Revision 3ef2e1bd
Added by Andreas Müller over 7 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/cyprus/CyprusAltitudeActivator.java | ||
|---|---|---|
| 41 | 41 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 42 | 42 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 43 | 43 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 44 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationship; |
|
| 45 | 44 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 46 | 45 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 47 | 46 |
|
| ... | ... | |
| 206 | 205 |
|
| 207 | 206 |
private boolean hasSynonym(Taxon t, TaxonBase<?> base) {
|
| 208 | 207 |
if (base.isInstanceOf(Synonym.class)){
|
| 209 |
for (SynonymRelationship rel : t.getSynonymRelations()){
|
|
| 210 |
if (rel.getSynonym().equals(base)){
|
|
| 208 |
for (Synonym syn : t.getSynonyms()){
|
|
| 209 |
if (syn.equals(base)){
|
|
| 211 | 210 |
return true; |
| 212 | 211 |
} |
| 213 | 212 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/app/util/TestDatabase.java | ||
|---|---|---|
| 47 | 47 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 48 | 48 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 49 | 49 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 50 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
|
|
| 50 |
import eu.etaxonomy.cdm.model.taxon.SynonymType; |
|
| 51 | 51 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 52 | 52 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 53 | 53 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
| ... | ... | |
| 284 | 284 |
syn12 = Synonym.NewInstance(synName12, sec); |
| 285 | 285 |
syn2 = Synonym.NewInstance(synName2, sec); |
| 286 | 286 |
|
| 287 |
child1.addSynonym(syn11, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF());
|
|
| 288 |
child1.addSynonym(syn12, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
|
|
| 289 |
child2.addSynonym(syn2, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
|
|
| 290 |
freeT.addSynonym(synFree, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
|
|
| 287 |
child1.addSynonym(syn11, SynonymType.HOMOTYPIC_SYNONYM_OF()); |
|
| 288 |
child1.addSynonym(syn12, SynonymType.HETEROTYPIC_SYNONYM_OF()); |
|
| 289 |
child2.addSynonym(syn2, SynonymType.HETEROTYPIC_SYNONYM_OF()); |
|
| 290 |
freeT.addSynonym(synFree, SynonymType.HETEROTYPIC_SYNONYM_OF()); |
|
| 291 | 291 |
|
| 292 | 292 |
taxonBases.add(synFree); |
| 293 | 293 |
taxonBases.add(syn11); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/palmae/PalmaePostImportUpdater.java | ||
|---|---|---|
| 1 | 1 |
// $Id$ |
| 2 | 2 |
/** |
| 3 | 3 |
* Copyright (C) 2007 EDIT |
| 4 |
* European Distributed Institute of Taxonomy
|
|
| 4 |
* European Distributed Institute of Taxonomy |
|
| 5 | 5 |
* http://www.e-taxonomy.eu |
| 6 |
*
|
|
| 6 |
* |
|
| 7 | 7 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 8 | 8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 9 | 9 |
*/ |
| ... | ... | |
| 42 | 42 |
private static final Logger logger = Logger.getLogger(PalmaePostImportUpdater.class); |
| 43 | 43 |
|
| 44 | 44 |
static final ICdmDataSource cdmDestination = CdmDestinations.localH2Palmae(); |
| 45 |
|
|
| 46 |
|
|
| 45 |
|
|
| 46 |
|
|
| 47 | 47 |
private String relationships = "relationships"; |
| 48 | 48 |
private String taxonomicAccounts = "taxonomic accounts"; |
| 49 | 49 |
private String fossilRecord = "fossil record"; |
| 50 |
|
|
| 50 |
|
|
| 51 | 51 |
public boolean updateMissingFeatures(ICdmDataSource dataSource) {
|
| 52 | 52 |
try{
|
| 53 | 53 |
int count = 0; |
| 54 | 54 |
UUID featureTreeUuid = PalmaeActivator.featureTreeUuid; |
| 55 | 55 |
CdmApplicationController cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE); |
| 56 |
|
|
| 56 |
|
|
| 57 | 57 |
TransactionStatus tx = cdmApp.startTransaction(); |
| 58 |
|
|
| 58 |
|
|
| 59 | 59 |
FeatureTree tree = cdmApp.getFeatureTreeService().find(featureTreeUuid); |
| 60 | 60 |
FeatureNode root = tree.getRoot(); |
| 61 |
|
|
| 61 |
|
|
| 62 | 62 |
List<Feature> featureList = cdmApp.getTermService().list(Feature.class, null, null, null, null); |
| 63 | 63 |
for (Feature feature : featureList){
|
| 64 | 64 |
String label = feature.getLabel(); |
| ... | ... | |
| 88 | 88 |
logger.error("ERROR in feature tree update");
|
| 89 | 89 |
return false; |
| 90 | 90 |
} |
| 91 |
|
|
| 91 |
|
|
| 92 | 92 |
} |
| 93 |
|
|
| 93 |
|
|
| 94 | 94 |
public boolean updateNameUsage(ICdmDataSource dataSource) {
|
| 95 | 95 |
try{
|
| 96 | 96 |
boolean result = true; |
| ... | ... | |
| 102 | 102 |
int count = cdmApp.getTaxonService().count(Taxon.class); |
| 103 | 103 |
List<TaxonBase> taxonList = cdmApp.getTaxonService().list(TaxonBase.class, 100000, page, null, null); |
| 104 | 104 |
int i = 0; |
| 105 |
|
|
| 105 |
|
|
| 106 | 106 |
IReference treatmentReference = (IReference) cdmApp.getCommonService().getSourcedObjectByIdInSource(Reference.class, "palm_pub_ed_999999", "PublicationCitation"); |
| 107 | 107 |
if (treatmentReference == null){
|
| 108 | 108 |
logger.error("Treatment reference could not be found");
|
| ... | ... | |
| 110 | 110 |
}else{
|
| 111 | 111 |
for (TaxonBase nameUsage : taxonList){
|
| 112 | 112 |
if ((i++ % 100) == 0){System.out.println(i);};
|
| 113 |
|
|
| 113 |
|
|
| 114 | 114 |
try {
|
| 115 | 115 |
//if not in treatment |
| 116 | 116 |
if (! isInTreatment(nameUsage, treatmentReference, false)){
|
| ... | ... | |
| 156 | 156 |
logger.error("ERROR in name usage update");
|
| 157 | 157 |
return false; |
| 158 | 158 |
} |
| 159 |
|
|
| 159 |
|
|
| 160 | 160 |
} |
| 161 | 161 |
|
| 162 | 162 |
/** |
| 163 |
* @param nameUsage
|
|
| 163 |
* @param nameUsage |
|
| 164 | 164 |
* @return |
| 165 | 165 |
*/ |
| 166 | 166 |
private Taxon getAcceptedTreatmentTaxon(TaxonBase nameUsage, IReference treatmentReference) {
|
| ... | ... | |
| 174 | 174 |
} |
| 175 | 175 |
}else if (candidate instanceof Synonym){
|
| 176 | 176 |
Synonym synonym = (Synonym)candidate; |
| 177 |
Set<Taxon> accTaxa = synonym.getAcceptedTaxa();
|
|
| 177 |
Taxon accTaxon = synonym.getAcceptedTaxon();
|
|
| 178 | 178 |
if (isInTreatment(synonym, treatmentReference, true)){
|
| 179 | 179 |
hasSynonymInTreatment = true; |
| 180 | 180 |
} |
| 181 |
for (Taxon accTaxon : accTaxa){
|
|
| 181 |
if (accTaxon != null){
|
|
| 182 | 182 |
if (isInTreatment(accTaxon, treatmentReference, false)){
|
| 183 | 183 |
return accTaxon; |
| 184 | 184 |
} |
| ... | ... | |
| 195 | 195 |
|
| 196 | 196 |
/** |
| 197 | 197 |
* @param taxonBase |
| 198 |
* @param treatmentReference
|
|
| 198 |
* @param treatmentReference |
|
| 199 | 199 |
* @return |
| 200 | 200 |
*/ |
| 201 | 201 |
private boolean isInTreatment(TaxonBase taxonBase, IReference treatmentReference, boolean silent) {
|
| ... | ... | |
| 209 | 209 |
}else if (taxonBase instanceof Synonym){
|
| 210 | 210 |
Synonym synonym = (Synonym)taxonBase; |
| 211 | 211 |
boolean hasAccTaxonInTreatment = false; |
| 212 |
for (Taxon accTaxon : synonym.getAcceptedTaxa()){
|
|
| 212 |
Taxon accTaxon = synonym.getAcceptedTaxon(); |
|
| 213 |
if (accTaxon != null){
|
|
| 213 | 214 |
hasAccTaxonInTreatment |= isInTreatment(accTaxon, treatmentReference, false); |
| 214 | 215 |
} |
| 215 | 216 |
if (hasAccTaxonInTreatment == false){
|
| ... | ... | |
| 230 | 231 |
}else if (taxonBase instanceof Synonym){
|
| 231 | 232 |
Synonym synonym = (Synonym)taxonBase; |
| 232 | 233 |
boolean hasAccTaxonInTreatment = false; |
| 233 |
for (Taxon accTaxon : synonym.getAcceptedTaxa()){
|
|
| 234 |
Taxon accTaxon = synonym.getAcceptedTaxon(); |
|
| 235 |
if (accTaxon != null){
|
|
| 234 | 236 |
hasAccTaxonInTreatment |= isInTreatment(accTaxon, treatmentReference, false); |
| 235 | 237 |
} |
| 236 | 238 |
if (hasAccTaxonInTreatment == true){
|
| ... | ... | |
| 243 | 245 |
return false; |
| 244 | 246 |
} |
| 245 | 247 |
} |
| 246 |
|
|
| 248 |
|
|
| 247 | 249 |
/** |
| 248 | 250 |
* @param taxonCandidate |
| 249 | 251 |
* @param taxon |
| ... | ... | |
| 266 | 268 |
myDescription.addElement(textData); |
| 267 | 269 |
return true; |
| 268 | 270 |
} |
| 269 |
|
|
| 270 |
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|
| 271 |
|
|
| 272 |
|
|
| 271 | 273 |
/** |
| 272 | 274 |
* @param args |
| 273 | 275 |
*/ |
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/palmae/UseImport.java | ||
|---|---|---|
| 149 | 149 |
ArrayList<String> lstTaxon = new ArrayList<String>(); |
| 150 | 150 |
while (cells.hasNext()) {
|
| 151 | 151 |
Cell cell = cells.next(); |
| 152 |
|
|
| 152 |
|
|
| 153 | 153 |
int intCellType = cell.getCellType(); |
| 154 | 154 |
switch (intCellType) {
|
| 155 | 155 |
case 0: |
| 156 |
int cellValue = (int) cell.getNumericCellValue();
|
|
| 156 |
int cellValue = (int) cell.getNumericCellValue(); |
|
| 157 | 157 |
lstTaxon.add(Integer.toString(cellValue)); |
| 158 | 158 |
break; |
| 159 | 159 |
case 1: |
| ... | ... | |
| 162 | 162 |
} |
| 163 | 163 |
} |
| 164 | 164 |
lstUpdates.add(lstTaxon); |
| 165 |
lstTaxonIDs.add(Integer.parseInt(lstTaxon.get(0)));
|
|
| 165 |
lstTaxonIDs.add(Integer.parseInt(lstTaxon.get(0))); |
|
| 166 | 166 |
} |
| 167 |
|
|
| 167 |
|
|
| 168 | 168 |
List<TaxonBase> taxa = service.findTaxaByID(lstTaxonIDs); |
| 169 | 169 |
for(TaxonBase idTaxa : taxa) {
|
| 170 | 170 |
//System.out.println(idTaxa.getUuid().toString()); |
| 171 | 171 |
System.out.println(idTaxa.getName()); |
| 172 | 172 |
} |
| 173 |
|
|
| 174 |
|
|
| 173 |
|
|
| 174 |
|
|
| 175 | 175 |
MarkerType useMarkerType = (MarkerType) termService.find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
|
| 176 | 176 |
Marker useMarker = Marker.NewInstance(useMarkerType, true); |
| 177 | 177 |
for (ArrayList<String> lstUpdate : lstUpdates) {
|
| ... | ... | |
| 185 | 185 |
authorTeam.setTitleCache(lstUpdate.get(3)); |
| 186 | 186 |
citation.setAuthorship(authorTeam); |
| 187 | 187 |
citation.setTitle(lstUpdate.get(4)); |
| 188 |
|
|
| 188 |
|
|
| 189 | 189 |
//citation. |
| 190 | 190 |
TimePeriod year = TimePeriod.NewInstance(Integer.parseInt(lstUpdate.get(5))); |
| 191 | 191 |
citation.setDatePublished(year); |
| 192 | 192 |
citation.setTitleCache(lstUpdate.get(6)); |
| 193 | 193 |
//citation. |
| 194 | 194 |
for(TaxonBase taxon : taxa) {
|
| 195 |
String taxonUUID = taxon.getUuid().toString();
|
|
| 195 |
String taxonUUID = taxon.getUuid().toString(); |
|
| 196 | 196 |
//System.out.println(idTaxonToUpdate + "|" + taxonUUID); |
| 197 | 197 |
if(idTaxonToUpdate.equals(taxonUUID)) {
|
| 198 | 198 |
logger.info("Processing Taxn " + taxon.getTitleCache() + " with UUID: " + taxon.getUuid());
|
| 199 | 199 |
if(taxon.isInstanceOf(Synonym.class)) {
|
| 200 | 200 |
Taxon bestCandidate = null; |
| 201 | 201 |
Synonym synonym = CdmBase.deproxy(taxon, Synonym.class); |
| 202 |
Set<Taxon> acceptetdCandidates = synonym.getAcceptedTaxa(); |
|
| 203 |
if(!acceptetdCandidates.isEmpty()){
|
|
| 204 |
bestCandidate = acceptetdCandidates.iterator().next(); |
|
| 205 |
if(acceptetdCandidates.size() == 1){
|
|
| 206 |
logger.info(acceptetdCandidates.size() + " Accepted taxa found for synonym " + taxon.getTitleCache() + ", using first one: " + bestCandidate.getTitleCache()); |
|
| 207 |
Set<TaxonDescription> taxonDescriptions = bestCandidate.getDescriptions(); |
|
| 208 |
if(!taxonDescriptions.isEmpty()) {
|
|
| 209 |
TaxonDescription firstDescription = taxonDescriptions.iterator().next(); |
|
| 210 |
//newUseSummary.addSource(null, null, citation, null); |
|
| 211 |
//firstDescription.addElement(newUseSummary); |
|
| 212 |
} |
|
| 213 |
else {
|
|
| 214 |
logger.warn("No description container for: " + bestCandidate.getName());
|
|
| 215 |
|
|
| 216 |
} |
|
| 217 |
} else {
|
|
| 218 |
logger.info("using accepted Taxon " + bestCandidate.getTitleCache() + "for synonym " + taxon.getTitleCache());
|
|
| 219 |
//List<DescriptionElementBase> descriptionElements = descService.getDescriptionElementsForTaxon((Taxon) bestCandidate, null, null, null, null, null); |
|
| 220 |
Set<TaxonDescription> taxonDescriptions = bestCandidate.getDescriptions(); |
|
| 221 |
if(!taxonDescriptions.isEmpty()) {
|
|
| 222 |
TaxonDescription firstDescription = taxonDescriptions.iterator().next(); |
|
| 223 |
//newUseSummary.addSource(null, null, citation, null); |
|
| 224 |
//firstDescription.addElement(newUseSummary); |
|
| 225 |
} |
|
| 226 |
else {
|
|
| 227 |
logger.warn("No description container for: " + bestCandidate.getName());
|
|
| 228 |
|
|
| 229 |
} |
|
| 202 |
Taxon acceptetdTaxon = synonym.getAcceptedTaxon(); |
|
| 203 |
if(acceptetdTaxon != null){
|
|
| 204 |
Set<TaxonDescription> taxonDescriptions = acceptetdTaxon.getDescriptions(); |
|
| 205 |
if(!taxonDescriptions.isEmpty()) {
|
|
| 206 |
TaxonDescription firstDescription = taxonDescriptions.iterator().next(); |
|
| 207 |
//newUseSummary.addSource(null, null, citation, null); |
|
| 208 |
//firstDescription.addElement(newUseSummary); |
|
| 209 |
} |
|
| 210 |
else {
|
|
| 211 |
logger.warn("No description container for: " + acceptetdTaxon.getName());
|
|
| 230 | 212 |
} |
| 231 | 213 |
} |
| 232 | 214 |
} |
| ... | ... | |
| 243 | 225 |
}*/ |
| 244 | 226 |
taxonAccepted.addDescription(newUseDescription); |
| 245 | 227 |
service.saveOrUpdate(taxonAccepted); |
| 246 |
|
|
| 228 |
|
|
| 247 | 229 |
} |
| 248 | 230 |
} |
| 249 | 231 |
} |
| 250 |
|
|
| 232 |
|
|
| 251 | 233 |
} |
| 252 | 234 |
conversation.commit(false); |
| 253 |
|
|
| 235 |
|
|
| 254 | 236 |
} catch (IOException e) {
|
| 255 | 237 |
success = false; |
| 256 | 238 |
e.printStackTrace(); |
| ... | ... | |
| 259 | 241 |
return success; |
| 260 | 242 |
|
| 261 | 243 |
} |
| 262 |
|
|
| 244 |
|
|
| 263 | 245 |
private boolean loadUses() throws InvalidFormatException {
|
| 264 | 246 |
boolean success = true; |
| 265 | 247 |
//String xslUseSummaryPathString = "C://workspace//Matched_UseSummary_referenceIdTaxEd_TaxonName.xls"; |
| 266 | 248 |
//String xslUseSummaryPathString = "C://workspace//testUseSummaries.xls"; |
| 267 |
|
|
| 268 |
|
|
| 249 |
|
|
| 250 |
|
|
| 269 | 251 |
String xslUseSummaryPathString = "//Users//alextheys//Projects//CDM_Trunk//Palm_Use_Data_Extension//CDMLib-apps//cdmlib-apps//UseImport//src//main//resources//Matched_UseSummary_referenceIdTaxEd_TaxonName.xls"; |
| 270 |
|
|
| 252 |
|
|
| 271 | 253 |
//String xslUseRecordPathString = "C://workspace//UseRecordTerms_UseSummaryId.xls"; |
| 272 | 254 |
//String xslUseRecordPathString = "C://workspace//testUseRecords.xls"; |
| 273 | 255 |
//String xslUseRecordPathString = "C://workspace//test_useRecord.xls"; |
| 274 | 256 |
String xslUseRecordPathString = "//Users//alextheys//Projects//CDM_Trunk//Palm_Use_Data_Extension//CDMLib-apps//cdmlib-apps//UseImport//src//main//resources//UseRecordTerms_UseSummaryId.xls"; |
| 275 |
|
|
| 257 |
|
|
| 276 | 258 |
InputStream inputStream = null; |
| 277 |
|
|
| 278 |
|
|
| 259 |
|
|
| 260 |
|
|
| 279 | 261 |
CdmApplicationController applicationController = CdmApplicationController.NewInstance(dataSource()); |
| 280 | 262 |
ConversationHolder conversation = applicationController.NewConversation(); |
| 281 | 263 |
conversation.startTransaction(); |
| 282 |
|
|
| 264 |
|
|
| 283 | 265 |
ITaxonService taxonService = applicationController.getTaxonService(); |
| 284 | 266 |
ITermService termService = applicationController.getTermService(); |
| 285 | 267 |
IDescriptionService descService = applicationController.getDescriptionService(); |
| 286 | 268 |
IReferenceService referenceService = applicationController.getReferenceService(); |
| 287 |
|
|
| 288 |
|
|
| 269 |
|
|
| 270 |
|
|
| 289 | 271 |
ArrayList<ArrayList<String>> lstUseSummaries = loadSpreadsheet(xslUseSummaryPathString); |
| 290 | 272 |
ArrayList<ArrayList<String>> lstUseRecords = loadSpreadsheet(xslUseRecordPathString); |
| 291 |
|
|
| 273 |
|
|
| 292 | 274 |
MarkerType useMarkerType = (MarkerType) termService.find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
|
| 293 | 275 |
Feature featureUseRecord = (Feature) termService.find(UUID.fromString("8125a59d-b4d5-4485-89ea-67306297b599"));
|
| 294 | 276 |
Feature featureUseSummary = (Feature) termService.find(UUID.fromString("6acb0348-c070-4512-a37c-67bcac016279"));
|
| 295 |
Pager<DefinedTermBase> notAvailModPager = (Pager<DefinedTermBase> ) termService.findByTitle(DefinedTerm.class, "N/A", null, null, null, null, null, null);
|
|
| 296 |
Pager<DefinedTermBase> notAvailStatePager = (Pager<DefinedTermBase> ) termService.findByTitle(State.class, "N/A", null, null, null, null, null, null);
|
|
| 277 |
Pager<DefinedTermBase> notAvailModPager = termService.findByTitle(DefinedTerm.class, "N/A", null, null, null, null, null, null); |
|
| 278 |
Pager<DefinedTermBase> notAvailStatePager = termService.findByTitle(State.class, "N/A", null, null, null, null, null, null); |
|
| 297 | 279 |
DefinedTerm notAvailMod = (DefinedTerm) notAvailModPager.getRecords().get(0); |
| 298 | 280 |
State notAvailState = (State) notAvailStatePager.getRecords().get(0); |
| 299 |
|
|
| 281 |
|
|
| 300 | 282 |
int i = 0; |
| 301 | 283 |
int j = 0; |
| 302 | 284 |
try {
|
| ... | ... | |
| 343 | 325 |
stateCatData.putModifyingText(Language.ENGLISH(), "Use Category"); |
| 344 | 326 |
modifyingText += useCategory.toString() + ";"; |
| 345 | 327 |
useRecord.addStateData(stateCatData); |
| 346 |
|
|
| 347 |
|
|
| 328 |
|
|
| 329 |
|
|
| 348 | 330 |
//useRecord.addState(stateData); |
| 349 | 331 |
} else {
|
| 350 | 332 |
State useCategory = notAvailState; |
| ... | ... | |
| 353 | 335 |
stateCatData.putModifyingText(Language.ENGLISH(), "Use Category"); |
| 354 | 336 |
modifyingText += useCategory.toString() + ";"; |
| 355 | 337 |
useRecord.addStateData(stateCatData); |
| 356 |
|
|
| 338 |
|
|
| 357 | 339 |
} |
| 358 |
|
|
| 340 |
|
|
| 359 | 341 |
if(lstUseRecord.get(4) != null && lstUseRecord.get(4).length() > 0) {
|
| 360 | 342 |
Pager<DefinedTermBase> useSubCategoryPager = termService.findByTitle(State.class, lstUseRecord.get(4), null, null, null, null, null, null); |
| 361 | 343 |
State useSubCategory = null; |
| 362 | 344 |
if(useSubCategoryPager.getCount() > 0) {
|
| 363 | 345 |
useSubCategory = (State) useSubCategoryPager.getRecords().get(0); |
| 364 |
|
|
| 346 |
|
|
| 365 | 347 |
} else {
|
| 366 | 348 |
useSubCategory = notAvailState; |
| 367 | 349 |
} |
| ... | ... | |
| 370 | 352 |
stateSubCatData.putModifyingText(Language.ENGLISH(), "Use SubCategory"); |
| 371 | 353 |
modifyingText += useSubCategory.toString() + ";"; |
| 372 | 354 |
useRecord.addStateData(stateSubCatData); |
| 373 |
|
|
| 355 |
|
|
| 374 | 356 |
} |
| 375 | 357 |
else {
|
| 376 | 358 |
State useSubCategory = notAvailState; |
| ... | ... | |
| 379 | 361 |
stateSubCatData.putModifyingText(Language.ENGLISH(), "Use SubCategory"); |
| 380 | 362 |
modifyingText += useSubCategory.toString() + ";"; |
| 381 | 363 |
useRecord.addStateData(stateSubCatData); |
| 382 |
|
|
| 364 |
|
|
| 383 | 365 |
} |
| 384 | 366 |
if(lstUseRecord.get(5) != null && lstUseRecord.get(5).length() > 0) {
|
| 385 | 367 |
Pager<DefinedTermBase> countryPager = termService.findByTitle(DefinedTerm.class, lstUseRecord.get(5), null, null, null, null, null, null); |
| ... | ... | |
| 396 | 378 |
modifyingText += country.toString() + ";"; |
| 397 | 379 |
useRecord.addModifier(country); |
| 398 | 380 |
} |
| 399 |
|
|
| 381 |
|
|
| 400 | 382 |
if(lstUseRecord.get(6) != null && lstUseRecord.get(6).length() > 0) {
|
| 401 | 383 |
Pager<DefinedTermBase> plantPartPager = termService.findByTitle(DefinedTerm.class, lstUseRecord.get(6), null, null, null, null, null, null); |
| 402 | 384 |
DefinedTerm plantPart = null; |
| ... | ... | |
| 448 | 430 |
newUseDescription.addElement(useRecord); |
| 449 | 431 |
} |
| 450 | 432 |
} |
| 451 |
|
|
| 452 |
|
|
| 453 |
|
|
| 433 |
|
|
| 434 |
|
|
| 435 |
|
|
| 454 | 436 |
if (taxon.isInstanceOf(Synonym.class)){
|
| 455 | 437 |
Taxon bestCandidate = null; |
| 456 | 438 |
Synonym synonym = CdmBase.deproxy(taxon, Synonym.class); |
| 457 |
Set<Taxon> acceptetdCandidates = synonym.getAcceptedTaxa(); |
|
| 458 |
if(!acceptetdCandidates.isEmpty()){
|
|
| 459 |
bestCandidate = acceptetdCandidates.iterator().next(); |
|
| 460 |
if(acceptetdCandidates.size() == 1){
|
|
| 461 |
logger.info(acceptetdCandidates.size() + " Accepted taxa found for synonym " + taxon.getTitleCache() + ", using first one: " + bestCandidate.getTitleCache()); |
|
| 462 |
bestCandidate.addDescription(newUseDescription); |
|
| 463 |
taxonService.saveOrUpdate(bestCandidate); |
|
| 464 |
conversation.commit(); |
|
| 465 |
} |
|
| 466 |
else {
|
|
| 467 |
logger.info("using accepted Taxon " + bestCandidate.getTitleCache() + "for synonym " + taxon.getTitleCache());
|
|
| 468 |
bestCandidate.addDescription(newUseDescription); |
|
| 469 |
taxonService.saveOrUpdate(bestCandidate); |
|
| 470 |
conversation.commit(); |
|
| 471 |
} |
|
| 439 |
Taxon acceptedTaxon = synonym.getAcceptedTaxon(); |
|
| 440 |
if(acceptedTaxon != null){
|
|
| 441 |
acceptedTaxon.addDescription(newUseDescription); |
|
| 442 |
taxonService.saveOrUpdate(bestCandidate); |
|
| 443 |
conversation.commit(); |
|
| 472 | 444 |
} |
| 473 | 445 |
} else {
|
| 474 | 446 |
Taxon taxonAccepted = (Taxon) taxon; |
| ... | ... | |
| 481 | 453 |
System.out.println("Processing UseSummary#: " + i + " ID:" + lstUseSummary.get(0));
|
| 482 | 454 |
} |
| 483 | 455 |
} |
| 484 |
|
|
| 456 |
|
|
| 485 | 457 |
conversation.close(); |
| 486 | 458 |
applicationController.close(); |
| 487 |
|
|
| 459 |
|
|
| 488 | 460 |
} catch (Exception e) {
|
| 489 | 461 |
success = false; |
| 490 | 462 |
e.printStackTrace(); |
| 491 | 463 |
} |
| 492 | 464 |
return success; |
| 493 |
|
|
| 465 |
|
|
| 494 | 466 |
} |
| 495 |
|
|
| 467 |
|
|
| 496 | 468 |
//Completed and tested! |
| 497 | 469 |
private boolean loadTerms() throws InvalidFormatException {
|
| 498 | 470 |
boolean success = true; |
| 499 |
|
|
| 471 |
|
|
| 500 | 472 |
//String xslPathString = "C://workspace//terms.xls"; |
| 501 | 473 |
String xslPathString = "//Users//alextheys//Projects//CDM_Trunk//Palm_Use_Data_Extension//CDMLib-apps//cdmlib-apps//UseImport//src//main//resources//terms.xls"; |
| 502 |
|
|
| 474 |
|
|
| 503 | 475 |
CdmApplicationController applicationController = CdmApplicationController.NewInstance(dataSource()); |
| 504 | 476 |
ConversationHolder conversation = applicationController.NewConversation(); |
| 505 | 477 |
conversation.startTransaction(); |
| 506 |
|
|
| 478 |
|
|
| 507 | 479 |
ITaxonService service = applicationController.getTaxonService(); |
| 508 | 480 |
ITermService termService = applicationController.getTermService(); |
| 509 | 481 |
IVocabularyService vocabularyService = applicationController.getVocabularyService(); |
| 510 |
IReferenceService referenceService = applicationController.getReferenceService();
|
|
| 511 |
|
|
| 512 |
TermVocabulary<State> stateVocabulary = (TermVocabulary<State>) vocabularyService.find(UUID.fromString("67430d7c-fd43-4e9d-af5e-d0dca3f74931"));
|
|
| 513 |
TermVocabulary<DefinedTermBase<?>> countryVocabulary = (TermVocabulary<DefinedTermBase<?>>) vocabularyService.find(UUID.fromString("116c51f1-e63a-46f7-a258-e1149a42868b"));
|
|
| 514 |
TermVocabulary<DefinedTerm> plantPartVocabulary = (TermVocabulary<DefinedTerm>) vocabularyService.find(UUID.fromString("369914fe-d54b-4063-99ce-abc81d30ad35"));
|
|
| 515 |
TermVocabulary<DefinedTerm> humanGroupVocabulary = (TermVocabulary<DefinedTerm>) vocabularyService.find(UUID.fromString("ca46cea5-bdf7-438d-9cd8-e2793d2178dc"));
|
|
| 516 |
|
|
| 482 |
IReferenceService referenceService = applicationController.getReferenceService(); |
|
| 483 |
|
|
| 484 |
TermVocabulary<State> stateVocabulary = vocabularyService.find(UUID.fromString("67430d7c-fd43-4e9d-af5e-d0dca3f74931"));
|
|
| 485 |
TermVocabulary<DefinedTermBase<?>> countryVocabulary = vocabularyService.find(UUID.fromString("116c51f1-e63a-46f7-a258-e1149a42868b"));
|
|
| 486 |
TermVocabulary<DefinedTerm> plantPartVocabulary = vocabularyService.find(UUID.fromString("369914fe-d54b-4063-99ce-abc81d30ad35"));
|
|
| 487 |
TermVocabulary<DefinedTerm> humanGroupVocabulary = vocabularyService.find(UUID.fromString("ca46cea5-bdf7-438d-9cd8-e2793d2178dc"));
|
|
| 488 |
|
|
| 517 | 489 |
IDescriptionService descService = applicationController.getDescriptionService(); |
| 518 | 490 |
InputStream inputStream = null; |
| 519 |
|
|
| 491 |
|
|
| 520 | 492 |
try {
|
| 521 | 493 |
inputStream = new FileInputStream(xslPathString); |
| 522 | 494 |
|
| ... | ... | |
| 547 | 519 |
ArrayList<String> lstTerms = new ArrayList<String>(); |
| 548 | 520 |
while (cells.hasNext()) {
|
| 549 | 521 |
Cell cell = cells.next(); |
| 550 |
|
|
| 522 |
|
|
| 551 | 523 |
int intCellType = cell.getCellType(); |
| 552 | 524 |
switch (intCellType) {
|
| 553 | 525 |
case 0: |
| 554 |
int cellValue = (int) cell.getNumericCellValue();
|
|
| 526 |
int cellValue = (int) cell.getNumericCellValue(); |
|
| 555 | 527 |
lstTerms.add(Integer.toString(cellValue)); |
| 556 | 528 |
break; |
| 557 | 529 |
case 1: |
| ... | ... | |
| 560 | 532 |
} |
| 561 | 533 |
} |
| 562 | 534 |
lstUpdates.add(lstTerms); |
| 563 |
//lstTaxonIDs.add(Integer.parseInt(lstTaxon.get(0)));
|
|
| 535 |
//lstTaxonIDs.add(Integer.parseInt(lstTaxon.get(0))); |
|
| 564 | 536 |
} |
| 565 | 537 |
for (ArrayList<String> lstUpdate : lstUpdates) {
|
| 566 |
int termType = Integer.parseInt(lstUpdate.get(0));
|
|
| 538 |
int termType = Integer.parseInt(lstUpdate.get(0)); |
|
| 567 | 539 |
switch (termType) {
|
| 568 | 540 |
//Case 0 = UseCategory |
| 569 | 541 |
case 0: |
| ... | ... | |
| 642 | 614 |
} |
| 643 | 615 |
conversation.commit(true); |
| 644 | 616 |
break; |
| 645 |
|
|
| 617 |
|
|
| 646 | 618 |
} |
| 647 | 619 |
} |
| 648 |
conversation.close();
|
|
| 620 |
conversation.close(); |
|
| 649 | 621 |
applicationController.close(); |
| 650 |
|
|
| 622 |
|
|
| 651 | 623 |
} catch (IOException e) {
|
| 652 | 624 |
success = false; |
| 653 | 625 |
e.printStackTrace(); |
| 654 | 626 |
} |
| 655 | 627 |
return success; |
| 656 |
|
|
| 628 |
|
|
| 657 | 629 |
} |
| 658 |
|
|
| 630 |
|
|
| 659 | 631 |
private ArrayList<ArrayList<String>> loadSpreadsheet(String xslPathString) throws InvalidFormatException {
|
| 660 | 632 |
ArrayList<ArrayList<String>> lstUpdates = new ArrayList<ArrayList<String>>(); |
| 661 | 633 |
InputStream inputStream = null; |
| 662 |
|
|
| 634 |
|
|
| 663 | 635 |
try {
|
| 664 | 636 |
inputStream = new FileInputStream(xslPathString); |
| 665 | 637 |
|
| ... | ... | |
| 689 | 661 |
ArrayList<String> lstTerms = new ArrayList<String>(); |
| 690 | 662 |
while (cells.hasNext()) {
|
| 691 | 663 |
Cell cell = cells.next(); |
| 692 |
|
|
| 664 |
|
|
| 693 | 665 |
int intCellType = cell.getCellType(); |
| 694 | 666 |
switch (intCellType) {
|
| 695 | 667 |
case 0: |
| 696 |
int cellValue = (int) cell.getNumericCellValue();
|
|
| 668 |
int cellValue = (int) cell.getNumericCellValue(); |
|
| 697 | 669 |
lstTerms.add(Integer.toString(cellValue)); |
| 698 | 670 |
break; |
| 699 | 671 |
case 1: |
| ... | ... | |
| 702 | 674 |
} |
| 703 | 675 |
} |
| 704 | 676 |
lstUpdates.add(lstTerms); |
| 705 |
//lstTaxonIDs.add(Integer.parseInt(lstTaxon.get(0)));
|
|
| 677 |
//lstTaxonIDs.add(Integer.parseInt(lstTaxon.get(0))); |
|
| 706 | 678 |
} |
| 707 | 679 |
} catch (IOException e) {
|
| 708 | 680 |
e.printStackTrace(); |
| 709 | 681 |
} |
| 710 | 682 |
return lstUpdates; |
| 711 | 683 |
} |
| 712 |
|
|
| 713 |
|
|
| 684 |
|
|
| 685 |
|
|
| 714 | 686 |
private boolean setupNecessaryItems() {
|
| 715 | 687 |
boolean success = false; |
| 716 | 688 |
CdmApplicationController applicationController = CdmApplicationController.NewInstance(dataSource()); |
| 717 | 689 |
ConversationHolder conversation = applicationController.NewConversation(); |
| 718 |
|
|
| 719 |
|
|
| 690 |
|
|
| 691 |
|
|
| 720 | 692 |
ITaxonService service = applicationController.getTaxonService(); |
| 721 | 693 |
ITermService termService = applicationController.getTermService(); |
| 722 | 694 |
IVocabularyService vocabularyService = applicationController.getVocabularyService(); |
| 723 | 695 |
IFeatureTreeService featureTreeService = applicationController.getFeatureTreeService(); |
| 724 |
|
|
| 696 |
|
|
| 725 | 697 |
MarkerType existingMarkertype = (MarkerType)termService.find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
|
| 726 | 698 |
Feature featureUseRecord = (Feature) termService.find(UUID.fromString("8125a59d-b4d5-4485-89ea-67306297b599"));
|
| 727 | 699 |
Feature featureUseSummary = (Feature) termService.find(UUID.fromString("6acb0348-c070-4512-a37c-67bcac016279"));
|
| 728 |
TermVocabulary<State> stateVocabulary = (TermVocabulary<State>) vocabularyService.find(UUID.fromString("67430d7c-fd43-4e9d-af5e-d0dca3f74931"));
|
|
| 729 |
TermVocabulary<DefinedTerm> countryVocabulary = (TermVocabulary<DefinedTerm>) vocabularyService.find(UUID.fromString("116c51f1-e63a-46f7-a258-e1149a42868b"));
|
|
| 730 |
TermVocabulary<DefinedTerm> plantPartVocabulary = (TermVocabulary<DefinedTerm>) vocabularyService.find(UUID.fromString("369914fe-d54b-4063-99ce-abc81d30ad35"));
|
|
| 731 |
TermVocabulary<DefinedTerm> humanGroupVocabulary = (TermVocabulary<DefinedTerm>) vocabularyService.find(UUID.fromString("ca46cea5-bdf7-438d-9cd8-e2793d2178dc"));
|
|
| 732 |
Pager<DefinedTermBase> notAvailModPager = (Pager<DefinedTermBase> ) termService.findByTitle(DefinedTerm.class, "N/A", null, null, null, null, null, null);
|
|
| 733 |
Pager<DefinedTermBase> notAvailStatePager = (Pager<DefinedTermBase> ) termService.findByTitle(State.class, "N/A", null, null, null, null, null, null);
|
|
| 734 |
|
|
| 700 |
TermVocabulary<State> stateVocabulary = vocabularyService.find(UUID.fromString("67430d7c-fd43-4e9d-af5e-d0dca3f74931"));
|
|
| 701 |
TermVocabulary<DefinedTerm> countryVocabulary = vocabularyService.find(UUID.fromString("116c51f1-e63a-46f7-a258-e1149a42868b"));
|
|
| 702 |
TermVocabulary<DefinedTerm> plantPartVocabulary = vocabularyService.find(UUID.fromString("369914fe-d54b-4063-99ce-abc81d30ad35"));
|
|
| 703 |
TermVocabulary<DefinedTerm> humanGroupVocabulary = vocabularyService.find(UUID.fromString("ca46cea5-bdf7-438d-9cd8-e2793d2178dc"));
|
|
| 704 |
Pager<DefinedTermBase> notAvailModPager = termService.findByTitle(DefinedTerm.class, "N/A", null, null, null, null, null, null); |
|
| 705 |
Pager<DefinedTermBase> notAvailStatePager = termService.findByTitle(State.class, "N/A", null, null, null, null, null, null); |
|
| 706 |
|
|
| 735 | 707 |
conversation.startTransaction(); |
| 736 | 708 |
if (existingMarkertype == null) {
|
| 737 | 709 |
existingMarkertype = MarkerType.NewInstance("use", "use", null);
|
| 738 | 710 |
existingMarkertype.setUuid( UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
|
| 739 |
TermVocabulary<MarkerType> markerTypeVocabulary = (TermVocabulary<MarkerType>)vocabularyService.find((UUID.fromString("19dffff7-e142-429c-a420-5d28e4ebe305")));
|
|
| 711 |
TermVocabulary<MarkerType> markerTypeVocabulary = vocabularyService.find((UUID.fromString("19dffff7-e142-429c-a420-5d28e4ebe305")));
|
|
| 740 | 712 |
markerTypeVocabulary.addTerm(existingMarkertype); |
| 741 | 713 |
vocabularyService.saveOrUpdate(markerTypeVocabulary); |
| 742 | 714 |
conversation.commit(true); |
| 743 | 715 |
} |
| 744 | 716 |
if (stateVocabulary == null) {
|
| 745 |
|
|
| 717 |
|
|
| 746 | 718 |
URI termSourceUri = null; |
| 747 | 719 |
try {
|
| 748 | 720 |
termSourceUri = new URI("eu.etaxonomy.cdm.model.description.State");
|
| ... | ... | |
| 792 | 764 |
conversation.commit(true); |
| 793 | 765 |
} |
| 794 | 766 |
if(featureUseRecord == null|| featureUseSummary == null) {
|
| 795 |
TermVocabulary<Feature> featureVocabulary = (TermVocabulary<Feature>)vocabularyService.find((UUID.fromString("b187d555-f06f-4d65-9e53-da7c93f8eaa8")));
|
|
| 767 |
TermVocabulary<Feature> featureVocabulary = vocabularyService.find((UUID.fromString("b187d555-f06f-4d65-9e53-da7c93f8eaa8")));
|
|
| 796 | 768 |
FeatureTree palmWebFeatureTree = featureTreeService.find(UUID.fromString("72ccce05-7cc8-4dab-8e47-bf3f5fd848a0"));
|
| 797 | 769 |
//List<FeatureTree> featureTrees = CdmStore.getService(IFeatureTreeService.class).list(FeatureTree.class, null, null, null, null); |
| 798 |
|
|
| 770 |
|
|
| 799 | 771 |
if (featureUseRecord == null ) {
|
| 800 | 772 |
featureUseRecord = Feature.NewInstance("Use Record", "Use Record", null);
|
| 801 | 773 |
featureUseRecord.setUuid(UUID.fromString("8125a59d-b4d5-4485-89ea-67306297b599"));
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelImportConfigurator.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 |
*/ |
| ... | ... | |
| 13 | 13 |
import java.lang.reflect.Method; |
| 14 | 14 |
import java.net.MalformedURLException; |
| 15 | 15 |
import java.net.URL; |
| 16 |
import java.util.HashSet; |
|
| 17 |
import java.util.Set; |
|
| 18 | 16 |
|
| 19 | 17 |
import org.apache.log4j.Logger; |
| 20 | 18 |
|
| ... | ... | |
| 26 | 24 |
import eu.etaxonomy.cdm.io.common.Source; |
| 27 | 25 |
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
| 28 | 26 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 29 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
|
| 30 | 27 |
|
| 31 | 28 |
/** |
| 32 | 29 |
* @author a.mueller |
| 33 | 30 |
* @created 20.03.2008 |
| 34 | 31 |
*/ |
| 35 | 32 |
public class BerlinModelImportConfigurator extends DbImportConfiguratorBase<BerlinModelImportState> implements IImportConfigurator{
|
| 36 |
private static Logger logger = Logger.getLogger(BerlinModelImportConfigurator.class); |
|
| 33 |
private static final long serialVersionUID = 70300913255425256L; |
|
| 34 |
|
|
| 35 |
private static Logger logger = Logger.getLogger(BerlinModelImportConfigurator.class); |
|
| 37 | 36 |
|
| 38 | 37 |
public static BerlinModelImportConfigurator NewInstance(Source berlinModelSource, ICdmDataSource destination){
|
| 39 | 38 |
return new BerlinModelImportConfigurator(berlinModelSource, destination); |
| 40 | 39 |
} |
| 41 | 40 |
|
| 42 | 41 |
private PublishMarkerChooser taxonPublishMarker = PublishMarkerChooser.ALL; |
| 43 |
|
|
| 42 |
|
|
| 44 | 43 |
//TODO |
| 45 | 44 |
private static IInputTransformer defaultTransformer = null; |
| 46 |
|
|
| 45 |
|
|
| 47 | 46 |
private boolean doNameStatus = true; |
| 48 | 47 |
private boolean doRelNames = true; |
| 49 | 48 |
private boolean doCommonNames = true; |
| ... | ... | |
| 56 | 55 |
private DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
| 57 | 56 |
private boolean doTaxonNames = true; |
| 58 | 57 |
private boolean doTypes = true; |
| 59 |
|
|
| 58 |
|
|
| 60 | 59 |
//taxa |
| 61 | 60 |
private boolean doTaxa = true; |
| 62 | 61 |
private boolean doRelTaxa = true; |
| ... | ... | |
| 64 | 63 |
private boolean useSingleClassification = false; |
| 65 | 64 |
private boolean includeFlatClassifications = false; //concepts with no taxon relationship (even no misapplied name or synonym rel) |
| 66 | 65 |
private boolean includeAllNonMisappliedRelatedClassifications = true; //all concepts with any relationship except for misapplied name relationships |
| 67 |
|
|
| 66 |
|
|
| 68 | 67 |
//occurrences |
| 69 | 68 |
private boolean isSplitTdwgCodes = true; |
| 70 |
|
|
| 69 |
|
|
| 71 | 70 |
private boolean useEmAreaVocabulary = false; |
| 72 | 71 |
|
| 73 | 72 |
private boolean includesEmCode = true; // in Campanula we do not have an EMCOde |
| 74 |
private boolean allowInfraSpecTaxonRank = true;
|
|
| 73 |
private boolean allowInfraSpecTaxonRank = true; |
|
| 75 | 74 |
|
| 76 | 75 |
private Method namerelationshipTypeMethod; |
| 77 | 76 |
private Method uuidForDefTermMethod; |
| 78 | 77 |
private Method nameTypeDesignationStatusMethod; |
| 79 |
|
|
| 80 |
private Set<Synonym> proParteSynonyms = new HashSet<Synonym>(); |
|
| 81 |
private Set<Synonym> partialSynonyms = new HashSet<Synonym>(); |
|
| 82 |
|
|
| 78 |
|
|
| 83 | 79 |
// NameFact stuff |
| 84 | 80 |
private URL mediaUrl; |
| 85 | 81 |
private File mediaPath; |
| ... | ... | |
| 87 | 83 |
private boolean isIgnore0AuthorTeam = false; |
| 88 | 84 |
|
| 89 | 85 |
private boolean switchSpeciesGroup = false; |
| 90 |
|
|
| 86 |
|
|
| 91 | 87 |
//Term labels |
| 92 | 88 |
private String infrGenericRankAbbrev = null; |
| 93 | 89 |
private String infrSpecificRankAbbrev = null; |
| 94 |
|
|
| 90 |
|
|
| 95 | 91 |
private boolean removeHttpMapsAnchor = false; |
| 96 |
|
|
| 92 |
|
|
| 97 | 93 |
//Data Filter |
| 98 | 94 |
|
| 99 | 95 |
private String taxonTable = "PTaxon"; |
| ... | ... | |
| 109 | 105 |
private String occurrenceFilter = null; |
| 110 | 106 |
private String occurrenceSourceFilter = null; |
| 111 | 107 |
private String webMarkerFilter = null; |
| 112 |
|
|
| 108 |
|
|
| 113 | 109 |
//specific functions |
| 114 | 110 |
private Method makeUrlForTaxon = null; |
| 115 | 111 |
|
| 116 |
protected void makeIoClassList(){
|
|
| 112 |
@Override |
|
| 113 |
protected void makeIoClassList(){
|
|
| 117 | 114 |
ioClassList = new Class[]{
|
| 118 | 115 |
BerlinModelGeneralImportValidator.class |
| 119 | 116 |
, BerlinModelUserImport.class |
| ... | ... | |
| 134 | 131 |
, BerlinModelOccurrenceSourceImport.class |
| 135 | 132 |
, BerlinModelWebMarkerCategoryImport.class |
| 136 | 133 |
, BerlinModelWebMarkerImport.class |
| 137 |
};
|
|
| 134 |
}; |
|
| 138 | 135 |
} |
| 139 |
|
|
| 140 |
|
|
| 141 |
|
|
| 136 |
|
|
| 137 |
|
|
| 138 |
|
|
| 142 | 139 |
/* (non-Javadoc) |
| 143 | 140 |
* @see eu.etaxonomy.cdm.io.common.IImportConfigurator#getNewState() |
| 144 | 141 |
*/ |
| 145 |
public BerlinModelImportState getNewState() {
|
|
| 142 |
@Override |
|
| 143 |
public BerlinModelImportState getNewState() {
|
|
| 146 | 144 |
return new BerlinModelImportState(this); |
| 147 | 145 |
} |
| 148 | 146 |
|
| ... | ... | |
| 156 | 154 |
protected BerlinModelImportConfigurator(Source berlinModelSource, ICdmDataSource destination) {
|
| 157 | 155 |
super(berlinModelSource, destination, NomenclaturalCode.ICNAFP, defaultTransformer); //default for Berlin Model |
| 158 | 156 |
} |
| 159 |
|
|
| 160 |
|
|
| 157 |
|
|
| 158 |
|
|
| 161 | 159 |
/** |
| 162 | 160 |
* Import name relationships yes/no?. |
| 163 | 161 |
* @return |
| ... | ... | |
| 168 | 166 |
public void setDoRelNames(boolean doRelNames) {
|
| 169 | 167 |
this.doRelNames = doRelNames; |
| 170 | 168 |
} |
| 171 |
|
|
| 172 |
|
|
| 173 |
|
|
| 174 |
protected void addProParteSynonym(Synonym proParteSynonym){
|
|
| 175 |
this.proParteSynonyms.add(proParteSynonym); |
|
| 176 |
} |
|
| 177 |
|
|
| 178 |
protected boolean isProParteSynonym(Synonym synonym){
|
|
| 179 |
return this.proParteSynonyms.contains(synonym); |
|
| 180 |
} |
|
| 181 |
|
|
| 182 |
protected void addPartialSynonym(Synonym partialSynonym){
|
|
| 183 |
this.partialSynonyms.add(partialSynonym); |
|
| 184 |
} |
|
| 185 |
|
|
| 186 |
protected boolean isPartialSynonym(Synonym synonym){
|
|
| 187 |
return this.partialSynonyms.contains(synonym); |
|
| 188 |
} |
|
| 189 | 169 |
|
| 190 | 170 |
/** |
| 191 | 171 |
* @return the mediaUrl |
| ... | ... | |
| 214 | 194 |
public void setMediaPath(File mediaPath) {
|
| 215 | 195 |
this.mediaPath = mediaPath; |
| 216 | 196 |
} |
| 217 |
|
|
| 197 |
|
|
| 218 | 198 |
public void setMediaPath(String mediaPathString){
|
| 219 | 199 |
this.mediaPath = new File(mediaPathString); |
| 220 | 200 |
} |
| ... | ... | |
| 236 | 216 |
|
| 237 | 217 |
/** |
| 238 | 218 |
* set to 0 for unlimited |
| 239 |
*
|
|
| 219 |
* |
|
| 240 | 220 |
* @param maximumNumberOfNameFacts the maximumNumberOfNameFacts to set |
| 241 | 221 |
*/ |
| 242 | 222 |
public void setMaximumNumberOfNameFacts(int maximumNumberOfNameFacts) {
|
| ... | ... | |
| 271 | 251 |
public void setNamerelationshipTypeMethod(Method namerelationshipTypeMethod) {
|
| 272 | 252 |
this.namerelationshipTypeMethod = namerelationshipTypeMethod; |
| 273 | 253 |
} |
| 274 |
|
|
| 254 |
|
|
| 275 | 255 |
/** |
| 276 | 256 |
* @return the taxonPublishMarker |
| 277 | 257 |
*/ |
| ... | ... | |
| 321 | 301 |
Method nameTypeDesignationStatusMethod) {
|
| 322 | 302 |
this.nameTypeDesignationStatusMethod = nameTypeDesignationStatusMethod; |
| 323 | 303 |
} |
| 324 |
|
|
| 304 |
|
|
| 325 | 305 |
public boolean isDoNameStatus() {
|
| 326 | 306 |
return doNameStatus; |
| 327 | 307 |
} |
| 328 | 308 |
public void setDoNameStatus(boolean doNameStatus) {
|
| 329 | 309 |
this.doNameStatus = doNameStatus; |
| 330 | 310 |
} |
| 331 |
|
|
| 332 |
|
|
| 311 |
|
|
| 312 |
|
|
| 333 | 313 |
public boolean isDoCommonNames() {
|
| 334 | 314 |
return doCommonNames; |
| 335 | 315 |
} |
| ... | ... | |
| 340 | 320 |
*/ |
| 341 | 321 |
public void setDoCommonNames(boolean doCommonNames) {
|
| 342 | 322 |
this.doCommonNames = doCommonNames; |
| 343 |
|
|
| 323 |
|
|
| 344 | 324 |
} |
| 345 |
|
|
| 325 |
|
|
| 346 | 326 |
public boolean isDoFacts() {
|
| 347 | 327 |
return doFacts; |
| 348 | 328 |
} |
| ... | ... | |
| 350 | 330 |
this.doFacts = doFacts; |
| 351 | 331 |
} |
| 352 | 332 |
|
| 353 |
|
|
| 333 |
|
|
| 354 | 334 |
public boolean isDoOccurrence() {
|
| 355 | 335 |
return doOccurrence; |
| 356 | 336 |
} |
| ... | ... | |
| 373 | 353 |
public void setDoUser(boolean doUser) {
|
| 374 | 354 |
this.doUser = doUser; |
| 375 | 355 |
} |
| 376 |
|
|
| 356 |
|
|
| 377 | 357 |
public boolean isDoNameFacts() {
|
| 378 | 358 |
return doNameFacts; |
| 379 | 359 |
} |
| 380 | 360 |
public void setDoNameFacts(boolean doNameFacts) {
|
| 381 | 361 |
this.doNameFacts = doNameFacts; |
| 382 | 362 |
} |
| 383 |
|
|
| 363 |
|
|
| 384 | 364 |
public boolean isDoAuthors() {
|
| 385 | 365 |
return doAuthors; |
| 386 | 366 |
} |
| ... | ... | |
| 394 | 374 |
public void setDoReferences(DO_REFERENCES doReferences) {
|
| 395 | 375 |
this.doReferences = doReferences; |
| 396 | 376 |
} |
| 397 |
|
|
| 377 |
|
|
| 398 | 378 |
public boolean isDoTaxonNames() {
|
| 399 | 379 |
return doTaxonNames; |
| 400 | 380 |
} |
| ... | ... | |
| 484 | 464 |
public String getFactFilter() {
|
| 485 | 465 |
return factFilter; |
| 486 | 466 |
} |
| 487 |
|
|
| 467 |
|
|
| 488 | 468 |
public void setRefDetailFilter(String refDetailFilter) {
|
| 489 | 469 |
this.refDetailFilter = refDetailFilter; |
| 490 | 470 |
} |
| ... | ... | |
| 620 | 600 |
} |
| 621 | 601 |
public void setIncludesEmCode(boolean includesEmCode) {
|
| 622 | 602 |
this.includesEmCode = includesEmCode; |
| 623 |
|
|
| 603 |
|
|
| 624 | 604 |
} |
| 625 | 605 |
|
| 626 | 606 |
|
| ... | ... | |
| 639 | 619 |
this.includeAllNonMisappliedRelatedClassifications = includeAllNonMisappliedRelatedClassifications; |
| 640 | 620 |
} |
| 641 | 621 |
|
| 642 |
|
|
| 622 |
|
|
| 643 | 623 |
public boolean isUseEmAreaVocabulary() {
|
| 644 | 624 |
return useEmAreaVocabulary; |
| 645 | 625 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonImport.java | ||
|---|---|---|
| 186 | 186 |
synonym = Synonym.NewInstance(taxonName, reference); |
| 187 | 187 |
taxonBase = synonym; |
| 188 | 188 |
if (statusFk == T_STATUS_PRO_PARTE_SYN){
|
| 189 |
config.addProParteSynonym(synonym);
|
|
| 189 |
synonym.setProParte(true);
|
|
| 190 | 190 |
} |
| 191 | 191 |
if (statusFk == T_STATUS_PARTIAL_SYN){
|
| 192 |
config.addPartialSynonym(synonym);
|
|
| 192 |
synonym.setPartial(true);
|
|
| 193 | 193 |
} |
| 194 | 194 |
}else{
|
| 195 | 195 |
logger.warn("TaxonStatus " + statusFk + " not yet implemented. Taxon (RIdentifier = " + taxonId + ") left out.");
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonRelationImport.java | ||
|---|---|---|
| 46 | 46 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 47 | 47 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 48 | 48 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 49 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationship; |
|
| 50 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
|
| 49 |
import eu.etaxonomy.cdm.model.taxon.SynonymType; |
|
| 51 | 50 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 52 | 51 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 53 | 52 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
| ... | ... | |
| 299 | 298 |
} |
| 300 | 299 |
handleAllRelatedTaxa(state, toTaxon, classificationMap, treeRefFk); |
| 301 | 300 |
Synonym synonym = (Synonym)taxon1; |
| 302 |
SynonymRelationship synRel = getSynRel(relQualifierFk, toTaxon, synonym, citation, microcitation); |
|
| 303 |
taxonRelationship = synRel; |
|
| 301 |
makeSynRel(relQualifierFk, toTaxon, synonym, citation, microcitation); |
|
| 302 |
if (isNotBlank(notes)){
|
|
| 303 |
logger.warn("Notes for synonym relationship or unknown taxon relationship not handled");
|
|
| 304 |
} |
|
| 304 | 305 |
|
| 305 | 306 |
if (relQualifierFk == TAX_REL_IS_SYNONYM_OF || |
| 306 | 307 |
relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF || |
| 307 | 308 |
relQualifierFk == TAX_REL_IS_HETEROTYPIC_SYNONYM_OF){
|
| 308 |
addProParteAndPartial(synRel, synonym, config);
|
|
| 309 |
//pro parte already set by taxon mapping
|
|
| 309 | 310 |
}else if (relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF || |
| 310 | 311 |
relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF || |
| 311 | 312 |
relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF ){
|
| 312 |
synRel.setProParte(true);
|
|
| 313 |
synonym.setProParte(true);
|
|
| 313 | 314 |
}else if(relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF || |
| 314 | 315 |
relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF || |
| 315 | 316 |
relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF ){
|
| 316 |
synRel.setPartial(true);
|
|
| 317 |
synonym.setPartial(true);
|
|
| 317 | 318 |
}else{
|
| 318 | 319 |
success = false; |
| 319 | 320 |
logger.warn("Proparte/Partial not yet implemented for TaxonRelationShipType " + relQualifierFk);
|
| ... | ... | |
| 343 | 344 |
} |
| 344 | 345 |
} catch (UnknownCdmTypeException e) {
|
| 345 | 346 |
logger.warn("TaxonRelationShipType " + relQualifierFk + " (conceptRelationship) not yet implemented");
|
| 346 |
success = false; |
|
| 347 |
success = false;
|
|
| 347 | 348 |
} |
| 348 | 349 |
}else {
|
| 349 | 350 |
logger.warn("TaxonRelationShipType " + relQualifierFk + " not yet implemented: RelPTaxonId = " + relPTaxonId );
|
| 350 | 351 |
success = false; |
| 351 | 352 |
} |
| 352 | 353 |
|
| 353 |
doNotes(taxonRelationship, notes); |
|
| 354 |
if (taxonRelationship != null){
|
|
| 355 |
doNotes(taxonRelationship, notes); |
|
| 356 |
}else if (isNotBlank(notes)){
|
|
| 357 |
logger.warn("Notes for synonym relationship or unknown taxon relationship not handled");
|
|
| 358 |
} |
|
| 354 | 359 |
taxaToSave.add(taxon2); |
| 355 | 360 |
|
| 356 | 361 |
//TODO |
| ... | ... | |
| 548 | 553 |
} |
| 549 | 554 |
|
| 550 | 555 |
|
| 551 |
private SynonymRelationship getSynRel (int relQualifierFk, Taxon toTaxon, Synonym synonym, Reference citation, String microcitation){
|
|
| 552 |
SynonymRelationship result; |
|
| 553 |
if (relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF || |
|
| 556 |
private void makeSynRel (int relQualifierFk, Taxon toTaxon, Synonym synonym, Reference citation, String microcitation){
|
|
| 557 |
if (citation != null && !citation.equals(synonym.getSec())){
|
|
| 558 |
logger.warn("A synonym relationship citation is given and differs from synonym secundum. This can not be handled in CDM");
|
|
| 559 |
} |
|
| 560 |
if (isNotBlank(microcitation) && !microcitation.equals(synonym.getSecMicroReference())){
|
|
| 561 |
logger.warn("A synonym relationship microcitation is given and differs from synonym secundum micro reference. This can not be handled in CDM");
|
|
| 562 |
} |
|
| 563 |
if (relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF || |
|
| 554 | 564 |
relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF || |
| 555 | 565 |
relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF){
|
| 556 |
result = toTaxon.addHomotypicSynonym(synonym, citation, microcitation);
|
|
| 566 |
toTaxon.addHomotypicSynonym(synonym);
|
|
| 557 | 567 |
}else if (relQualifierFk == TAX_REL_IS_HETEROTYPIC_SYNONYM_OF || |
| 558 | 568 |
relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF || |
| 559 | 569 |
relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF){
|
| 560 |
result = toTaxon.addSynonym(synonym, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), citation, microcitation);
|
|
| 570 |
toTaxon.addSynonym(synonym, SynonymType.HETEROTYPIC_SYNONYM_OF());
|
|
| 561 | 571 |
}else if (relQualifierFk == TAX_REL_IS_SYNONYM_OF || |
| 562 | 572 |
relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF || |
| 563 | 573 |
relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF){
|
| 564 |
result = toTaxon.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF(), citation, microcitation);
|
|
| 574 |
toTaxon.addSynonym(synonym, SynonymType.SYNONYM_OF());
|
|
| 565 | 575 |
}else{
|
| 566 | 576 |
logger.warn("SynonymyRelationShipType could not be defined for relQualifierFk " + relQualifierFk + ". 'Unknown'-Type taken instead.");
|
| 567 |
result = toTaxon.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF(), citation, microcitation);
|
|
| 577 |
toTaxon.addSynonym(synonym, SynonymType.SYNONYM_OF());
|
|
| 568 | 578 |
} |
| 569 |
return result;
|
|
| 579 |
return; |
|
| 570 | 580 |
|
| 571 | 581 |
} |
| 572 | 582 |
|
| ... | ... | |
| 596 | 606 |
} |
| 597 | 607 |
} |
| 598 | 608 |
|
| 599 |
private void addProParteAndPartial(SynonymRelationship synRel, Synonym synonym, BerlinModelImportConfigurator bmiConfig){
|
|
| 600 |
if (bmiConfig.isPartialSynonym(synonym)){
|
|
| 601 |
synRel.setPartial(true); |
|
| 602 |
} |
|
| 603 |
if (bmiConfig.isProParteSynonym(synonym)){
|
|
| 604 |
synRel.setProParte(true); |
|
| 605 |
} |
|
| 606 |
} |
|
| 607 |
|
|
| 608 | 609 |
private TaxonNode makeTaxonomicallyIncluded(BerlinModelImportState state, Map<Integer, Classification> classificationMap, int treeRefFk, Taxon child, Taxon parent, Reference citation, String microCitation){
|
| 609 | 610 |
Classification tree = getClassificationTree(state, classificationMap, treeRefFk); |
| 610 | 611 |
return tree.addParentChild(parent, child, citation, microCitation); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/out/BerlinModelTaxonRelationExport.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 |
*/ |
| ... | ... | |
| 25 | 25 |
import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper; |
| 26 | 26 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 27 | 27 |
import eu.etaxonomy.cdm.model.common.RelationshipBase; |
| 28 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationship; |
|
| 29 | 28 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 30 | 29 |
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship; |
| 31 | 30 |
|
| ... | ... | |
| 48 | 47 |
public BerlinModelTaxonRelationExport(){
|
| 49 | 48 |
super(); |
| 50 | 49 |
} |
| 51 |
|
|
| 50 |
|
|
| 52 | 51 |
/* (non-Javadoc) |
| 53 | 52 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
| 54 | 53 |
*/ |
| ... | ... | |
| 58 | 57 |
logger.warn("Checking for " + pluralString + " not yet implemented");
|
| 59 | 58 |
//result &= checkArticlesWithoutJournal(bmiConfig); |
| 60 | 59 |
//result &= checkPartOfJournal(bmiConfig); |
| 61 |
|
|
| 60 |
|
|
| 62 | 61 |
return result; |
| 63 | 62 |
} |
| 64 |
|
|
| 63 |
|
|
| 65 | 64 |
private CdmDbExportMapping<BerlinModelExportState, BerlinModelExportConfigurator, IExportTransformer> getMapping(){
|
| 66 | 65 |
String tableName = dbTableName; |
| 67 | 66 |
CdmDbExportMapping<BerlinModelExportState, BerlinModelExportConfigurator, IExportTransformer> mapping = new CdmDbExportMapping<BerlinModelExportState, BerlinModelExportConfigurator, IExportTransformer>(tableName); |
| 68 | 67 |
// mapping.addMapper(IdMapper.NewInstance("RelPTaxonId")); //is Identity column
|
| 69 |
|
|
| 68 |
|
|
| 70 | 69 |
mapping.addMapper(MethodMapper.NewInstance("PTNameFk1", this.getClass(), "getPTNameFk1", standardMethodParameter, DbExportStateBase.class));
|
| 71 | 70 |
mapping.addMapper(MethodMapper.NewInstance("PTRefFk1", this.getClass(), "getPTRefFk1", standardMethodParameter, DbExportStateBase.class));
|
| 72 |
|
|
| 71 |
|
|
| 73 | 72 |
mapping.addMapper(MethodMapper.NewInstance("PTNameFk2", this.getClass(), "getPTNameFk2", standardMethodParameter, DbExportStateBase.class));
|
| 74 | 73 |
mapping.addMapper(MethodMapper.NewInstance("PTRefFk2", this.getClass(), "getPTRefFk2", standardMethodParameter, DbExportStateBase.class));
|
| 75 |
|
|
| 74 |
|
|
| 76 | 75 |
mapping.addMapper(MethodMapper.NewInstance("RelQualifierFk", this));
|
| 77 |
|
|
| 76 |
|
|
| 78 | 77 |
mapping.addMapper(DbObjectMapper.NewInstance("citation", "RelRefFk"));
|
| 79 | 78 |
// mapping.addMapper(RefDetailMapper.NewInstance("citationMicroReference","citation", "FactRefDetailFk"));
|
| 80 | 79 |
mapping.addMapper(CreatedAndNotesMapper.NewInstance()); |
| 81 | 80 |
|
| 82 | 81 |
return mapping; |
| 83 | 82 |
} |
| 84 |
|
|
| 85 |
protected void doInvoke(BerlinModelExportState state){
|
|
| 83 |
|
|
| 84 |
@Override |
|
| 85 |
protected void doInvoke(BerlinModelExportState state){
|
|
| 86 | 86 |
try{
|
| 87 | 87 |
logger.info("start make " + pluralString + " ...");
|
| 88 | 88 |
boolean success = true ; |
| 89 | 89 |
doDelete(state); |
| 90 |
|
|
| 90 |
|
|
| 91 | 91 |
TransactionStatus txStatus = startTransaction(true); |
| 92 |
|
|
| 92 |
|
|
| 93 | 93 |
List<RelationshipBase> list = getTaxonService().getAllRelationships(100000000, 0); |
| 94 |
|
|
| 94 |
|
|
| 95 | 95 |
CdmDbExportMapping<BerlinModelExportState, BerlinModelExportConfigurator, IExportTransformer> mapping = getMapping(); |
| 96 | 96 |
mapping.initialize(state); |
| 97 |
|
|
| 97 |
|
|
| 98 | 98 |
int count = 0; |
| 99 | 99 |
for (RelationshipBase<?,?,?> rel : list){
|
| 100 | 100 |
if (rel.isInstanceOf(TaxonRelationship.class) || rel.isInstanceOf(SynonymRelationship.class)){
|
| ... | ... | |
| 116 | 116 |
} |
| 117 | 117 |
} |
| 118 | 118 |
|
| 119 |
|
|
| 119 |
|
|
| 120 | 120 |
protected boolean doDelete(BerlinModelExportState state){
|
| 121 | 121 |
BerlinModelExportConfigurator bmeConfig = state.getConfig(); |
| 122 |
|
|
| 122 |
|
|
| 123 | 123 |
String sql; |
| 124 | 124 |
Source destination = bmeConfig.getDestination(); |
| 125 | 125 |
//RelPTaxon |
| ... | ... | |
| 129 | 129 |
|
| 130 | 130 |
return true; |
| 131 | 131 |
} |
| 132 |
|
|
| 133 |
|
|
| 132 |
|
|
| 133 |
|
|
| 134 | 134 |
/* (non-Javadoc) |
| 135 | 135 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
| 136 | 136 |
*/ |
| 137 |
protected boolean isIgnore(BerlinModelExportState state){
|
|
| 137 |
@Override |
|
| 138 |
protected boolean isIgnore(BerlinModelExportState state){
|
|
| 138 | 139 |
return ! state.getConfig().isDoRelTaxa(); |
| 139 | 140 |
} |
| 140 |
|
|
| 141 |
|
|
| 141 | 142 |
//called by MethodMapper |
| 142 | 143 |
@SuppressWarnings("unused")
|
| 143 | 144 |
private static Integer getRelQualifierFk(RelationshipBase<?, ?, ?> rel){
|
| 144 | 145 |
return BerlinModelTransformer.taxRelation2relPtQualifierFk(rel); |
| 145 | 146 |
} |
| 146 |
|
|
| 147 |
|
|
| 147 | 148 |
@SuppressWarnings("unused")
|
| 148 | 149 |
private static Integer getPTNameFk1(RelationshipBase<?, ?, ?> rel, DbExportStateBase<?, IExportTransformer> state){
|
| 149 | 150 |
return getObjectFk(rel, state, true, true); |
| 150 | 151 |
} |
| 151 |
|
|
| 152 |
|
|
| 152 | 153 |
@SuppressWarnings("unused")
|
| 153 | 154 |
private static Integer getPTRefFk1(RelationshipBase<?, ?, ?> rel, DbExportStateBase<?, IExportTransformer> state){
|
| 154 | 155 |
return getObjectFk(rel, state, false, true); |
| 155 | 156 |
} |
| 156 |
|
|
| 157 |
|
|
| 157 | 158 |
@SuppressWarnings("unused")
|
| 158 | 159 |
private static Integer getPTNameFk2(RelationshipBase<?, ?, ?> rel, DbExportStateBase<?, IExportTransformer> state){
|
| 159 | 160 |
return getObjectFk(rel, state, true, false); |
| 160 | 161 |
} |
| 161 |
|
|
| 162 |
|
|
| 162 | 163 |
@SuppressWarnings("unused")
|
| 163 | 164 |
private static Integer getPTRefFk2(RelationshipBase<?, ?, ?> rel, DbExportStateBase<?, IExportTransformer> state){
|
| 164 | 165 |
return getObjectFk(rel, state, false, false); |
| ... | ... | |
| 180 | 181 |
logger.warn("No taxon found for relationship: " + rel.toString());
|
| 181 | 182 |
return null; |
| 182 | 183 |
} |
| 183 |
|
|
| 184 |
|
|
| 184 |
|
|
| 185 |
|
|
| 185 | 186 |
/* (non-Javadoc) |
| 186 | 187 |
* @see eu.etaxonomy.cdm.io.berlinModel.out.BerlinModelExportBase#getStandardMethodParameter() |
| 187 | 188 |
*/ |
| app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoTaxonImport.java | ||
|---|---|---|
| 45 | 45 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 46 | 46 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 47 | 47 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 48 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
|
|
| 48 |
import eu.etaxonomy.cdm.model.taxon.SynonymType; |
|
| 49 | 49 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 50 | 50 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 51 | 51 |
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; |
| ... | ... | |
| 203 | 203 |
} |
| 204 | 204 |
name.addBasionym(basionym); |
| 205 | 205 |
Synonym syn = Synonym.NewInstance(basionym, state.getTransactionalSourceReference()); |
| 206 |
taxon.addSynonym(syn, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF());
|
|
| 206 |
taxon.addSynonym(syn, SynonymType.HOMOTYPIC_SYNONYM_OF()); |
|
| 207 | 207 |
getTaxonService().save(syn); |
| 208 | 208 |
} |
| 209 | 209 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/cuba/CubaExcelImport.java | ||
|---|---|---|
| 58 | 58 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 59 | 59 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 60 | 60 |
import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode; |
| 61 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
|
|
| 62 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
|
|
| 61 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
|
| 62 |
import eu.etaxonomy.cdm.model.taxon.SynonymType; |
|
| 63 | 63 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 64 | 64 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
| 65 | 65 |
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; |
| ... | ... | |
| 429 | 429 |
name.addSource(makeOriginalSource(state)); |
| 430 | 430 |
NomenclaturalStatus status = NomenclaturalStatus.NewInstance( NomenclaturalStatusType.INVALID()); |
| 431 | 431 |
name.addStatus(status); |
| 432 |
SynonymRelationship sr = state.getCurrentTaxon().addSynonymName(name, SynonymRelationshipType.SYNONYM_OF());
|
|
| 433 |
sr.getSynonym().addSource(makeOriginalSource(state));
|
|
| 432 |
Synonym syn = state.getCurrentTaxon().addSynonymName(name, SynonymType.SYNONYM_OF());
|
|
| 433 |
syn.addSource(makeOriginalSource(state));
|
|
| 434 | 434 |
}else if (sphalmMatcher.matches()){
|
| 435 | 435 |
String firstPart = sphalmMatcher.group(1); |
| 436 | 436 |
String sphalmPart = synonymStr.replace(firstPart, "").replace("“","").replace("”","").trim();
|
| ... | ... | |
| 438 | 438 |
// NomenclaturalStatus status = NomenclaturalStatus.NewInstance( NomenclaturalStatusType.INVALID()); |
| 439 | 439 |
// name.addStatus(status); |
| 440 | 440 |
name.addSource(makeOriginalSource(state)); |
| 441 |
SynonymRelationship sr = state.getCurrentTaxon().addSynonymName(name, SynonymRelationshipType.SYNONYM_OF());
|
|
| 442 |
sr.getSynonym().setAppendedPhrase(sphalmPart);
|
|
| 443 |
sr.getSynonym().setSec(null);
|
|
| 444 |
sr.getSynonym().addSource(makeOriginalSource(state));
|
|
| 441 |
Synonym syn = state.getCurrentTaxon().addSynonymName(name, SynonymType.SYNONYM_OF());
|
|
| 442 |
syn.setAppendedPhrase(sphalmPart);
|
|
| 443 |
syn.setSec(null);
|
|
| 444 |
syn.addSource(makeOriginalSource(state));
|
|
| 445 | 445 |
}else if (acceptedMatcher.matches()){
|
| 446 | 446 |
String firstPart = acceptedMatcher.group(1); |
| 447 | 447 |
String homonymPart = acceptedMatcher.groupCount() < 2 ? null : acceptedMatcher.group(2); |
| ... | ... | |
| 461 | 461 |
if (isHomonym){
|
| 462 | 462 |
homonyms.add(synName); |
| 463 | 463 |
} |
| 464 |
SynonymRelationship sr = state.getCurrentTaxon().addHeterotypicSynonymName(synName);
|
|
| 465 |
sr.getSynonym().setDoubtful(isDoubtful);
|
|
| 466 |
sr.getSynonym().addSource(makeOriginalSource(state));
|
|
| 464 |
Synonym syn = state.getCurrentTaxon().addHeterotypicSynonymName(synName);
|
|
| 465 |
syn.setDoubtful(isDoubtful);
|
|
| 466 |
syn.addSource(makeOriginalSource(state));
|
|
| 467 | 467 |
List<BotanicalName> list = handleHomotypicGroup(secondPart, state, synName, true, homonyms, homonymPart, isDoubtful); |
| 468 | 468 |
checkFirstSynonym(state, list, isFirstSynonym, synonymStr, true); |
| 469 | 469 |
|
| ... | ... | |
| 472 | 472 |
if (synName.isProtectedTitleCache()){
|
| 473 | 473 |
logger.warn(line + "Special heterotypic synonym could not be parsed correctly:" + synonymStr); |
| 474 | 474 |
} |
| 475 |
SynonymRelationship sr = state.getCurrentTaxon().addHeterotypicSynonymName(synName);
|
|
| 476 |
sr.getSynonym().addSource(makeOriginalSource(state));
|
|
| 475 |
Synonym syn = state.getCurrentTaxon().addHeterotypicSynonymName(synName);
|
|
| 476 |
syn.addSource(makeOriginalSource(state));
|
|
| 477 | 477 |
}else{
|
| 478 | 478 |
logger.warn(line + "Synonym entry does not match: " + synonymStr); |
| 479 | 479 |
} |
| ... | ... | |
| 615 | 615 |
homonyms.add(newName); |
| 616 | 616 |
} |
| 617 | 617 |
if (isHeterotypic){
|
| 618 |
SynonymRelationship sr = state.getCurrentTaxon().addHeterotypicSynonymName(newName, homotypicGroup, null, null);
|
|
| 619 |
sr.getSynonym().setDoubtful(isDoubtful);
|
|
| 620 |
sr.getSynonym().addSource(makeOriginalSource(state));
|
|
| 618 |
Synonym syn = state.getCurrentTaxon().addHeterotypicSynonymName(newName, null, null, homotypicGroup);
|
|
| 619 |
syn.setDoubtful(isDoubtful);
|
|
| 620 |
syn.addSource(makeOriginalSource(state));
|
|
| 621 | 621 |
// newName.addBasionym(homotypicName); |
| 622 | 622 |
}else{
|
| 623 |
state.getCurrentTaxon().addHomotypicSynonymName(newName, null, null);
|
|
| 623 |
state.getCurrentTaxon().addHomotypicSynonymName(newName); |
|
| 624 | 624 |
} |
| 625 | 625 |
handleBasionym(state, homotypicNameList, homonyms, newName); |
| 626 | 626 |
homotypicNameList.add(newName); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/cyprus/CyprusExcelImport.java | ||
|---|---|---|
| 39 | 39 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 40 | 40 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 41 | 41 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 42 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
|
|
| 42 |
import eu.etaxonomy.cdm.model.taxon.SynonymType; |
|
| 43 | 43 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 44 | 44 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 45 | 45 |
import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser; |
| ... | ... | |
| 333 | 333 |
if (! speciesIsExisting){
|
| 334 | 334 |
makeHigherTaxa(state, taxonLight, speciesTaxon, citation, microCitation); |
| 335 | 335 |
} |
| 336 |
makeHomotypicSynonyms(state, citation, microCitation, homotypicSynonymList, mainTaxon);
|
|
| 337 |
makeHeterotypicSynonyms(state, citation, microCitation, heterotypicSynonymList, mainTaxon);
|
|
| 336 |
makeHomotypicSynonyms(state, homotypicSynonymList, mainTaxon); |
|
| 337 |
makeHeterotypicSynonyms(state, heterotypicSynonymList, mainTaxon); |
|
| 338 | 338 |
makeSystematics(systematicsString, mainTaxon); |
| 339 | 339 |
makeEndemism(endemismString, mainTaxon); |
| 340 | 340 |
makeStatus(statusString, mainTaxon); |
| ... | ... | |
| 378 | 378 |
|
| 379 | 379 |
|
| 380 | 380 |
private void makeHomotypicSynonyms(CyprusImportState state, |
| 381 |
Reference citation, String microCitation, List<String> homotypicSynonymList, Taxon mainTaxon) {
|
|
| 381 |
List<String> homotypicSynonymList, Taxon mainTaxon) {
|
|
| 382 | 382 |
for (String homotypicSynonym: homotypicSynonymList){
|
| 383 | 383 |
if (StringUtils.isNotBlank(homotypicSynonym)){
|
| 384 | 384 |
Synonym synonym = (Synonym)createTaxon(state, null, homotypicSynonym, Synonym.class, nc); |
| 385 |
mainTaxon.addHomotypicSynonym(synonym, citation, microCitation);
|
|
| 385 |
mainTaxon.addHomotypicSynonym(synonym); |
|
| 386 | 386 |
} |
| 387 | 387 |
} |
| 388 | 388 |
} |
| 389 | 389 |
|
| 390 | 390 |
|
| 391 |
private void makeHeterotypicSynonyms(CyprusImportState state, Reference citation, String microCitation, List<String> heterotypicSynonymList, Taxon mainTaxon) {
|
|
| 391 |
private void makeHeterotypicSynonyms(CyprusImportState state, List<String> heterotypicSynonymList, Taxon mainTaxon) {
|
|
| 392 | 392 |
for (String heterotypicSynonym: heterotypicSynonymList){
|
| 393 | 393 |
if (StringUtils.isNotBlank(heterotypicSynonym)){
|
| 394 | 394 |
Synonym synonym = (Synonym)createTaxon(state, null, heterotypicSynonym, Synonym.class, nc); |
| 395 |
mainTaxon.addSynonym(synonym, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), citation, microCitation);
|
|
| 395 |
mainTaxon.addSynonym(synonym, SynonymType.HETEROTYPIC_SYNONYM_OF());
|
|
| 396 | 396 |
} |
| 397 | 397 |
} |
| 398 | 398 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/edaphobase/EdaphobaseClassificationImport.java | ||
|---|---|---|
| 128 | 128 |
// logger.warn(message); |
| 129 | 129 |
// }else{
|
| 130 | 130 |
// Taxon accepted = CdmBase.deproxy(parent, Taxon.class); |
| 131 |
//// accepted.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF());
|
|
| 131 |
//// accepted.addSynonym(synonym, SynonymType.SYNONYM_OF()); |
|
| 132 | 132 |
// taxaToSave.add(accepted); |
| 133 | 133 |
// } |
| 134 | 134 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/edaphobase/EdaphobaseSynonymyImport.java | ||
|---|---|---|
| 24 | 24 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 25 | 25 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 26 | 26 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 27 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
|
|
| 27 |
import eu.etaxonomy.cdm.model.taxon.SynonymType; |
|
| 28 | 28 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 29 | 29 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 30 | 30 |
|
| ... | ... | |
| 41 | 41 |
|
| 42 | 42 |
private static final String tableName = "tax_synonym"; |
| 43 | 43 |
|
| 44 |
private static final String pluralString = "synonym relationships";
|
|
| 44 |
private static final String pluralString = "related synonyms";
|
|
| 45 | 45 |
|
| 46 | 46 |
|
| 47 | 47 |
/** |
| ... | ... | |
| 92 | 92 |
if (synonymCandidate == null){
|
| 93 | 93 |
logger.warn("Synonym " + synId + " not found for synonymRelations (tax_synonym): " + id);
|
| 94 | 94 |
}else if (synonymCandidate.isInstanceOf(Taxon.class)){
|
| 95 |
String message = "Synonym ("+synId+") is not synonym but accepted (valid). Can't add synonym relationship for tax_synonym: "+id;
|
|
| 95 |
String message = "Synonym ("+synId+") is not synonym but accepted (valid). Can't add synonym for tax_synonym: "+id;
|
|
| 96 | 96 |
logger.warn(message); |
| 97 | 97 |
}else{
|
| 98 | 98 |
Synonym synonym = CdmBase.deproxy(synonymCandidate, Synonym.class); |
| ... | ... | |
| 100 | 100 |
if (accepted == null){
|
| 101 | 101 |
logger.warn("Accepted(parent) taxon " + accId + " not found for tax_synonym " + id );
|
| 102 | 102 |
}else if(accepted.isInstanceOf(Synonym.class)){
|
| 103 |
String message = "Taxon ("+accId+") is not accepted but synonym. Can't add synonym relationship for tax_synonym: "+id;
|
|
| 103 |
String message = "Taxon ("+accId+") is not accepted but synonym. Can't add synonym for tax_synonym: "+id;
|
|
| 104 | 104 |
logger.warn(message); |
| 105 | 105 |
}else{
|
| 106 | 106 |
Taxon taxon = CdmBase.deproxy(accepted, Taxon.class); |
| 107 |
taxon.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF());
|
|
| 107 |
taxon.addSynonym(synonym, SynonymType.SYNONYM_OF()); |
|
| 108 | 108 |
taxaToSave.add(synonym); |
| 109 | 109 |
taxaToSave.add(taxon); |
| 110 | 110 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisSpecTaxImport.java | ||
|---|---|---|
| 54 | 54 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType; |
| 55 | 55 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 56 | 56 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
Also available in: Unified diff
ref #5974 Remove synonym relationships (not finished yet)