Revision bb38665e
Added by Andreas Müller over 10 years ago
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonImport.java | ||
|---|---|---|
| 57 | 57 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 58 | 58 |
import eu.etaxonomy.cdm.model.name.TypeDesignationBase; |
| 59 | 59 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
| 60 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase; |
|
| 61 |
import eu.etaxonomy.cdm.model.occurrence.Specimen; |
|
| 60 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
|
| 62 | 61 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 63 | 62 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 64 | 63 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 65 | 64 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 66 | 65 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 67 | 66 |
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
| 67 |
import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser; |
|
| 68 | 68 |
|
| 69 | 69 |
|
| 70 | 70 |
/** |
| ... | ... | |
| 262 | 262 |
designation.setNotDesignated(true); |
| 263 | 263 |
} |
| 264 | 264 |
|
| 265 |
DerivedUnitBase specimen = designation.getTypeSpecimen();
|
|
| 265 |
DerivedUnit specimen = designation.getTypeSpecimen(); |
|
| 266 | 266 |
|
| 267 | 267 |
if (lastFacade != null){
|
| 268 | 268 |
lastFacade.addDuplicate(specimen); |
| ... | ... | |
| 335 | 335 |
private SpecimenTypeDesignation makeCachedSpecimenDesignation(String split) {
|
| 336 | 336 |
SpecimenTypeDesignation lastDesignation; |
| 337 | 337 |
lastDesignation = SpecimenTypeDesignation.NewInstance(); |
| 338 |
Specimen specimen = Specimen.NewInstance();
|
|
| 338 |
DerivedUnit specimen = DerivedUnit.NewPreservedSpecimenInstance();
|
|
| 339 | 339 |
specimen.setTitleCache(split, true); |
| 340 | 340 |
lastDesignation.setTypeSpecimen(specimen); |
| 341 | 341 |
return lastDesignation; |
| ... | ... | |
| 345 | 345 |
|
| 346 | 346 |
private SpecimenTypeDesignation makeSpecimenTypeCollection(SpecimenTypeDesignation designation, String collectionString, String strCollectionPattern, String strNumberPattern, String strAddInfoPattern) {
|
| 347 | 347 |
SpecimenTypeDesignation result = SpecimenTypeDesignation.NewInstance(); |
| 348 |
Specimen specimen = Specimen.NewInstance();
|
|
| 348 |
DerivedUnit specimen = DerivedUnit.NewPreservedSpecimenInstance();
|
|
| 349 | 349 |
result.setTypeSpecimen(specimen); |
| 350 | 350 |
|
| 351 | 351 |
//collection |
| ... | ... | |
| 513 | 513 |
if (strName.endsWith(",")){
|
| 514 | 514 |
strName = strName.substring(0, strName.length() -1); |
| 515 | 515 |
} |
| 516 |
BotanicalName result = (BotanicalName)NonViralNameParserImpl.NewInstance().parseFullName(strName, NomenclaturalCode.ICBN, Rank.SPECIES());
|
|
| 516 |
BotanicalName result = (BotanicalName)NonViralNameParserImpl.NewInstance().parseFullName(strName, NomenclaturalCode.ICNAFP, Rank.SPECIES());
|
|
| 517 | 517 |
return result; |
| 518 | 518 |
} |
| 519 | 519 |
|
| ... | ... | |
| 537 | 537 |
acceptedName = acceptedName.substring(0, acceptedName.length()-1); |
| 538 | 538 |
} |
| 539 | 539 |
acceptedName = acceptedName.replaceFirst("=", "").trim();
|
| 540 |
result[1] = (BotanicalName)NonViralNameParserImpl.NewInstance().parseFullName(acceptedName, NomenclaturalCode.ICBN, null);
|
|
| 540 |
result[1] = (BotanicalName)NonViralNameParserImpl.NewInstance().parseFullName(acceptedName, NomenclaturalCode.ICNAFP, null);
|
|
| 541 | 541 |
strName = notAcceptedName; |
| 542 | 542 |
} |
| 543 | 543 |
|
| 544 |
result[0] = (BotanicalName)NonViralNameParserImpl.NewInstance().parseFullName(strName, NomenclaturalCode.ICBN, Rank.SPECIES());
|
|
| 544 |
result[0] = (BotanicalName)NonViralNameParserImpl.NewInstance().parseFullName(strName, NomenclaturalCode.ICNAFP, Rank.SPECIES());
|
|
| 545 | 545 |
return result; |
| 546 | 546 |
} |
| 547 | 547 |
|
| 548 | 548 |
|
| 549 | 549 |
|
| 550 |
private String handleDesignatedBy(TypeDesignationBase typeDesignation, String typeString) {
|
|
| 550 |
private String handleDesignatedBy(TypeDesignationBase<?> typeDesignation, String typeString) {
|
|
| 551 | 551 |
String[] splitDesignated = typeString.split(", designated by ");
|
| 552 | 552 |
if (splitDesignated.length > 1){
|
| 553 | 553 |
Reference designationCitation = getDesignationCitation(typeDesignation, splitDesignated[1]); |
| ... | ... | |
| 561 | 561 |
|
| 562 | 562 |
|
| 563 | 563 |
|
| 564 |
private Reference getDesignationCitation(TypeDesignationBase typeDesignation, String citationString) {
|
|
| 564 |
private Reference getDesignationCitation(TypeDesignationBase<?> typeDesignation, String citationString) {
|
|
| 565 | 565 |
// TODO try to find an existing Reference |
| 566 | 566 |
Reference result = ReferenceFactory.newGeneric(); |
| 567 | 567 |
String strBracketPattern = "\\((10 Oct. )?\\d{4}:\\s?(\\d{1,3}(--\\d{1,3})?|[XLVI]{1,7}|\\.{1,8})\\)\\.?";
|
| ... | ... | |
| 589 | 589 |
Team team = Team.NewTitledInstance(authorPart, authorPart); |
| 590 | 590 |
result.setAuthorTeam(team); |
| 591 | 591 |
String[] bracketSplit = bracket.split(":");
|
| 592 |
TimePeriod datePublished = TimePeriod.parseString(bracketSplit[0].trim()); |
|
| 592 |
TimePeriod datePublished = TimePeriodParser.parseString(bracketSplit[0].trim());
|
|
| 593 | 593 |
result.setDatePublished(datePublished); |
| 594 | 594 |
String citationMicroReference = bracketSplit[1].trim(); |
| 595 | 595 |
citationMicroReference = citationMicroReference.replace("--", "-");
|
| ... | ... | |
| 657 | 657 |
if (StringUtils.isNotBlank(referenceString) || StringUtils.isNotBlank(volume) || |
| 658 | 658 |
StringUtils.isNotBlank(pages) || StringUtils.isNotBlank(illustrations) || |
| 659 | 659 |
StringUtils.isNotBlank(datePublishedString) || StringUtils.isNotBlank(paperTitle)){
|
| 660 |
NonViralName name = CdmBase.deproxy(taxonBase.getName(), NonViralName.class); |
|
| 661 |
Reference reference = ReferenceFactory.newGeneric(); |
|
| 662 |
reference.setAuthorTeam((TeamOrPersonBase)name.getCombinationAuthorTeam()); |
|
| 660 |
NonViralName<?> name = CdmBase.deproxy(taxonBase.getName(), NonViralName.class);
|
|
| 661 |
Reference<?> reference = ReferenceFactory.newGeneric();
|
|
| 662 |
reference.setAuthorTeam((TeamOrPersonBase<?>)name.getCombinationAuthorTeam());
|
|
| 663 | 663 |
reference.setTitle(referenceString); |
| 664 | 664 |
reference.setVolume(volume); |
| 665 | 665 |
reference.setEdition(part); |
| 666 |
Reference inrefernce = null; |
|
| 666 |
Reference<?> inrefernce = null;
|
|
| 667 | 667 |
//TODO parser |
| 668 |
TimePeriod datePublished = TimePeriod.parseString(datePublishedString); |
|
| 668 |
TimePeriod datePublished = TimePeriodParser.parseString(datePublishedString);
|
|
| 669 | 669 |
reference.setDatePublished(datePublished); |
| 670 | 670 |
if (StringUtils.isNotBlank(paperTitle)){
|
| 671 |
Reference innerReference = ReferenceFactory.newGeneric(); |
|
| 671 |
Reference<?> innerReference = ReferenceFactory.newGeneric();
|
|
| 672 | 672 |
innerReference.setDatePublished(datePublished); |
| 673 | 673 |
name.setNomenclaturalReference(innerReference); |
| 674 | 674 |
innerReference.setInReference(reference); |
Also available in: Unified diff
reintegrate cdmlib-app-3.3 branch into trunk