Revision 94dab8de
Added by Andreas Müller over 2 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/cyprus/CyprusImagesActivator.java | ||
|---|---|---|
| 100 | 100 |
CdmApplicationController app = CdmIoApplicationController.NewInstance(cdmDestination, DbSchemaValidation.VALIDATE); |
| 101 | 101 |
TransactionStatus tx = app.startTransaction(); |
| 102 | 102 |
|
| 103 |
deduplicationHelper = (ImportDeduplicationHelper)ImportDeduplicationHelper.NewInstance(app); |
|
| 103 |
deduplicationHelper = (ImportDeduplicationHelper)ImportDeduplicationHelper.NewInstance(app, null);
|
|
| 104 | 104 |
|
| 105 | 105 |
File file = new File(path); |
| 106 | 106 |
String[] fileList = file.list(); |
| ... | ... | |
| 635 | 635 |
CdmApplicationController app = CdmIoApplicationController.NewInstance(cdmDestination, DbSchemaValidation.VALIDATE); |
| 636 | 636 |
TransactionStatus tx = app.startTransaction(); |
| 637 | 637 |
|
| 638 |
deduplicationHelper = (ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>>)ImportDeduplicationHelper.NewInstance(app);
|
|
| 638 |
deduplicationHelper = (ImportDeduplicationHelper)ImportDeduplicationHelper.NewInstance(app, null);
|
|
| 639 | 639 |
|
| 640 | 640 |
List<Media> list = app.getMediaService().list(Media.class, null, null, null, null); |
| 641 | 641 |
for (Media media : list){
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/bogota/BogotaChecklistTaxonImport.java | ||
|---|---|---|
| 17 | 17 |
import org.springframework.transaction.TransactionStatus; |
| 18 | 18 |
|
| 19 | 19 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 20 |
import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper; |
|
| 21 | 20 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport; |
| 22 | 21 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| 23 | 22 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
| ... | ... | |
| 57 | 56 |
private static UUID rootUuid = UUID.fromString("d66eda18-4c11-4472-bfe8-f6cd5ed95c9f");
|
| 58 | 57 |
private static UUID plantaeUuid = UUID.fromString("032fc183-eb4f-4f19-a290-28597a849096");
|
| 59 | 58 |
|
| 60 |
@SuppressWarnings("unchecked")
|
|
| 61 |
private ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>> deduplicationHelper |
|
| 62 |
= (ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>>)ImportDeduplicationHelper.NewStandaloneInstance(); |
|
| 63 |
|
|
| 64 | 59 |
private String lastGenus; |
| 65 | 60 |
private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance(); |
| 66 | 61 |
private BasionymRelationCreator basionymCreator = new BasionymRelationCreator(); |
| ... | ... | |
| 174 | 169 |
} |
| 175 | 170 |
IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank); |
| 176 | 171 |
name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null); |
| 177 |
name = deduplicationHelper.getExistingName(state, name);
|
|
| 172 |
name = state.getDeduplicationHelper().getExistingName(state, name);
|
|
| 178 | 173 |
if (name.isProtectedTitleCache()){
|
| 179 | 174 |
logger.warn(line + "Misapplied name could not be parsed: " + nameStr); |
| 180 | 175 |
} |
| 181 |
deduplicationHelper.replaceAuthorNamesAndNomRef(state, name);
|
|
| 176 |
state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(state, name);
|
|
| 182 | 177 |
|
| 183 | 178 |
Taxon misApp = Taxon.NewInstance(name, null); |
| 184 | 179 |
if (auctRequired){
|
| ... | ... | |
| 211 | 206 |
Rank rank = Rank.SPECIES(); |
| 212 | 207 |
IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank); |
| 213 | 208 |
name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null); |
| 214 |
name = deduplicationHelper.getExistingName(state, name);
|
|
| 209 |
name = state.getDeduplicationHelper().getExistingName(state, name);
|
|
| 215 | 210 |
if (name.isProtectedTitleCache()){
|
| 216 | 211 |
logger.warn(line + "Synonym could not be parsed: " + nameStr); |
| 217 | 212 |
} |
| 218 |
deduplicationHelper.replaceAuthorNamesAndNomRef(state, name);
|
|
| 213 |
state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(state, name);
|
|
| 219 | 214 |
|
| 220 | 215 |
Synonym synonym = Synonym.NewInstance(name, getSecReference(state)); |
| 221 | 216 |
synonym.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null); |
| ... | ... | |
| 242 | 237 |
Rank rank = Rank.SUBSPECIES(); |
| 243 | 238 |
IBotanicalName name = (IBotanicalName)parser.parseFullName(split.trim(), state.getConfig().getNomenclaturalCode(), rank); |
| 244 | 239 |
name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null); |
| 245 |
name = deduplicationHelper.getExistingName(state, name);
|
|
| 240 |
name = state.getDeduplicationHelper().getExistingName(state, name);
|
|
| 246 | 241 |
if (name.isProtectedTitleCache()){
|
| 247 | 242 |
logger.warn(line + "Infraspecific taxon could not be parsed: " + split.trim()); |
| 248 | 243 |
} |
| 249 |
deduplicationHelper.replaceAuthorNamesAndNomRef(state, name);
|
|
| 244 |
state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(state, name);
|
|
| 250 | 245 |
|
| 251 | 246 |
Taxon subSpecies = Taxon.NewInstance(name, getSecReference(state)); |
| 252 | 247 |
subSpecies.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null); |
| ... | ... | |
| 279 | 274 |
Rank rank = Rank.SPECIES(); |
| 280 | 275 |
IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank); |
| 281 | 276 |
name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null); |
| 282 |
name = deduplicationHelper.getExistingName(state, name);
|
|
| 277 |
name = state.getDeduplicationHelper().getExistingName(state, name);
|
|
| 283 | 278 |
if (name.isProtectedTitleCache()){
|
| 284 | 279 |
logger.warn(line + "Name could not be parsed: " + nameStr); |
| 285 | 280 |
} |
| 286 |
deduplicationHelper.replaceAuthorNamesAndNomRef(state, name);
|
|
| 281 |
state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(state, name);
|
|
| 287 | 282 |
|
| 288 | 283 |
Taxon taxon = Taxon.NewInstance(name, getSecReference(state)); |
| 289 | 284 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoAizoaceaeExcelImport.java | ||
|---|---|---|
| 23 | 23 |
import eu.etaxonomy.cdm.api.service.config.SynonymDeletionConfigurator; |
| 24 | 24 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 25 | 25 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
| 26 |
import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper; |
|
| 27 | 26 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport; |
| 28 | 27 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| 29 | 28 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
| ... | ... | |
| 68 | 67 |
private Set<UUID> createdNames = new HashSet<>(); |
| 69 | 68 |
|
| 70 | 69 |
private SimpleExcelTaxonImportState<CaryoAizoaceaeExcelImportConfigurator> state; |
| 71 |
private ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>> dedupHelper = null; |
|
| 72 | 70 |
|
| 73 | 71 |
@Override |
| 74 | 72 |
protected void firstPass(SimpleExcelTaxonImportState<CaryoAizoaceaeExcelImportConfigurator> state) {
|
| ... | ... | |
| 235 | 233 |
|
| 236 | 234 |
private TaxonName dedupliateNameParts(TaxonName name) {
|
| 237 | 235 |
if (state.getConfig().isDoDeduplicate()){
|
| 238 |
getDedupHelper().replaceAuthorNamesAndNomRef(state, name);
|
|
| 236 |
state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(state, name);
|
|
| 239 | 237 |
} |
| 240 | 238 |
return name; |
| 241 | 239 |
} |
| 242 | 240 |
|
| 243 |
private ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>> getDedupHelper() {
|
|
| 244 |
if (dedupHelper == null){
|
|
| 245 |
dedupHelper |
|
| 246 |
= ImportDeduplicationHelper.NewInstance(this, state); |
|
| 247 |
} |
|
| 248 |
return dedupHelper; |
|
| 249 |
} |
|
| 250 |
|
|
| 251 | 241 |
private String getOtherAuthors(List<TaxonName> otherNames) {
|
| 252 | 242 |
String result = ""; |
| 253 | 243 |
for (TaxonName name : otherNames){
|
| ... | ... | |
| 383 | 373 |
private void newTransaction(SimpleExcelTaxonImportState<CaryoAizoaceaeExcelImportConfigurator> state) {
|
| 384 | 374 |
commitTransaction(state.getTransactionStatus()); |
| 385 | 375 |
secRef = null; |
| 386 |
dedupHelper = null;
|
|
| 376 |
state.getDeduplicationHelper().reset();
|
|
| 387 | 377 |
state.setSourceReference(null); |
| 388 | 378 |
System.gc(); |
| 389 | 379 |
state.setTransactionStatus(startTransaction()); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaImageImport.java | ||
|---|---|---|
| 28 | 28 |
import eu.etaxonomy.cdm.api.service.config.MatchingTaxonConfigurator; |
| 29 | 29 |
import eu.etaxonomy.cdm.common.URI; |
| 30 | 30 |
import eu.etaxonomy.cdm.io.common.CdmImportBase; |
| 31 |
import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper; |
|
| 32 | 31 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| 33 | 32 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 34 | 33 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| ... | ... | |
| 60 | 59 |
private static final String BASE_URL = "https://media.e-taxonomy.eu/flora-greece/"; |
| 61 | 60 |
private static final String IMAGE_FOLDER = "////BGBM-PESIHPC/Greece/thumbs/"; |
| 62 | 61 |
|
| 63 |
@SuppressWarnings("unchecked")
|
|
| 64 |
private ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>> deduplicationHelper = (ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>>)ImportDeduplicationHelper.NewInstance(this); |
|
| 65 |
|
|
| 66 | 62 |
@Override |
| 67 | 63 |
protected void doInvoke(SimpleExcelTaxonImportState<CONFIG> state) {
|
| 68 | 64 |
TransactionStatus tx = this.startTransaction(); |
| ... | ... | |
| 158 | 154 |
}else{
|
| 159 | 155 |
person.setTitleCache("artistStr", true);
|
| 160 | 156 |
} |
| 161 |
person = deduplicationHelper.getExistingAuthor(state, person);
|
|
| 157 |
person = state.getDeduplicationHelper().getExistingAuthor(state, person);
|
|
| 162 | 158 |
|
| 163 | 159 |
media.setArtist(person); |
| 164 | 160 |
//copyright |
| 165 | 161 |
Rights right = Rights.NewInstance(); |
| 166 | 162 |
right.setType(RightsType.COPYRIGHT()); |
| 167 | 163 |
right.setAgent(person); |
| 168 |
right = deduplicationHelper.getExistingCopyright(state, right);
|
|
| 164 |
right = state.getDeduplicationHelper().getExistingCopyright(state, right);
|
|
| 169 | 165 |
media.addRights(right); |
| 170 | 166 |
} |
| 171 | 167 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaImportBase.java | ||
|---|---|---|
| 15 | 15 |
|
| 16 | 16 |
import org.apache.log4j.Logger; |
| 17 | 17 |
|
| 18 |
import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper; |
|
| 19 | 18 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport; |
| 20 | 19 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| 21 | 20 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
| ... | ... | |
| 44 | 43 |
private Reference secReference; |
| 45 | 44 |
private Reference secReference2; |
| 46 | 45 |
|
| 47 |
@SuppressWarnings("unchecked")
|
|
| 48 |
private ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>> deduplicationHelper = (ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>>)ImportDeduplicationHelper.NewInstance(this); |
|
| 49 |
|
|
| 50 |
|
|
| 51 |
|
|
| 52 |
/** |
|
| 53 |
* @param taxon |
|
| 54 |
* @return |
|
| 55 |
*/ |
|
| 56 | 46 |
protected TaxonDescription getTaxonDescription(Taxon taxon) {
|
| 57 | 47 |
if (!taxon.getDescriptions().isEmpty()){
|
| 58 | 48 |
return taxon.getDescriptions().iterator().next(); |
| ... | ... | |
| 161 | 151 |
} |
| 162 | 152 |
|
| 163 | 153 |
protected <NAME extends INonViralName> NAME replaceNameAuthorsAndReferences(SimpleExcelTaxonImportState<CONFIG> state, NAME name) {
|
| 164 |
NAME result = deduplicationHelper.getExistingName(state, name);
|
|
| 165 |
deduplicationHelper.replaceAuthorNamesAndNomRef(state, result);
|
|
| 154 |
NAME result = state.getDeduplicationHelper().getExistingName(state, name);
|
|
| 155 |
state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(state, result);
|
|
| 166 | 156 |
return result; |
| 167 | 157 |
} |
| 168 | 158 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/lichenes/LichenesGeneraTaxonImport.java | ||
|---|---|---|
| 18 | 18 |
import org.springframework.stereotype.Component; |
| 19 | 19 |
|
| 20 | 20 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 21 |
import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper; |
|
| 22 | 21 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport; |
| 23 | 22 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| 24 | 23 |
import eu.etaxonomy.cdm.model.common.Annotation; |
| ... | ... | |
| 399 | 398 |
} |
| 400 | 399 |
|
| 401 | 400 |
private void replaceNameAuthorsAndReferences(SimpleExcelTaxonImportState<CONFIG> state, INonViralName name) {
|
| 402 |
dedupHelper().replaceAuthorNamesAndNomRef(state, name); |
|
| 403 |
} |
|
| 404 |
|
|
| 405 |
private ImportDeduplicationHelper<SimpleExcelTaxonImportState<CONFIG>> dedupHelper; |
|
| 406 |
private ImportDeduplicationHelper<SimpleExcelTaxonImportState<CONFIG>> dedupHelper() {
|
|
| 407 |
if (dedupHelper == null) {
|
|
| 408 |
dedupHelper = (ImportDeduplicationHelper)ImportDeduplicationHelper.NewStandaloneInstance(); |
|
| 409 |
} |
|
| 410 |
return dedupHelper; |
|
| 401 |
state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(state, name); |
|
| 411 | 402 |
} |
| 412 | 403 |
|
| 413 | 404 |
@Override |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/excel/RedListGefaesspflanzenTaxonExcelImport.java | ||
|---|---|---|
| 18 | 18 |
import org.springframework.transaction.TransactionStatus; |
| 19 | 19 |
|
| 20 | 20 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 21 |
import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper; |
|
| 22 | 21 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport; |
| 23 | 22 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| 24 | 23 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
| ... | ... | |
| 61 | 60 |
private static UUID rootUuid = UUID.fromString("235ae474-227f-438a-b132-4508053fcb1c");
|
| 62 | 61 |
private static UUID plantaeUuid = UUID.fromString("31bd1b7c-245a-416d-b076-aa090c7469ce");
|
| 63 | 62 |
|
| 64 |
@SuppressWarnings("unchecked")
|
|
| 65 |
private ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>> deduplicationHelper |
|
| 66 |
= (ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>>)ImportDeduplicationHelper.NewStandaloneInstance(); |
|
| 67 |
|
|
| 68 | 63 |
private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance(); |
| 69 | 64 |
private BasionymRelationCreator basionymCreator = new BasionymRelationCreator(); |
| 70 | 65 |
|
| ... | ... | |
| 161 | 156 |
Rank rank = Rank.SPECIES(); |
| 162 | 157 |
IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank); |
| 163 | 158 |
name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null); |
| 164 |
name = deduplicationHelper.getExistingName(state, name);
|
|
| 159 |
name = state.getDeduplicationHelper().getExistingName(state, name);
|
|
| 165 | 160 |
if (name.isProtectedTitleCache()){
|
| 166 | 161 |
logger.warn(line + "Name could not be parsed: " + nameStr); |
| 167 | 162 |
} |
| 168 | 163 |
|
| 169 |
deduplicationHelper.replaceAuthorNamesAndNomRef(state, name);
|
|
| 164 |
state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(state, name);
|
|
| 170 | 165 |
|
| 171 | 166 |
TaxonBase<?> taxon; |
| 172 | 167 |
if ("1".equals(synFlag) || isAuct){
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/germanSL/GermanSLTaxonImport.java | ||
|---|---|---|
| 20 | 20 |
|
| 21 | 21 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 22 | 22 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
| 23 |
import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper; |
|
| 24 | 23 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| 25 | 24 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 26 | 25 |
import eu.etaxonomy.cdm.model.common.Language; |
| ... | ... | |
| 76 | 75 |
|
| 77 | 76 |
private static final String UUID_ = "UUID"; |
| 78 | 77 |
|
| 79 |
|
|
| 80 | 78 |
public static final String TAXON_NAMESPACE = "1.3.4"; |
| 81 | 79 |
|
| 82 |
@SuppressWarnings("unchecked")
|
|
| 83 |
protected ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>> deduplicationHelper |
|
| 84 |
= (ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>>)ImportDeduplicationHelper.NewStandaloneInstance(); |
|
| 85 |
|
|
| 86 |
|
|
| 87 | 80 |
@Override |
| 88 | 81 |
protected String getWorksheetName(GermanSLImportConfigurator config) {
|
| 89 | 82 |
return "1.3.4"; |
| ... | ... | |
| 283 | 276 |
if (fullName.isProtectedTitleCache()){
|
| 284 | 277 |
logger.warn(line + "Name could not be parsed: " + fullNameStr ); |
| 285 | 278 |
}else{
|
| 286 |
getDeduplicationHelper(state).replaceAuthorNamesAndNomRef(state, fullName);
|
|
| 279 |
state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(state, fullName);
|
|
| 287 | 280 |
// replaceAuthorNamesAndNomRef(state, fullName); |
| 288 | 281 |
} |
| 289 | 282 |
// BotanicalName existingName = getExistingName(state, fullName); |
| ... | ... | |
| 296 | 289 |
return result; |
| 297 | 290 |
} |
| 298 | 291 |
|
| 299 |
/** |
|
| 300 |
* @param state |
|
| 301 |
* @return |
|
| 302 |
*/ |
|
| 303 |
protected ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>> getDeduplicationHelper(SimpleExcelTaxonImportState<?> state) {
|
|
| 304 |
if (deduplicationHelper == null){
|
|
| 305 |
deduplicationHelper = ImportDeduplicationHelper.NewInstance(this, state); |
|
| 306 |
} |
|
| 307 |
return deduplicationHelper; |
|
| 308 |
} |
|
| 309 |
|
|
| 310 |
|
|
| 311 |
|
|
| 312 |
/** |
|
| 313 |
* @param line |
|
| 314 |
* @param state |
|
| 315 |
* @param rankStr |
|
| 316 |
* @return |
|
| 317 |
*/ |
|
| 318 | 292 |
private Rank makeRank(String line, SimpleExcelTaxonImportState<GermanSLImportConfigurator> state, String rankStr) {
|
| 319 | 293 |
Rank rank = null; |
| 320 | 294 |
try {
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/salvador/SalvadorSpecimenImport.java | ||
|---|---|---|
| 25 | 25 |
|
| 26 | 26 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
| 27 | 27 |
import eu.etaxonomy.cdm.common.URI; |
| 28 |
import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper; |
|
| 29 | 28 |
import eu.etaxonomy.cdm.io.csv.in.CsvImportBase; |
| 30 | 29 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 31 | 30 |
import eu.etaxonomy.cdm.model.agent.Team; |
| ... | ... | |
| 63 | 62 |
|
| 64 | 63 |
private static final long serialVersionUID = -2165916187195347780L; |
| 65 | 64 |
|
| 66 |
private ImportDeduplicationHelper<?> dedupHelper; |
|
| 67 |
|
|
| 68 |
/** |
|
| 69 |
* {@inheritDoc}
|
|
| 70 |
*/ |
|
| 71 | 65 |
@Override |
| 72 | 66 |
protected void handleSingleLine(SalvadorSpecimenImportState state) {
|
| 73 | 67 |
|
| 74 |
initDedupHelper(); |
|
| 75 | 68 |
try {
|
| 76 | 69 |
UUID factUuid = UUID.fromString(state.getCurrentRecord().get("specimenFactUuid"));
|
| 77 | 70 |
|
| ... | ... | |
| 101 | 94 |
} |
| 102 | 95 |
} |
| 103 | 96 |
|
| 104 |
|
|
| 105 |
/** |
|
| 106 |
* |
|
| 107 |
*/ |
|
| 108 |
private void initDedupHelper() {
|
|
| 109 |
if (dedupHelper == null){
|
|
| 110 |
dedupHelper = ImportDeduplicationHelper.NewStandaloneInstance(); |
|
| 111 |
} |
|
| 112 |
} |
|
| 113 |
|
|
| 114 |
|
|
| 115 |
/** |
|
| 116 |
* @param config |
|
| 117 |
* @param facade |
|
| 118 |
* @param importResult |
|
| 119 |
*/ |
|
| 120 | 97 |
private void makeSpecimenDuplicate(SalvadorSpecimenImportState state, |
| 121 | 98 |
DerivedUnitFacade facade) {
|
| 122 | 99 |
|
| ... | ... | |
| 285 | 262 |
//collector |
| 286 | 263 |
TeamOrPersonBase<?> collector = makeCollectorTeam(state, record, row); |
| 287 | 264 |
if (collector != null){
|
| 288 |
collector = dedupHelper.getExistingAuthor(null, collector);
|
|
| 265 |
collector = state.getDeduplicationHelper().getExistingAuthor(null, collector);
|
|
| 289 | 266 |
facade.setCollector(collector); |
| 290 | 267 |
} |
| 291 | 268 |
|
| ... | ... | |
| 592 | 569 |
state.getResult().addWarning(message, row); |
| 593 | 570 |
result.setTitleCache(str, true); |
| 594 | 571 |
} |
| 595 |
result = dedupHelper.getExistingAuthor(null, result);
|
|
| 572 |
result = state.getDeduplicationHelper().getExistingAuthor(null, result);
|
|
| 596 | 573 |
|
| 597 | 574 |
team.addTeamMember(result); |
| 598 | 575 |
return ; |
| ... | ... | |
| 605 | 582 |
collectionMap = new HashMap<>(); |
| 606 | 583 |
fieldUnitMap = new HashMap<>(); |
| 607 | 584 |
taxonDescMap = new HashMap<>(); |
| 608 |
dedupHelper.restartSession(this, state.getResult());
|
|
| 585 |
state.getDeduplicationHelper().restartSession(this, state.getResult());
|
|
| 609 | 586 |
} |
| 610 | 587 |
|
| 611 | 588 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/uzbekistan/UzbekistanTaxonImport.java | ||
|---|---|---|
| 17 | 17 |
import org.apache.log4j.Logger; |
| 18 | 18 |
import org.springframework.stereotype.Component; |
| 19 | 19 |
|
| 20 |
import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper; |
|
| 21 | 20 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport; |
| 22 | 21 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| 23 | 22 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| ... | ... | |
| 464 | 463 |
} |
| 465 | 464 |
|
| 466 | 465 |
private void replaceNameAuthorsAndReferences(SimpleExcelTaxonImportState<CONFIG> state, INonViralName name) {
|
| 467 |
dedupHelper().replaceAuthorNamesAndNomRef(state, name);
|
|
| 466 |
state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(state, name);
|
|
| 468 | 467 |
} |
| 469 | 468 |
|
| 470 |
private ImportDeduplicationHelper<SimpleExcelTaxonImportState<CONFIG>> dedupHelper; |
|
| 471 |
@SuppressWarnings({ "rawtypes", "unchecked" })
|
|
| 472 |
private ImportDeduplicationHelper<SimpleExcelTaxonImportState<CONFIG>> dedupHelper() {
|
|
| 473 |
if (dedupHelper == null) {
|
|
| 474 |
dedupHelper = (ImportDeduplicationHelper)ImportDeduplicationHelper.NewInstance(this); |
|
| 475 |
} |
|
| 476 |
return dedupHelper; |
|
| 477 |
} |
|
| 478 | 469 |
|
| 479 | 470 |
@Override |
| 480 | 471 |
protected IdentifiableSource makeOriginalSource(SimpleExcelTaxonImportState<CONFIG> state) {
|
Also available in: Unified diff
ref #9890 use common state based deduplication helper in app-import