalName.NewInstance(Rank.FAMILY());
|
|
| 103 |
BotanicalName nameRubiaceae = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());
|
|
| 103 | 104 |
nameRubiaceae.setGenusOrUninomial("Rubiaceae");
|
| 104 | 105 |
Taxon rubiaceaeTaxon = Taxon.NewInstance(nameRubiaceae, classification.getReference()); |
| 105 | 106 |
rubiaceaeNode = classification.addChildTaxon(rubiaceaeTaxon, null, null); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/mexico/SimpleExcelTaxonImport.java | ||
|---|---|---|
| 26 | 26 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
| 27 | 27 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 28 | 28 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 29 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 29 | 30 |
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference; |
| 30 | 31 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 31 | 32 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| ... | ... | |
| 113 | 114 |
if (genus != null){
|
| 114 | 115 |
higherNode = genus.getTaxonNodes().iterator().next(); |
| 115 | 116 |
}else{
|
| 116 |
BotanicalName genusName = BotanicalName.NewInstance(Rank.GENUS());
|
|
| 117 |
BotanicalName genusName = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
|
|
| 117 | 118 |
genusName.addSource(makeOriginalSource(state)); |
| 118 | 119 |
genusName.setGenusOrUninomial(genusStr); |
| 119 | 120 |
genus = Taxon.NewInstance(genusName, sec); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/RoteListeDbTaxonImport.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 |
*/ |
| ... | ... | |
| 28 | 28 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 29 | 29 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 30 | 30 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 31 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 31 | 32 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 32 | 33 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 33 | 34 |
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
| ... | ... | |
| 42 | 43 |
public class RoteListeDbTaxonImport extends RoteListeDbImportBase<TaxonBase> implements IMappingImport<TaxonBase, RoteListeDbImportState>{
|
| 43 | 44 |
@SuppressWarnings("unused")
|
| 44 | 45 |
private static final Logger logger = Logger.getLogger(RoteListeDbTaxonImport.class); |
| 45 |
|
|
| 46 |
|
|
| 46 | 47 |
private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance(); |
| 47 |
|
|
| 48 |
|
|
| 48 | 49 |
private Map<UUID, Taxon> higherTaxonMap; |
| 49 |
|
|
| 50 |
|
|
| 50 | 51 |
private Integer TREE_ID = null; |
| 51 |
|
|
| 52 |
|
|
| 52 | 53 |
private DbImportMapping mapping; |
| 53 |
|
|
| 54 |
|
|
| 54 | 55 |
private int modCount = 10000; |
| 55 | 56 |
private static final String pluralString = "taxa"; |
| 56 | 57 |
private static final String dbTableName = "checklist"; |
| ... | ... | |
| 60 | 61 |
public RoteListeDbTaxonImport(){
|
| 61 | 62 |
super(pluralString, dbTableName, cdmTargetClass); |
| 62 | 63 |
} |
| 63 |
|
|
| 64 |
|
|
| 64 |
|
|
| 65 |
|
|
| 65 | 66 |
@Override |
| 66 | 67 |
protected String getIdQuery() {
|
| 67 | 68 |
String strQuery = " SELECT pk FROM " + dbTableName + |
| ... | ... | |
| 73 | 74 |
protected DbImportMapping getMapping() {
|
| 74 | 75 |
if (mapping == null){
|
| 75 | 76 |
mapping = new DbImportMapping(); |
| 76 |
|
|
| 77 |
|
|
| 77 | 78 |
// mapping.addMapper(DbImportObjectCreationMapper.NewInstance(this, "pk", TAXON_NAMESPACE)); //id + tu_status |
| 78 |
//
|
|
| 79 |
// |
|
| 79 | 80 |
// UUID uuidKew = RoteListeDbTransformer.uuidAcceptedKew; |
| 80 | 81 |
// mapping.addMapper(DbImportMarkerMapper.NewInstance("accepted kew", uuidKew, "Accepted Kew", "Accepted Kew", "Kew", null));
|
| 81 |
|
|
| 82 |
|
|
| 82 | 83 |
} |
| 83 |
|
|
| 84 |
|
|
| 84 | 85 |
return mapping; |
| 85 | 86 |
} |
| 86 | 87 |
|
| ... | ... | |
| 93 | 94 |
return strRecordQuery; |
| 94 | 95 |
} |
| 95 | 96 |
|
| 96 |
|
|
| 97 |
|
|
| 97 | 98 |
@Override |
| 98 | 99 |
public boolean doPartition(ResultSetPartitioner partitioner, RoteListeDbImportState state) {
|
| 99 | 100 |
boolean success = super.doPartition(partitioner, state); |
| ... | ... | |
| 109 | 110 |
Class<?> cdmClass; |
| 110 | 111 |
Set<String> idSet; |
| 111 | 112 |
Set<String> referenceIdSet = new HashSet<String>(); |
| 112 |
|
|
| 113 |
|
|
| 113 | 114 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>(); |
| 114 |
|
|
| 115 |
|
|
| 115 | 116 |
try{
|
| 116 | 117 |
while (rs.next()){
|
| 117 | 118 |
handleForeignKey(rs, referenceIdSet, "source"); |
| ... | ... | |
| 129 | 130 |
} |
| 130 | 131 |
return result; |
| 131 | 132 |
} |
| 132 |
|
|
| 133 |
|
|
| 133 | 134 |
|
| 134 | 135 |
@Override |
| 135 | 136 |
public TaxonBase createObject(ResultSet rs, RoteListeDbImportState state) throws SQLException {
|
| 136 |
BotanicalName speciesName = BotanicalName.NewInstance(Rank.SPECIES());
|
|
| 137 |
|
|
| 137 |
BotanicalName speciesName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 138 |
|
|
| 138 | 139 |
// Reference sec = state.getConfig().getSourceReference(); |
| 139 | 140 |
// getReferenceService().saveOrUpdate(sec); |
| 140 |
//
|
|
| 141 |
// |
|
| 141 | 142 |
// String familyString = rs.getString("family");
|
| 142 | 143 |
// String genusString = rs.getString("genus");
|
| 143 | 144 |
// String speciesString = rs.getString("species");
|
| 144 | 145 |
// String authorityString = rs.getString("authority");
|
| 145 |
//
|
|
| 146 |
// |
|
| 146 | 147 |
// if (logger.isDebugEnabled()){
|
| 147 | 148 |
// System.out.println(familyString + " " + genusString + " " + speciesString); |
| 148 | 149 |
// } |
| 149 |
//
|
|
| 150 |
// |
|
| 150 | 151 |
// Taxon speciesTaxon = Taxon.NewInstance(speciesName, sec);; |
| 151 | 152 |
// speciesName.setGenusOrUninomial(genusString); |
| 152 | 153 |
// speciesName.setSpecificEpithet(speciesString); |
| 153 | 154 |
// parser.handleAuthors(speciesName, CdmUtils.concat(" ", new String[] {"", genusString, speciesString, authorityString}), authorityString);
|
| 154 |
//
|
|
| 155 |
// |
|
| 155 | 156 |
// //family |
| 156 | 157 |
// Taxon familyTaxon = null; |
| 157 | 158 |
// if (StringUtils.isNotBlank(familyString)){
|
| 158 | 159 |
// familyTaxon = getHigherTaxon(state, familyString, null); |
| 159 | 160 |
// if (familyTaxon == null){
|
| 160 |
// BotanicalName familyName = BotanicalName.NewInstance(Rank.FAMILY());
|
|
| 161 |
// BotanicalName familyName = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());
|
|
| 161 | 162 |
// familyName.setGenusOrUninomial(familyString); |
| 162 | 163 |
// familyTaxon = Taxon.NewInstance(familyName, sec); |
| 163 | 164 |
// saveHigherTaxon(state, familyTaxon, familyString, null); |
| 164 | 165 |
// } |
| 165 |
// getTaxonService().saveOrUpdate(familyTaxon);
|
|
| 166 |
// getTaxonService().saveOrUpdate(familyTaxon); |
|
| 166 | 167 |
// } |
| 167 |
//
|
|
| 168 |
//
|
|
| 168 |
// |
|
| 169 |
// |
|
| 169 | 170 |
// //genus |
| 170 | 171 |
// Taxon genusTaxon = getHigherTaxon(state, familyString, genusString); |
| 171 | 172 |
// if (genusTaxon == null){
|
| 172 |
// BotanicalName genusName = BotanicalName.NewInstance(Rank.GENUS());
|
|
| 173 |
// BotanicalName genusName = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
|
|
| 173 | 174 |
// genusName.setGenusOrUninomial(genusString); |
| 174 | 175 |
// genusTaxon = Taxon.NewInstance(genusName, sec); |
| 175 | 176 |
// saveHigherTaxon(state, genusTaxon, familyString, genusString); |
| ... | ... | |
| 182 | 183 |
// |
| 183 | 184 |
// String sourceString = rs.getString("source");
|
| 184 | 185 |
// String sourceId = rs.getString("source_id");
|
| 185 |
//
|
|
| 186 |
// |
|
| 186 | 187 |
// Reference sourceRef = state.getRelatedObject(REFERENCE_NAMESPACE, sourceString, Reference.class); |
| 187 | 188 |
// speciesTaxon.addSource(sourceId, REFERENCE_NAMESPACE, sourceRef, null); |
| 188 |
//
|
|
| 189 |
//
|
|
| 189 |
// |
|
| 190 |
// |
|
| 190 | 191 |
// //distribution |
| 191 | 192 |
// handleDistribution(rs, speciesTaxon); |
| 192 |
//
|
|
| 193 |
// |
|
| 193 | 194 |
// return speciesTaxon; |
| 194 |
|
|
| 195 |
|
|
| 195 | 196 |
return null; |
| 196 | 197 |
} |
| 197 | 198 |
|
| ... | ... | |
| 201 | 202 |
IOValidator<RoteListeDbImportState> validator = new RoteListeDbTaxonImportValidator(); |
| 202 | 203 |
return validator.validate(state); |
| 203 | 204 |
} |
| 204 |
|
|
| 205 |
|
|
| 205 |
|
|
| 206 |
|
|
| 206 | 207 |
@Override |
| 207 | 208 |
protected boolean isIgnore(RoteListeDbImportState state){
|
| 208 | 209 |
return ! state.getConfig().isDoTaxa(); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportFamily.java | ||
|---|---|---|
| 25 | 25 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 26 | 26 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 27 | 27 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 28 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 28 | 29 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 29 | 30 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 30 | 31 |
|
| ... | ... | |
| 81 | 82 |
ResultSet rs = state.getConfig().getSource().getResultSet(query); |
| 82 | 83 |
while(rs.next()){
|
| 83 | 84 |
String familieStr = rs.getString("FAMILIE");
|
| 84 |
BotanicalName name = BotanicalName.NewInstance(Rank.FAMILY());
|
|
| 85 |
BotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());
|
|
| 85 | 86 |
name.setGenusOrUninomial(familieStr); |
| 86 | 87 |
Taxon family = Taxon.NewInstance(name, null); |
| 87 | 88 |
familyMap.put(familieStr, family.getUuid()); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java | ||
|---|---|---|
| 38 | 38 |
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
| 40 | 40 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 41 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
|
| 42 | 41 |
import eu.etaxonomy.cdm.model.name.CultivarPlantName; |
| 43 | 42 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 44 | 43 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
| ... | ... | |
| 47 | 46 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 48 | 47 |
import eu.etaxonomy.cdm.model.name.RankClass; |
| 49 | 48 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 49 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 50 | 50 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 51 | 51 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 52 | 52 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| ... | ... | |
| 342 | 342 |
Rank rank = makeRank(id, state, rangString, CdmUtils.isNotBlank(ep3String)); |
| 343 | 343 |
//cultivar |
| 344 | 344 |
if(rank!= null && rank.equals(Rank.CULTIVAR())){
|
| 345 |
CultivarPlantName cultivar = CultivarPlantName.NewInstance(rank);
|
|
| 345 |
CultivarPlantName cultivar = TaxonNameFactory.NewCultivarInstance(rank);
|
|
| 346 | 346 |
cultivar.setGenusOrUninomial(ep1String); |
| 347 | 347 |
cultivar.setSpecificEpithet(ep2String); |
| 348 | 348 |
cultivar.setCultivarName(ep3String); |
| ... | ... | |
| 350 | 350 |
} |
| 351 | 351 |
//botanical names |
| 352 | 352 |
else{
|
| 353 |
name = BotanicalName.NewInstance(rank);
|
|
| 353 |
name = TaxonNameFactory.NewBotanicalInstance(rank);
|
|
| 354 | 354 |
|
| 355 | 355 |
//ep1 should always be present |
| 356 | 356 |
if(CdmUtils.isBlank(ep1String)){
|
| ... | ... | |
| 392 | 392 |
//more than two hybrids not yet handled by name parser |
| 393 | 393 |
//TODO: use parser when implemented to fully support hybrids |
| 394 | 394 |
if(taxNameString.split(RedListUtil.HYB_SIGN).length>2){
|
| 395 |
name = BotanicalName.NewInstance(rank);
|
|
| 395 |
name = TaxonNameFactory.NewBotanicalInstance(rank);
|
|
| 396 | 396 |
name.setTitleCache(taxNameString, true); |
| 397 | 397 |
} |
| 398 | 398 |
else if(hybString.equals(RedListUtil.HYB_X)){
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/wp6/CommonNameExcelImport.java | ||
|---|---|---|
| 222 | 222 |
desc = taxonStore.get(taxonNameStr); |
| 223 | 223 |
}else{
|
| 224 | 224 |
taxon = getTaxonService().findBestMatchingTaxon(taxonNameStr); |
| 225 |
// TaxonNameBase name = BotanicalName.NewInstance(Rank.SPECIES());
|
|
| 225 |
// TaxonNameBase name = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 226 | 226 |
// name.setTitleCache(taxonNameStr, true); |
| 227 | 227 |
// |
| 228 | 228 |
// result = Taxon.NewInstance(name, null); |
| app-import/src/test/java/eu/etaxonomy/cdm/app/util/TestTransaction.java | ||
|---|---|---|
| 19 | 19 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
| 20 | 20 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 21 | 21 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 22 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 22 | 23 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 23 | 24 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 24 | 25 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| ... | ... | |
| 80 | 81 |
List<Taxon> taxa = appCtr.getTaxonService().list(Taxon.class, MAX_ENTRIES, 0, null, null); |
| 81 | 82 |
|
| 82 | 83 |
name1 = |
| 83 |
BotanicalName.NewInstance(rankSpecies, "Hyoseris", null, "lucida", null, author, null, "1", null);
|
|
| 84 |
TaxonNameFactory.NewBotanicalInstance(rankSpecies, "Hyoseris", null, "lucida", null, author, null, "1", null);
|
|
| 84 | 85 |
// Calendula L. |
| 85 | 86 |
taxon1 = taxa.get(0); |
| 86 | 87 |
child1 = Taxon.NewInstance(name1, sec); |
| ... | ... | |
| 93 | 94 |
TransactionStatus txStatTwo = appCtr.startTransaction(); |
| 94 | 95 |
|
| 95 | 96 |
name2 = |
| 96 |
BotanicalName.NewInstance(rankSpecies, "Hyoseris", null, "scabra", null, author, null, "2", null);
|
|
| 97 |
TaxonNameFactory.NewBotanicalInstance(rankSpecies, "Hyoseris", null, "scabra", null, author, null, "2", null);
|
|
| 97 | 98 |
// Sonchus L. |
| 98 | 99 |
taxon2 = taxa.get(1); |
| 99 | 100 |
child2 = Taxon.NewInstance(name2, sec); |
| ... | ... | |
| 158 | 159 |
List<Taxon> taxa = appCtr.getTaxonService().list(Taxon.class, MAX_ENTRIES, 0, null, null); |
| 159 | 160 |
|
| 160 | 161 |
name1 = |
| 161 |
BotanicalName.NewInstance(rankSpecies, "Launaea", null, "child1", null, author, null, "1", null);
|
|
| 162 |
TaxonNameFactory.NewBotanicalInstance(rankSpecies, "Launaea", null, "child1", null, author, null, "1", null);
|
|
| 162 | 163 |
// Cichorium intybus L. |
| 163 | 164 |
taxon1 = taxa.get(5); |
| 164 | 165 |
child1 = Taxon.NewInstance(name1, sec); |
| ... | ... | |
| 171 | 172 |
TransactionStatus txStatTwo = appCtr.startTransaction(); |
| 172 | 173 |
|
| 173 | 174 |
name2 = |
| 174 |
BotanicalName.NewInstance(rankSpecies, "Reichardia", null, "child2", null, author, null, "2", null);
|
|
| 175 |
TaxonNameFactory.NewBotanicalInstance(rankSpecies, "Reichardia", null, "child2", null, author, null, "2", null);
|
|
| 175 | 176 |
// Cichorium intybus L. |
| 176 | 177 |
taxon2 = taxa.get(5); |
| 177 | 178 |
child2 = Taxon.NewInstance(name2, sec); |
| ... | ... | |
| 257 | 258 |
Reference sec = references.get(0); |
| 258 | 259 |
|
| 259 | 260 |
name1 = |
| 260 |
BotanicalName.NewInstance(rankSpecies, "NewTaxon1", null, "taxon1", null, author, null, "1", null);
|
|
| 261 |
TaxonNameFactory.NewBotanicalInstance(rankSpecies, "NewTaxon1", null, "taxon1", null, author, null, "1", null);
|
|
| 261 | 262 |
taxon1 = Taxon.NewInstance(name1, sec); |
| 262 | 263 |
t1uuid = appCtr.getTaxonService().saveOrUpdate(taxon1); |
| 263 | 264 |
//t1uuid = appCtr.getTaxonService().saveTaxon(taxon1, txStatOne); |
| ... | ... | |
| 270 | 271 |
//getSession(). |
| 271 | 272 |
|
| 272 | 273 |
name1_ = |
| 273 |
BotanicalName.NewInstance(rankSpecies, "NewTaxon1_", null, "taxon1_", null, author, null, "1_", null);
|
|
| 274 |
TaxonNameFactory.NewBotanicalInstance(rankSpecies, "NewTaxon1_", null, "taxon1_", null, author, null, "1_", null);
|
|
| 274 | 275 |
taxon1_ = appCtr.getTaxonService().find(t1uuid); |
| 275 | 276 |
|
| 276 | 277 |
/* ************** Commit Transaction #1 ******************************** */ |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/EfloraTaxonImport.java | ||
|---|---|---|
| 66 | 66 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 67 | 67 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| 68 | 68 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 69 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 69 | 70 |
import eu.etaxonomy.cdm.model.name.TypeDesignationBase; |
| 70 | 71 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
| 71 | 72 |
import eu.etaxonomy.cdm.model.reference.IBook; |
| ... | ... | |
| 150 | 151 |
logger.warn("body has element other than 'taxon'");
|
| 151 | 152 |
} |
| 152 | 153 |
|
| 153 |
BotanicalName botanicalName = BotanicalName.NewInstance(Rank.SPECIES());
|
|
| 154 |
BotanicalName botanicalName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 154 | 155 |
Taxon taxon = Taxon.NewInstance(botanicalName, state.getConfig().getSourceReference()); |
| 155 | 156 |
|
| 156 | 157 |
handleTaxonAttributes(elTaxon, taxon, state); |
| ... | ... | |
| 1279 | 1280 |
verifyNoAttribute(elHomonym); |
| 1280 | 1281 |
|
| 1281 | 1282 |
//hommonym name |
| 1282 |
BotanicalName homonymName = BotanicalName.NewInstance(upperName.getRank());
|
|
| 1283 |
BotanicalName homonymName = TaxonNameFactory.NewBotanicalInstance(upperName.getRank());
|
|
| 1283 | 1284 |
homonymName.setGenusOrUninomial(upperName.getGenusOrUninomial()); |
| 1284 | 1285 |
homonymName.setInfraGenericEpithet(upperName.getInfraGenericEpithet()); |
| 1285 | 1286 |
homonymName.setSpecificEpithet(upperName.getSpecificEpithet()); |
| ... | ... | |
| 1515 | 1516 |
String homonymString = detail.substring(end); |
| 1516 | 1517 |
|
| 1517 | 1518 |
//hommonym name |
| 1518 |
BotanicalName homonymName = BotanicalName.NewInstance(name.getRank());
|
|
| 1519 |
BotanicalName homonymName = TaxonNameFactory.NewBotanicalInstance(name.getRank());
|
|
| 1519 | 1520 |
homonymName.setGenusOrUninomial(name.getGenusOrUninomial()); |
| 1520 | 1521 |
homonymName.setInfraGenericEpithet(name.getInfraGenericEpithet()); |
| 1521 | 1522 |
homonymName.setSpecificEpithet(name.getSpecificEpithet()); |
| ... | ... | |
| 1650 | 1651 |
private TaxonNameBase makeName(Taxon taxon,HomotypicalGroup homotypicalGroup, boolean isSynonym) {
|
| 1651 | 1652 |
TaxonNameBase<?,?> name; |
| 1652 | 1653 |
if (isSynonym){
|
| 1653 |
name = BotanicalName.NewInstance(Rank.SPECIES(), homotypicalGroup);
|
|
| 1654 |
name = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES(), homotypicalGroup);
|
|
| 1654 | 1655 |
SynonymType synonymType = SynonymType.HETEROTYPIC_SYNONYM_OF(); |
| 1655 | 1656 |
if (taxon.getHomotypicGroup().equals(homotypicalGroup)){
|
| 1656 | 1657 |
synonymType = SynonymType.HOMOTYPIC_SYNONYM_OF(); |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/checklist/CentralAfricaChecklistSynonymImport.java | ||
|---|---|---|
| 28 | 28 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 29 | 29 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 30 | 30 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 31 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 31 | 32 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 32 | 33 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 33 | 34 |
import eu.etaxonomy.cdm.model.taxon.SynonymType; |
| ... | ... | |
| 42 | 43 |
*/ |
| 43 | 44 |
@Component |
| 44 | 45 |
public class CentralAfricaChecklistSynonymImport extends CentralAfricaChecklistImportBase<TaxonBase> implements IMappingImport<TaxonBase, CentralAfricaChecklistImportState>{
|
| 45 |
private static final Logger logger = Logger.getLogger(CentralAfricaChecklistSynonymImport.class); |
|
| 46 |
private static final long serialVersionUID = 954395388404224712L; |
|
| 47 |
|
|
| 48 |
private static final Logger logger = Logger.getLogger(CentralAfricaChecklistSynonymImport.class); |
|
| 46 | 49 |
|
| 47 | 50 |
private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance(); |
| 48 | 51 |
|
| ... | ... | |
| 63 | 66 |
} |
| 64 | 67 |
|
| 65 | 68 |
|
| 66 |
|
|
| 67 |
/* (non-Javadoc) |
|
| 68 |
* @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getIdQuery() |
|
| 69 |
*/ |
|
| 70 | 69 |
@Override |
| 71 | 70 |
protected String getIdQuery() {
|
| 72 | 71 |
String strQuery = " SELECT syn_id FROM " + dbTableName + strOrderBy; |
| 73 | 72 |
return strQuery; |
| 74 | 73 |
} |
| 75 | 74 |
|
| 76 |
|
|
| 77 |
/* (non-Javadoc) |
|
| 78 |
* @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getMapping() |
|
| 79 |
*/ |
|
| 80 | 75 |
@Override |
| 81 | 76 |
protected DbImportMapping getMapping() {
|
| 82 | 77 |
if (mapping == null){
|
| ... | ... | |
| 89 | 84 |
return mapping; |
| 90 | 85 |
} |
| 91 | 86 |
|
| 92 |
/* (non-Javadoc) |
|
| 93 |
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator) |
|
| 94 |
*/ |
|
| 95 | 87 |
@Override |
| 96 | 88 |
protected String getRecordQuery(CentralAfricaChecklistImportConfigurator config) {
|
| 97 | 89 |
String strSelect = " SELECT * "; |
| ... | ... | |
| 127 | 119 |
return result; |
| 128 | 120 |
} |
| 129 | 121 |
|
| 130 |
|
|
| 131 |
/* (non-Javadoc) |
|
| 132 |
* @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet) |
|
| 133 |
*/ |
|
| 134 | 122 |
@Override |
| 135 | 123 |
public TaxonBase createObject(ResultSet rs, CentralAfricaChecklistImportState state) throws SQLException {
|
| 136 |
BotanicalName speciesName = BotanicalName.NewInstance(Rank.SPECIES());
|
|
| 124 |
BotanicalName speciesName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 137 | 125 |
|
| 138 | 126 |
|
| 139 | 127 |
Integer accId = rs.getInt("acc_id");
|
| ... | ... | |
| 160 | 148 |
} |
| 161 | 149 |
|
| 162 | 150 |
|
| 163 |
/* (non-Javadoc) |
|
| 164 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
|
| 165 |
*/ |
|
| 166 | 151 |
@Override |
| 167 | 152 |
protected boolean doCheck(CentralAfricaChecklistImportState state){
|
| 168 | 153 |
IOValidator<CentralAfricaChecklistImportState> validator = new CentralAfricaChecklistTaxonImportValidator(); |
| 169 | 154 |
return validator.validate(state); |
| 170 | 155 |
} |
| 171 | 156 |
|
| 172 |
|
|
| 173 |
/* (non-Javadoc) |
|
| 174 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
|
| 175 |
*/ |
|
| 176 | 157 |
@Override |
| 177 | 158 |
protected boolean isIgnore(CentralAfricaChecklistImportState state){
|
| 178 | 159 |
return ! state.getConfig().isDoTaxa(); |
| 179 | 160 |
} |
| 180 | 161 |
|
| 181 |
|
|
| 182 |
|
|
| 183 | 162 |
} |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/checklist/CentralAfricaChecklistTaxonImport.java | ||
|---|---|---|
| 40 | 40 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 41 | 41 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 42 | 42 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 43 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 43 | 44 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 44 | 45 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 45 | 46 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| ... | ... | |
| 169 | 170 |
|
| 170 | 171 |
@Override |
| 171 | 172 |
public TaxonBase<?> createObject(ResultSet rs, CentralAfricaChecklistImportState state) throws SQLException {
|
| 172 |
BotanicalName speciesName = BotanicalName.NewInstance(Rank.SPECIES());
|
|
| 173 |
BotanicalName speciesName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
| 173 | 174 |
|
| 174 | 175 |
Reference sec = state.getConfig().getSourceReference(); |
| 175 | 176 |
getReferenceService().saveOrUpdate(sec); |
| ... | ... | |
| 193 | 194 |
if (StringUtils.isNotBlank(familyString)){
|
| 194 | 195 |
familyTaxon = getHigherTaxon(state, familyString, null); |
| 195 | 196 |
if (familyTaxon == null){
|
| 196 |
BotanicalName familyName = BotanicalName.NewInstance(Rank.FAMILY());
|
|
| 197 |
BotanicalName familyName = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());
|
|
| 197 | 198 |
familyName.setGenusOrUninomial(familyString); |
| 198 | 199 |
familyTaxon = Taxon.NewInstance(familyName, sec); |
| 199 | 200 |
saveHigherTaxon(state, familyTaxon, familyString, null); |
| ... | ... | |
| 205 | 206 |
//genus |
| 206 | 207 |
Taxon genusTaxon = getHigherTaxon(state, familyString, genusString); |
| 207 | 208 |
if (genusTaxon == null){
|
| 208 |
BotanicalName genusName = BotanicalName.NewInstance(Rank.GENUS());
|
|
| 209 |
BotanicalName genusName = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
|
|
| 209 | 210 |
genusName.setGenusOrUninomial(genusString); |
| 210 | 211 |
genusTaxon = Taxon.NewInstance(genusName, sec); |
| 211 | 212 |
saveHigherTaxon(state, genusTaxon, familyString, genusString); |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonImport.java | ||
|---|---|---|
| 55 | 55 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 56 | 56 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| 57 | 57 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 58 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 58 | 59 |
import eu.etaxonomy.cdm.model.name.TypeDesignationBase; |
| 59 | 60 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
| 60 | 61 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
| ... | ... | |
| 771 | 772 |
*/ |
| 772 | 773 |
@Override |
| 773 | 774 |
public TaxonBase createObject(ResultSet rs, CentralAfricaFernsImportState state) throws SQLException {
|
| 774 |
BotanicalName taxonName = BotanicalName.NewInstance(null);
|
|
| 775 |
BotanicalName taxonName = TaxonNameFactory.NewBotanicalInstance(null);
|
|
| 775 | 776 |
Reference sec = state.getConfig().getSourceReference(); |
| 776 | 777 |
|
| 777 | 778 |
String taxonNumber = rs.getString("Taxon number");
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonRelationImport.java | ||
|---|---|---|
| 51 | 51 |
import eu.etaxonomy.cdm.model.name.INonViralName; |
| 52 | 52 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 53 | 53 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 54 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 54 | 55 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 55 | 56 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 56 | 57 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| ... | ... | |
| 789 | 790 |
|
| 790 | 791 |
private BotanicalName handleInfraSpecific(Rank lowerTaxonRank, Epithets epithets) {
|
| 791 | 792 |
|
| 792 |
BotanicalName taxonName = BotanicalName.NewInstance(null);
|
|
| 793 |
BotanicalName taxonName = TaxonNameFactory.NewBotanicalInstance(null);
|
|
| 793 | 794 |
Rank newRank = null; |
| 794 | 795 |
|
| 795 | 796 |
if (StringUtils.isNotBlank(epithets.subFormaName) && lowerTaxonRank.isLower(Rank.SUBFORM())){
|
Also available in: Unified diff
ref #6365 use TaxonNameFactory for factory methods in cdmlib-app