Revision 51171c9d
Added by Andreas Müller almost 13 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/taxa/NormalExplicitImport.java | ||
|---|---|---|
| 27 | 27 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 28 | 28 |
import eu.etaxonomy.cdm.io.excel.common.ExcelRowBase.SourceDataHolder; |
| 29 | 29 |
import eu.etaxonomy.cdm.model.agent.Team; |
| 30 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
|
| 30 | 31 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 31 | 32 |
import eu.etaxonomy.cdm.model.common.DescriptionElementSource; |
| 33 |
import eu.etaxonomy.cdm.model.common.Extension; |
|
| 34 |
import eu.etaxonomy.cdm.model.common.ExtensionType; |
|
| 32 | 35 |
import eu.etaxonomy.cdm.model.common.Language; |
| 33 | 36 |
import eu.etaxonomy.cdm.model.common.TimePeriod; |
| 34 | 37 |
import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
| ... | ... | |
| 68 | 71 |
|
| 69 | 72 |
public static Set<String> validMarkers = new HashSet<String>(Arrays.asList(new String[]{"", "valid", "accepted", "a", "v", "t"}));
|
| 70 | 73 |
public static Set<String> synonymMarkers = new HashSet<String>(Arrays.asList(new String[]{"", "invalid", "synonym", "s", "i"}));
|
| 71 |
|
|
| 74 |
public static final UUID uuidRefExtension = UUID.fromString("a46533df-7a78-448f-9b80-36d087fbdf2a");
|
|
| 72 | 75 |
|
| 73 | 76 |
/* (non-Javadoc) |
| 74 | 77 |
* @see eu.etaxonomy.cdm.io.excel.common.ExcelTaxonOrSpecimenImportBase#analyzeSingleValue(eu.etaxonomy.cdm.io.excel.common.ExcelTaxonOrSpecimenImportBase.KeyValue, eu.etaxonomy.cdm.io.excel.common.ExcelImportState) |
| 75 | 78 |
*/ |
| 76 | 79 |
@Override |
| 77 |
protected boolean analyzeSingleValue(KeyValue keyValue, TaxonExcelImportState state) {
|
|
| 78 |
boolean success = true; |
|
| 80 |
protected void analyzeSingleValue(KeyValue keyValue, TaxonExcelImportState state) {
|
|
| 79 | 81 |
|
| 80 | 82 |
NormalExplicitRow normalExplicitRow = state.getCurrentRow(); |
| 81 | 83 |
String key = keyValue.key; |
| ... | ... | |
| 124 | 126 |
}else{
|
| 125 | 127 |
String message = "Unexpected column header " + key; |
| 126 | 128 |
fireWarningEvent(message, state, 10); |
| 127 |
success = false;
|
|
| 129 |
state.setUnsuccessfull();
|
|
| 128 | 130 |
logger.error(message); |
| 129 | 131 |
} |
| 130 | 132 |
} |
| 131 |
return success;
|
|
| 133 |
return; |
|
| 132 | 134 |
} |
| 133 | 135 |
|
| 134 | 136 |
|
| 135 | 137 |
/** |
| 136 |
* Stores taxa records in DB
|
|
| 138 |
* Create base taxa and add all information attached to it's name.
|
|
| 137 | 139 |
*/ |
| 138 | 140 |
@Override |
| 139 |
protected boolean firstPass(TaxonExcelImportState state) {
|
|
| 140 |
boolean success = true; |
|
| 141 |
protected void firstPass(TaxonExcelImportState state) {
|
|
| 142 |
|
|
| 143 |
// if (1==1){
|
|
| 144 |
// return true; |
|
| 145 |
// } |
|
| 146 |
// System.out.println("FP:" + state.getCurrentLine());
|
|
| 141 | 147 |
Rank rank = null; |
| 142 | 148 |
NormalExplicitRow taxonDataHolder = state.getCurrentRow(); |
| 143 | 149 |
|
| ... | ... | |
| 161 | 167 |
try {
|
| 162 | 168 |
rank = Rank.getRankByEnglishName(rankStr, state.getConfig().getNomenclaturalCode(), false); |
| 163 | 169 |
} catch (UnknownCdmTypeException e) {
|
| 164 |
success = false;
|
|
| 170 |
state.setUnsuccessfull();
|
|
| 165 | 171 |
logger.error(rankStr + " is not a valid rank."); |
| 166 | 172 |
} |
| 167 | 173 |
} |
| ... | ... | |
| 169 | 175 |
//taxon |
| 170 | 176 |
taxonBase = createTaxon(state, rank, taxonNameStr, authorStr, nameStatus); |
| 171 | 177 |
}else{
|
| 172 |
return true;
|
|
| 178 |
return; |
|
| 173 | 179 |
} |
| 174 | 180 |
} |
| 175 | 181 |
if (taxonBase == null){
|
| 176 | 182 |
String message = "Taxon could not be created. Record will not be handled"; |
| 177 | 183 |
fireWarningEvent(message, "Record: " + state.getCurrentLine(), 6); |
| 178 | 184 |
logger.warn(message); |
| 179 |
return false; |
|
| 185 |
state.setUnsuccessfull(); |
|
| 186 |
return; |
|
| 180 | 187 |
} |
| 181 | 188 |
|
| 182 | 189 |
//protologue |
| ... | ... | |
| 190 | 197 |
} catch (URISyntaxException e) {
|
| 191 | 198 |
String warning = "URISyntaxException when trying to convert to URI: " + protologue; |
| 192 | 199 |
logger.error(warning); |
| 200 |
state.setUnsuccessfull(); |
|
| 193 | 201 |
} |
| 194 | 202 |
} |
| 195 |
|
|
| 196 |
//media |
|
| 197 |
for (String imageUrl : taxonDataHolder.getImages()){
|
|
| 198 |
//TODO |
|
| 199 |
Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
|
| 200 |
TaxonDescription td = taxon.getImageGallery(true); |
|
| 201 |
DescriptionElementBase mediaHolder; |
|
| 202 |
if (td.getElements().size() != 0){
|
|
| 203 |
mediaHolder = td.getElements().iterator().next(); |
|
| 204 |
}else{
|
|
| 205 |
mediaHolder = TextData.NewInstance(Feature.IMAGE()); |
|
| 206 |
td.addElement(mediaHolder); |
|
| 207 |
} |
|
| 208 |
try {
|
|
| 209 |
Media media = getImageMedia(imageUrl, true); |
|
| 210 |
mediaHolder.addMedia(media); |
|
| 211 |
} catch (MalformedURLException e) {
|
|
| 212 |
logger.warn("Can't add media: " + e.getMessage());
|
|
| 213 |
} |
|
| 214 |
} |
|
| 215 |
|
|
| 216 |
//tdwg label |
|
| 217 |
for (String tdwg : taxonDataHolder.getDistributions()){
|
|
| 218 |
//TODO |
|
| 219 |
Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
|
| 220 |
TaxonDescription td = this.getTaxonDescription(taxon, false, true); |
|
| 221 |
NamedArea area = TdwgArea.getAreaByTdwgAbbreviation(tdwg); |
|
| 222 |
if (area == null){
|
|
| 223 |
area = TdwgArea.getAreaByTdwgLabel(tdwg); |
|
| 224 |
} |
|
| 225 |
if (area != null){
|
|
| 226 |
Distribution distribution = Distribution.NewInstance(area, PresenceTerm.PRESENT()); |
|
| 227 |
td.addElement(distribution); |
|
| 228 |
}else{
|
|
| 229 |
String message = "TDWG area could not be recognized: " + tdwg; |
|
| 230 |
logger.warn(message); |
|
| 231 |
} |
|
| 232 |
|
|
| 233 |
} |
|
| 234 |
|
|
| 235 |
|
|
| 236 | 203 |
|
| 237 | 204 |
state.putTaxon(id, taxonBase); |
| 238 | 205 |
getTaxonService().save(taxonBase); |
| 239 | 206 |
|
| 240 |
return success;
|
|
| 207 |
return; |
|
| 241 | 208 |
} |
| 242 | 209 |
|
| 243 | 210 |
|
| 244 | 211 |
|
| 245 | 212 |
/** |
| 246 |
* Stores parent-child, synonym and common name relationships |
|
| 213 |
* Stores parent-child, synonym and common name relationships. |
|
| 214 |
* Adds all taxon related descriptive information (this is not done in the first pass |
|
| 215 |
* because the information may also be attached to a synonym). |
|
| 247 | 216 |
*/ |
| 248 | 217 |
@Override |
| 249 |
protected boolean secondPass(TaxonExcelImportState state) {
|
|
| 250 |
// System.out.println(state.getCurrentLine()); |
|
| 251 |
boolean success = true; |
|
| 218 |
protected void secondPass(TaxonExcelImportState state) {
|
|
| 219 |
System.out.println(state.getCurrentLine()); |
|
| 252 | 220 |
try {
|
| 253 | 221 |
NormalExplicitRow taxonDataHolder = state.getCurrentRow(); |
| 254 | 222 |
String taxonNameStr = taxonDataHolder.getScientificName(); |
| ... | ... | |
| 282 | 250 |
Reference citation = state.getConfig().getSourceReference(); |
| 283 | 251 |
String microCitation = null; |
| 284 | 252 |
Taxon childTaxon = taxon; |
| 285 |
success &= makeParent(state, parentTaxon, childTaxon, citation, microCitation);
|
|
| 253 |
makeParent(state, parentTaxon, childTaxon, citation, microCitation); |
|
| 286 | 254 |
getTaxonService().saveOrUpdate(parentTaxon); |
| 287 | 255 |
} else {
|
| 288 | 256 |
String message = "Taxonomic parent not found for " + taxonNameStr; |
| 289 | 257 |
logger.warn(message); |
| 290 | 258 |
fireWarningEvent(message, state, 6); |
| 291 |
success = false;
|
|
| 259 |
state.setUnsuccessfull();
|
|
| 292 | 260 |
} |
| 293 | 261 |
}else{
|
| 294 | 262 |
//do nothing (parent == 0) no parent exists |
| ... | ... | |
| 309 | 277 |
String message = "Unhandled exception (%s) occurred during synonym import/update"; |
| 310 | 278 |
message = String.format(message, e.getMessage()); |
| 311 | 279 |
fireWarningEvent(message, state, 10); |
| 312 |
success = false;
|
|
| 280 |
state.setUnsuccessfull();
|
|
| 313 | 281 |
} |
| 314 | 282 |
}else{
|
| 315 | 283 |
acceptedTaxon = null; |
| ... | ... | |
| 328 | 296 |
String message = "Accepted taxon could not be found. Can't add additional data (common names, descriptive data, ...) to taxon"; |
| 329 | 297 |
fireWarningEvent(message, state, 6); |
| 330 | 298 |
}else{
|
| 299 |
//common names |
|
| 331 | 300 |
if (CdmUtils.isNotEmpty(commonNameStr)){ // add common name to taxon
|
| 332 | 301 |
handleCommonName(state, taxonNameStr, commonNameStr, acceptedTaxon); |
| 333 | 302 |
} |
| 334 | 303 |
|
| 304 |
|
|
| 305 |
//media |
|
| 306 |
for (String imageUrl : taxonDataHolder.getImages()){
|
|
| 307 |
TaxonDescription td = acceptedTaxon.getImageGallery(true); |
|
| 308 |
DescriptionElementBase mediaHolder; |
|
| 309 |
if (td.getElements().size() != 0){
|
|
| 310 |
mediaHolder = td.getElements().iterator().next(); |
|
| 311 |
}else{
|
|
| 312 |
mediaHolder = TextData.NewInstance(Feature.IMAGE()); |
|
| 313 |
td.addElement(mediaHolder); |
|
| 314 |
} |
|
| 315 |
try {
|
|
| 316 |
Media media = getImageMedia(imageUrl, true); |
|
| 317 |
mediaHolder.addMedia(media); |
|
| 318 |
} catch (MalformedURLException e) {
|
|
| 319 |
logger.warn("Can't add media: " + e.getMessage());
|
|
| 320 |
state.setUnsuccessfull(); |
|
| 321 |
} |
|
| 322 |
} |
|
| 323 |
|
|
| 324 |
//tdwg label |
|
| 325 |
for (String tdwg : taxonDataHolder.getDistributions()){
|
|
| 326 |
TaxonDescription td = this.getTaxonDescription(acceptedTaxon, state.getConfig().getSourceReference() ,false, true); |
|
| 327 |
NamedArea area = TdwgArea.getAreaByTdwgAbbreviation(tdwg); |
|
| 328 |
if (area == null){
|
|
| 329 |
area = TdwgArea.getAreaByTdwgLabel(tdwg); |
|
| 330 |
} |
|
| 331 |
if (area != null){
|
|
| 332 |
Distribution distribution = Distribution.NewInstance(area, PresenceTerm.PRESENT()); |
|
| 333 |
td.addElement(distribution); |
|
| 334 |
}else{
|
|
| 335 |
String message = "TDWG area could not be recognized: " + tdwg; |
|
| 336 |
logger.warn(message); |
|
| 337 |
state.setUnsuccessfull(); |
|
| 338 |
} |
|
| 339 |
} |
|
| 340 |
|
|
| 341 |
//features |
|
| 335 | 342 |
handleFeatures(state, taxonDataHolder, acceptedTaxon, nameUsedInSource); |
| 336 | 343 |
} |
| 337 | 344 |
} catch (Exception e) {
|
| 338 | 345 |
e.printStackTrace(); |
| 339 | 346 |
} |
| 340 |
return success;
|
|
| 347 |
return; |
|
| 341 | 348 |
} |
| 342 | 349 |
|
| 343 | 350 |
|
| ... | ... | |
| 355 | 362 |
|
| 356 | 363 |
for (int i = 0; i < textList.size(); i++){
|
| 357 | 364 |
String featureText = textList.get(i); |
| 358 |
String featureLanguage = languageList.get(i); |
|
| 365 |
String featureLanguage = languageList == null ? null :languageList.get(i);
|
|
| 359 | 366 |
Language language = getFeatureLanguage(featureLanguage, state); |
| 360 | 367 |
//TODO |
| 361 |
TaxonDescription td = this.getTaxonDescription(acceptedTaxon, false, true); |
|
| 368 |
TaxonDescription td = this.getTaxonDescription(acceptedTaxon, state.getConfig().getSourceReference() ,false, true);
|
|
| 362 | 369 |
TextData textData = TextData.NewInstance(feature); |
| 363 | 370 |
textData.putText(language, featureText); |
| 364 | 371 |
td.addElement(textData); |
| ... | ... | |
| 374 | 381 |
for (SourceType type : sourceMap.keySet()){
|
| 375 | 382 |
String value = sourceMap.get(type); |
| 376 | 383 |
if (type.equals(SourceType.Author)){
|
| 377 |
Team team = Team.NewInstance(); |
|
| 378 |
team.setTitleCache(value, true); |
|
| 379 |
ref.setAuthorTeam(team); |
|
| 384 |
TeamOrPersonBase author = getAuthorAccordingToConfig(value, state); |
|
| 385 |
ref.setAuthorTeam(author); |
|
| 380 | 386 |
}else if (type.equals(SourceType.Title)) {
|
| 381 | 387 |
ref.setTitle(value); |
| 382 | 388 |
}else if (type.equals(SourceType.Year)) {
|
| 383 | 389 |
ref.setDatePublished(TimePeriod.parseString(value)); |
| 390 |
}else if (type.equals(SourceType.RefExtension)) {
|
|
| 391 |
ExtensionType extensionType = getExtensionType(state, uuidRefExtension, "RefExtension", "Reference Extension", "RefExt."); |
|
| 392 |
Extension extension = Extension.NewInstance(ref, value, extensionType); |
|
| 384 | 393 |
} |
| 385 | 394 |
refExists = true; |
| 386 | 395 |
} |
| 387 | 396 |
if (refExists){
|
| 397 |
ref = getReferenceAccordingToConfig(ref, state); |
|
| 388 | 398 |
source.setCitation(ref); |
| 389 | 399 |
source.setNameUsedInSource(nameUsedInSource); |
| 390 | 400 |
} |
| ... | ... | |
| 394 | 404 |
} |
| 395 | 405 |
} |
| 396 | 406 |
|
| 407 |
private Map<String, UUID> referenceMapping = new HashMap<String, UUID>(); |
|
| 408 |
private Map<UUID, Reference> referenceStore = new HashMap<UUID, Reference>(); |
|
| 409 |
|
|
| 410 |
private Reference getReferenceAccordingToConfig(Reference value, TaxonExcelImportState state) {
|
|
| 411 |
Reference result = null; |
|
| 412 |
String titleCache = value.getTitleCache(); |
|
| 413 |
UUID referenceUuid = referenceMapping.get(titleCache); |
|
| 414 |
if (referenceUuid != null){
|
|
| 415 |
result = referenceStore.get(referenceUuid); |
|
| 416 |
} |
|
| 417 |
if (result == null){
|
|
| 418 |
result = value; |
|
| 419 |
referenceStore.put(result.getUuid(), result); |
|
| 420 |
} |
|
| 421 |
if (referenceUuid == null){
|
|
| 422 |
referenceMapping.put(titleCache, result.getUuid()); |
|
| 423 |
} |
|
| 424 |
return result; |
|
| 425 |
} |
|
| 426 |
|
|
| 427 |
|
|
| 428 |
private Map<String, UUID> authorMapping = new HashMap<String, UUID>(); |
|
| 429 |
private Map<UUID, TeamOrPersonBase> authorStore = new HashMap<UUID, TeamOrPersonBase>(); |
|
| 430 |
|
|
| 431 |
private TeamOrPersonBase getAuthorAccordingToConfig(String value, TaxonExcelImportState state) {
|
|
| 432 |
TeamOrPersonBase result = null; |
|
| 433 |
UUID authorUuid = authorMapping.get(value); |
|
| 434 |
if (authorUuid != null){
|
|
| 435 |
result = authorStore.get(authorUuid); |
|
| 436 |
} |
|
| 437 |
if (result == null){
|
|
| 438 |
//TODO parsing |
|
| 439 |
TeamOrPersonBase author = Team.NewInstance(); |
|
| 440 |
author.setTitleCache(value, true); |
|
| 441 |
result = author; |
|
| 442 |
authorStore.put(result.getUuid(), result); |
|
| 443 |
} |
|
| 444 |
if (authorUuid == null){
|
|
| 445 |
authorMapping.put(value, result.getUuid()); |
|
| 446 |
} |
|
| 447 |
return result; |
|
| 448 |
} |
|
| 449 |
|
|
| 397 | 450 |
|
| 398 | 451 |
private Map<String, UUID> languageMapping = new HashMap<String, UUID>(); |
| 399 | 452 |
|
| ... | ... | |
| 545 | 598 |
} |
| 546 | 599 |
} |
| 547 | 600 |
|
| 548 |
private boolean makeParent(TaxonExcelImportState state, Taxon parentTaxon, Taxon childTaxon, Reference citation, String microCitation){
|
|
| 549 |
boolean success = true; |
|
| 601 |
private void makeParent(TaxonExcelImportState state, Taxon parentTaxon, Taxon childTaxon, Reference citation, String microCitation){
|
|
| 550 | 602 |
Reference sec = state.getConfig().getSourceReference(); |
| 551 | 603 |
|
| 552 | 604 |
// Reference sec = parentTaxon.getSec(); |
| ... | ... | |
| 555 | 607 |
tree = makeTree(state, sec); |
| 556 | 608 |
} |
| 557 | 609 |
if (sec.equals(childTaxon.getSec())){
|
| 558 |
success &= (null != tree.addParentChild(parentTaxon, childTaxon, citation, microCitation)); |
|
| 610 |
boolean success = (null != tree.addParentChild(parentTaxon, childTaxon, citation, microCitation)); |
|
| 611 |
if (success == false){
|
|
| 612 |
state.setUnsuccessfull(); |
|
| 613 |
} |
|
| 559 | 614 |
}else{
|
| 560 | 615 |
logger.warn("No relationship added for child " + childTaxon.getTitleCache());
|
| 561 | 616 |
} |
| 562 |
return success;
|
|
| 617 |
return; |
|
| 563 | 618 |
} |
| 564 | 619 |
|
| 565 | 620 |
|
Also available in: Unified diff
last updates for Taxon Excel Import and moving all success variables to state