Revision cfd4c9cb
Added by Andreas Müller over 6 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/salvador/SalvadorSpecimenImport.java | ||
|---|---|---|
| 74 | 74 |
initDedupHelper(); |
| 75 | 75 |
try {
|
| 76 | 76 |
UUID factUuid = UUID.fromString(state.getCurrentRecord().get("specimenFactUuid"));
|
| 77 |
|
|
| 77 | 78 |
if (existingFieldUnits.get(factUuid)== null){
|
| 78 |
FieldUnit fieldUnit = getFieldUnit(state); |
|
| 79 |
|
|
| 80 |
FieldUnit fieldUnit = makeFieldUnit(state); |
|
| 79 | 81 |
DerivedUnitFacade facade = DerivedUnitFacade.NewInstance( |
| 80 | 82 |
SpecimenOrObservationType.PreservedSpecimen, fieldUnit); |
| 81 | 83 |
makeFieldUnitData(state, facade); |
| ... | ... | |
| 117 | 119 |
*/ |
| 118 | 120 |
private void makeSpecimenDuplicate(SalvadorSpecimenImportState state, |
| 119 | 121 |
DerivedUnitFacade facade) {
|
| 122 |
|
|
| 120 | 123 |
Map<String, String> record = state.getCurrentRecord(); |
| 124 |
|
|
| 125 |
TaxonDescription desc = getTaxonDescription(state, record); |
|
| 126 |
|
|
| 121 | 127 |
int row = state.getRow(); |
| 122 | 128 |
String herbariaStr = record.get("Herbaria");
|
| 123 | 129 |
String[] splits = herbariaStr.split(";");
|
| ... | ... | |
| 133 | 139 |
URI uri = URI.create(uriStr); |
| 134 | 140 |
facade.setPreferredStableUri(uri); |
| 135 | 141 |
} |
| 142 |
IndividualsAssociation assoc = IndividualsAssociation.NewInstance(facade.innerDerivedUnit()); |
|
| 143 |
assoc.setFeature(Feature.SPECIMEN()); |
|
| 144 |
desc.addElement(assoc); |
|
| 136 | 145 |
} |
| 146 |
|
|
| 137 | 147 |
} |
| 138 | 148 |
} |
| 139 | 149 |
|
| 140 | 150 |
|
| 141 | 151 |
private Map<UUID, FieldUnit> fieldUnitMap = new HashMap<>(); |
| 142 | 152 |
private Map<UUID, UUID> existingFieldUnits = new HashMap<>(); |
| 143 |
private FieldUnit getFieldUnit(SalvadorSpecimenImportState state) {
|
|
| 153 |
private FieldUnit makeFieldUnit(SalvadorSpecimenImportState state) {
|
|
| 144 | 154 |
|
| 145 | 155 |
Map<String, String> record = state.getCurrentRecord(); |
| 146 |
int row = state.getRow(); |
|
| 147 | 156 |
UUID factUuid = UUID.fromString(record.get("specimenFactUuid"));
|
| 148 | 157 |
|
| 149 | 158 |
TextData textSpecimen = (TextData)getDescriptionService().getDescriptionElementByUuid(factUuid); |
| 150 | 159 |
textSpecimen.setFeature(getTexSpecimenFeature()); |
| 151 | 160 |
|
| 152 |
TaxonDescription desc = getTaxonDescription(state, textSpecimen, record, row); |
|
| 153 | 161 |
FieldUnit fieldUnit = FieldUnit.NewInstance(); |
| 154 |
IndividualsAssociation assoc = IndividualsAssociation.NewInstance(fieldUnit); |
|
| 155 |
assoc.setFeature(Feature.SPECIMEN()); |
|
| 156 |
desc.addElement(assoc); |
|
| 162 |
|
|
| 157 | 163 |
fieldUnitMap.put(factUuid, fieldUnit); |
| 158 | 164 |
existingFieldUnits.put(factUuid, fieldUnit.getUuid()); |
| 159 | 165 |
|
| 160 | 166 |
return fieldUnit; |
| 161 | 167 |
} |
| 162 | 168 |
|
| 169 |
//taxonUuid, TaxonDescription map |
|
| 163 | 170 |
private Map<UUID, TaxonDescription> taxonDescMap = new HashMap<>(); |
| 171 |
//taxonUuid, TaxonDescription.uuid map |
|
| 164 | 172 |
private Map<UUID, UUID> existingTaxonDescs = new HashMap<>(); |
| 165 | 173 |
|
| 166 | 174 |
private TaxonDescription getTaxonDescription(SalvadorSpecimenImportState state, |
| 167 |
TextData textSpecimen, Map<String, String> record, int row) {
|
|
| 175 |
Map<String, String> record) {
|
|
| 176 |
|
|
| 177 |
int row = state.getRow(); |
|
| 168 | 178 |
UUID taxonUuid = UUID.fromString(record.get("taxonUuid"));
|
| 169 | 179 |
TaxonDescription taxonDesc = taxonDescMap.get(taxonUuid); |
| 170 | 180 |
if (taxonDesc == null && existingTaxonDescs.get(taxonUuid) != null){
|
| ... | ... | |
| 172 | 182 |
taxonDescMap.put(taxonUuid, taxonDesc); |
| 173 | 183 |
} |
| 174 | 184 |
if (taxonDesc == null){
|
| 175 |
Taxon taxon = CdmBase.deproxy(textSpecimen.getInDescription(), |
|
| 176 |
TaxonDescription.class).getTaxon(); |
|
| 185 |
|
|
| 186 |
Taxon taxon = (Taxon)getTaxonService().find(taxonUuid); |
|
| 187 |
|
|
| 177 | 188 |
taxonDesc = TaxonDescription.NewInstance(taxon); |
| 178 | 189 |
taxonDesc.setTitleCache("JACQ import for " + taxon.getName().getTitleCache(), true);
|
| 179 | 190 |
taxonDesc.addImportSource(null, null, state.getConfig().getSourceReference(), String.valueOf(row)); |
| ... | ... | |
| 194 | 205 |
private void makeSpecimen(SalvadorSpecimenImportState state, DerivedUnitFacade facade) {
|
| 195 | 206 |
|
| 196 | 207 |
Map<String, String> record = state.getCurrentRecord(); |
| 208 |
|
|
| 209 |
TaxonDescription desc = getTaxonDescription(state, record); |
|
| 210 |
|
|
| 197 | 211 |
int row = state.getRow(); |
| 198 | 212 |
String herbariaStr = record.get("Herbaria");
|
| 199 | 213 |
String laguUuidStr = record.get("LAGU_UUID");
|
| ... | ... | |
| 226 | 240 |
unit.setPreferredStableUri(uri); |
| 227 | 241 |
} |
| 228 | 242 |
} |
| 243 |
|
|
| 244 |
IndividualsAssociation assoc = IndividualsAssociation.NewInstance(unit); |
|
| 245 |
assoc.setFeature(Feature.SPECIMEN()); |
|
| 246 |
desc.addElement(assoc); |
|
| 229 | 247 |
} |
| 230 | 248 |
} |
| 231 | 249 |
|
| ... | ... | |
| 282 | 300 |
//CollectionDate |
| 283 | 301 |
String collectionDate = record.get("CollectionDate");
|
| 284 | 302 |
if (collectionDate != null){
|
| 285 |
DateTimeFormatter f = DateTimeFormat.forPattern("yyyy-MM-dd");
|
|
| 286 |
collectionDate = collectionDate.replace(" 00:00:00", "");
|
|
| 287 |
DateTime dateTime = f.parseDateTime(collectionDate); |
|
| 288 |
TimePeriod tp = TimePeriod.NewInstance(dateTime, null); |
|
| 303 |
TimePeriod tp; |
|
| 304 |
if (collectionDate.equals("1987")){
|
|
| 305 |
tp = TimePeriod.NewInstance(1987); |
|
| 306 |
state.getResult().addWarning("Only year is not correct: " + collectionDate, state.getRow());
|
|
| 307 |
}else{
|
|
| 308 |
DateTimeFormatter f = DateTimeFormat.forPattern("yyyy-MM-dd");
|
|
| 309 |
collectionDate = collectionDate.replace(" 00:00:00", "");
|
|
| 310 |
DateTime dateTime = f.parseDateTime(collectionDate); |
|
| 311 |
tp = TimePeriod.NewInstance(dateTime, null); |
|
| 312 |
} |
|
| 289 | 313 |
facade.getGatheringEvent(true).setTimeperiod(tp); |
| 290 | 314 |
} |
| 291 | 315 |
//Country |
| ... | ... | |
| 404 | 428 |
*/ |
| 405 | 429 |
private ExtensionType getExtensionType() {
|
| 406 | 430 |
if (identificationHistoryType == null){
|
| 407 |
identificationHistoryType = ExtensionType.NewInstance("Identification History", "IdentificationHistory", null);
|
|
| 431 |
identificationHistoryType = ExtensionType.NewInstance("Identification History", "Identification History", null);
|
|
| 408 | 432 |
UUID vocUuid = uuidUserDefinedExtensionTypeVocabulary; |
| 409 | 433 |
TermVocabulary<ExtensionType> voc = getVocabularyService().find(vocUuid); |
| 410 | 434 |
if (voc == null){
|
| ... | ... | |
| 506 | 530 |
private TeamOrPersonBase<?> makeCollectorTeam(SalvadorSpecimenImportState state, Map<String, String> record, int row) {
|
| 507 | 531 |
|
| 508 | 532 |
Team team = Team.NewInstance(); |
| 509 |
makeCollector(state, 0, team, record, row); |
|
| 510 |
makeCollector(state, 1, team, record, row); |
|
| 511 |
makeCollector(state, 2, team, record, row); |
|
| 512 |
makeCollector(state, 3, team, record, row); |
|
| 513 |
makeCollector(state, 4, team, record, row); |
|
| 514 |
if (team.getTeamMembers().size() == 0){
|
|
| 515 |
return null; |
|
| 516 |
}else if (team.getTeamMembers().size() == 1){
|
|
| 517 |
return team.getTeamMembers().get(0); |
|
| 518 |
}else{
|
|
| 533 |
String first = record.get("COLLECTOR_0");
|
|
| 534 |
if(first != null && first.startsWith("Grupo Ecológico")){
|
|
| 535 |
team.setTitleCache(first, true); |
|
| 519 | 536 |
return team; |
| 537 |
}else{
|
|
| 538 |
makeCollector(state, 0, team, record, row); |
|
| 539 |
makeCollector(state, 1, team, record, row); |
|
| 540 |
makeCollector(state, 2, team, record, row); |
|
| 541 |
makeCollector(state, 3, team, record, row); |
|
| 542 |
makeCollector(state, 4, team, record, row); |
|
| 543 |
if (team.getTeamMembers().size() == 0){
|
|
| 544 |
return null; |
|
| 545 |
}else if (team.getTeamMembers().size() == 1){
|
|
| 546 |
return team.getTeamMembers().get(0); |
|
| 547 |
}else{
|
|
| 548 |
return team; |
|
| 549 |
} |
|
| 520 | 550 |
} |
| 521 | 551 |
} |
| 522 | 552 |
|
| ... | ... | |
| 527 | 557 |
if (str == null){
|
| 528 | 558 |
return; |
| 529 | 559 |
}else{
|
| 530 |
Person person = parsePerson(state, str, row); |
|
| 531 |
team.addTeamMember(person); |
|
| 560 |
parsePerson(state, str, team, row); |
|
| 532 | 561 |
} |
| 533 | 562 |
return ; |
| 534 | 563 |
} |
| 535 | 564 |
|
| 536 | 565 |
/** |
| 537 | 566 |
* @param str |
| 567 |
* @param team |
|
| 538 | 568 |
* @param row |
| 539 | 569 |
* @param importResult |
| 540 | 570 |
*/ |
| 541 |
private Person parsePerson(SalvadorSpecimenImportState state, String str, int row) {
|
|
| 571 |
private void parsePerson(SalvadorSpecimenImportState state, String str, Team team, int row) {
|
|
| 542 | 572 |
Person result = Person.NewInstance(); |
| 543 |
String regEx = "(.*),([A-Z]\\.)+";
|
|
| 573 |
String regEx = "(.*),(([A-Z]\\.)+(\\sde)?)";
|
|
| 544 | 574 |
Pattern pattern = Pattern.compile(regEx); |
| 545 | 575 |
Matcher matcher = pattern.matcher(str); |
| 546 | 576 |
|
| 577 |
String noInitials = "(Campo|Chinchilla|Campos|Claus|Desconocido|Fomtg|Huezo|Martínez|" |
|
| 578 |
+ "Quezada|Romero|Ruíz|Sandoval|Serrano|Vásquez|Cabrera|Calderón)"; |
|
| 547 | 579 |
|
| 548 | 580 |
if (matcher.matches()){
|
| 549 | 581 |
String lastname = matcher.group(1); |
| 550 | 582 |
result.setLastname(lastname); |
| 551 | 583 |
String initials = matcher.group(2); |
| 552 | 584 |
result.setInitials(initials); |
| 585 |
}else if (str.matches(noInitials)){
|
|
| 586 |
result.setLastname(str); |
|
| 587 |
}else if (str.matches("Martínez, F. de M.")){
|
|
| 588 |
result.setLastname("Martínez");
|
|
| 589 |
result.setInitials("F. de M.");
|
|
| 590 |
}else if (str.equals("et al.")){
|
|
| 591 |
team.setHasMoreMembers(true); |
|
| 592 |
return; |
|
| 593 |
}else if (str.startsWith("Grupo Ecológico")){
|
|
| 594 |
result.setLastname(str); |
|
| 553 | 595 |
}else{
|
| 554 | 596 |
String message = "Collector did not match pattern: " + str; |
| 555 | 597 |
state.getResult().addWarning(message, row); |
| ... | ... | |
| 557 | 599 |
} |
| 558 | 600 |
result = (Person)dedupHelper.getExistingAuthor(null, result); |
| 559 | 601 |
|
| 560 |
return result; |
|
| 602 |
team.addTeamMember(result); |
|
| 603 |
return ; |
|
| 561 | 604 |
} |
| 562 | 605 |
|
| 563 | 606 |
|
Also available in: Unified diff
ref #6792 fix latest issues in SalvadorSpecimenImport