Revision ac5fb7af
Added by Andreas Müller about 7 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/cyprus/CyprusExcelImport.java | ||
|---|---|---|
| 32 | 32 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 33 | 33 |
import eu.etaxonomy.cdm.model.description.TextData; |
| 34 | 34 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 35 |
import eu.etaxonomy.cdm.model.name.BotanicalName;
|
|
| 35 |
import eu.etaxonomy.cdm.model.name.INonViralName;
|
|
| 36 | 36 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 37 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
|
| 38 | 37 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 39 | 38 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 40 | 39 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| ... | ... | |
| 517 | 516 |
private TaxonBase createTaxon(CyprusImportState state, Rank rank, String taxonNameStr, |
| 518 | 517 |
Class statusClass, NomenclaturalCode nc) {
|
| 519 | 518 |
TaxonBase taxonBase; |
| 520 |
NonViralName taxonNameBase = null; |
|
| 519 |
INonViralName taxonNameBase = null;
|
|
| 521 | 520 |
if (nc == NomenclaturalCode.ICVCN){
|
| 522 | 521 |
logger.warn("ICVCN not yet supported");
|
| 523 | 522 |
|
| 524 | 523 |
}else{
|
| 525 |
taxonNameBase =(NonViralName) nc.getNewTaxonNameInstance(rank); |
|
| 526 |
//NonViralName nonViralName = (NonViralName)taxonNameBase; |
|
| 527 |
INonViralNameParser parser = nameParser;//NonViralNameParserImpl.NewInstance(); |
|
| 528 |
taxonNameBase = (NonViralName<BotanicalName>)parser.parseFullName(taxonNameStr, nc, rank); |
|
| 524 |
taxonNameBase = nc.getNewTaxonNameInstance(rank); |
|
| 525 |
INonViralNameParser<INonViralName> parser = nameParser;//NonViralNameParserImpl.NewInstance(); |
|
| 526 |
taxonNameBase = parser.parseFullName(taxonNameStr, nc, rank); |
|
| 529 | 527 |
|
| 530 | 528 |
//taxonNameBase.setNameCache(taxonNameStr); |
| 531 | 529 |
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/EfloraTaxonImport.java | ||
|---|---|---|
| 58 | 58 |
import eu.etaxonomy.cdm.model.description.TextData; |
| 59 | 59 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 60 | 60 |
import eu.etaxonomy.cdm.model.name.HomotypicalGroup; |
| 61 |
import eu.etaxonomy.cdm.model.name.INonViralName; |
|
| 61 | 62 |
import eu.etaxonomy.cdm.model.name.NameRelationshipType; |
| 62 | 63 |
import eu.etaxonomy.cdm.model.name.NameTypeDesignation; |
| 63 | 64 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 64 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
|
| 65 | 65 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 66 | 66 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 67 | 67 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| ... | ... | |
| 610 | 610 |
if (strGoto == null){
|
| 611 | 611 |
return ""; |
| 612 | 612 |
} |
| 613 |
String strGenusName = CdmBase.deproxy(taxon.getName(), NonViralName.class).getGenusOrUninomial();
|
|
| 613 |
String strGenusName = taxon.getName().getGenusOrUninomial();
|
|
| 614 | 614 |
strGoto = strGoto.replaceAll("\\([^\\(\\)]*\\)", ""); //replace all brackets
|
| 615 | 615 |
strGoto = strGoto.replaceAll("\\s+", " "); //replace multiple whitespaces by exactly one whitespace
|
| 616 | 616 |
|
| ... | ... | |
| 622 | 622 |
split[i] = strGenusName; |
| 623 | 623 |
} |
| 624 | 624 |
// if (isInfraSpecificMarker(single)){
|
| 625 |
// String strSpeciesName = CdmBase.deproxy(taxon.getName(), NonViralName.class).getSpecificEpithet();
|
|
| 625 |
// String strSpeciesName = taxon.getName().getSpecificEpithet();
|
|
| 626 | 626 |
// split[i] = strGenusName + " " + strSpeciesName + " "; |
| 627 | 627 |
// } |
| 628 | 628 |
result = (result + " " + split[i]).trim(); |
| ... | ... | |
| 1152 | 1152 |
*/ |
| 1153 | 1153 |
//body/taxon/ |
| 1154 | 1154 |
private HomotypicalGroup handleNomTaxon(EfloraImportState state, Element elNom, Taxon taxon, HomotypicalGroup homotypicalGroup, boolean isSynonym) {
|
| 1155 |
NonViralName name = makeName(taxon, homotypicalGroup, isSynonym); |
|
| 1156 |
String num = null; |
|
| 1155 |
INonViralName nvn = makeName(taxon, homotypicalGroup, isSynonym); |
|
| 1156 |
TaxonNameBase<?,?> name = TaxonNameBase.castAndDeproxy(nvn); |
|
| 1157 |
String num = null; |
|
| 1157 | 1158 |
|
| 1158 | 1159 |
boolean hasGenusInfo = false; |
| 1159 |
TeamOrPersonBase lastTeam = null; |
|
| 1160 |
TeamOrPersonBase<?> lastTeam = null;
|
|
| 1160 | 1161 |
|
| 1161 | 1162 |
//genus |
| 1162 | 1163 |
List<Element> elGenus = XmlHelp.getAttributedChildListWithValue(elNom, "name", "class", "genus"); |
| ... | ... | |
| 1262 | 1263 |
} |
| 1263 | 1264 |
|
| 1264 | 1265 |
|
| 1265 |
private void handleQuestionMark(NonViralName name, Taxon taxon) {
|
|
| 1266 |
private void handleQuestionMark(INonViralName name, Taxon taxon) {
|
|
| 1266 | 1267 |
int count = name.getTaxonBases().size(); |
| 1267 | 1268 |
if (count != 1){
|
| 1268 | 1269 |
logger.warn("Name has " + count + " taxa. This is not handled for question mark");
|
| 1269 | 1270 |
}else{
|
| 1270 |
TaxonBase taxonBase = (TaxonBase)name.getTaxonBases().iterator().next();
|
|
| 1271 |
TaxonBase taxonBase = name.getTaxonBases().iterator().next(); |
|
| 1271 | 1272 |
taxonBase.setDoubtful(true); |
| 1272 | 1273 |
} |
| 1273 | 1274 |
} |
| 1274 | 1275 |
|
| 1275 | 1276 |
|
| 1276 | 1277 |
//merge with handleNomTaxon |
| 1277 |
private void handleHomonym(EfloraImportState state, Element elHomonym, NonViralName upperName) {
|
|
| 1278 |
private void handleHomonym(EfloraImportState state, Element elHomonym, TaxonNameBase upperName) {
|
|
| 1278 | 1279 |
verifyNoAttribute(elHomonym); |
| 1279 | 1280 |
|
| 1280 | 1281 |
//hommonym name |
| ... | ... | |
| 1326 | 1327 |
}else{
|
| 1327 | 1328 |
upperName.addRelationshipToName(homonymName, relType, null); |
| 1328 | 1329 |
} |
| 1329 |
|
|
| 1330 | 1330 |
} |
| 1331 | 1331 |
|
| 1332 | 1332 |
|
| ... | ... | |
| 1347 | 1347 |
} |
| 1348 | 1348 |
|
| 1349 | 1349 |
|
| 1350 |
private void handleNameNote(NonViralName name, String value) {
|
|
| 1350 |
private void handleNameNote(INonViralName name, String value) {
|
|
| 1351 | 1351 |
logger.warn("Name note: " + value + ". Available in portal?");
|
| 1352 | 1352 |
Annotation annotation = Annotation.NewInstance(value, AnnotationType.EDITORIAL(), Language.DEFAULT()); |
| 1353 | 1353 |
name.addAnnotation(annotation); |
| ... | ... | |
| 1359 | 1359 |
* @param name |
| 1360 | 1360 |
* @param value |
| 1361 | 1361 |
*/ |
| 1362 |
protected TeamOrPersonBase handleNameUsage(Taxon taxon, NonViralName<?> name, String referenceTitle, TeamOrPersonBase lastTeam) {
|
|
| 1362 |
protected TeamOrPersonBase handleNameUsage(Taxon taxon, INonViralName name, String referenceTitle, TeamOrPersonBase lastTeam) {
|
|
| 1363 | 1363 |
Reference ref = ReferenceFactory.newGeneric(); |
| 1364 | 1364 |
referenceTitle = removeStartingSymbols(referenceTitle, ref); |
| 1365 | 1365 |
|
| ... | ... | |
| 1374 | 1374 |
|
| 1375 | 1375 |
TaxonDescription description = getDescription(taxon); |
| 1376 | 1376 |
TextData textData = TextData.NewInstance(Feature.CITATION()); |
| 1377 |
textData.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, ref, microReference, name, null); |
|
| 1377 |
textData.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, ref, microReference, (TaxonNameBase)name, null);
|
|
| 1378 | 1378 |
description.addElement(textData); |
| 1379 | 1379 |
return team; |
| 1380 | 1380 |
} |
| ... | ... | |
| 1489 | 1489 |
* @param name |
| 1490 | 1490 |
* @return |
| 1491 | 1491 |
*/ |
| 1492 |
protected String parseHomonym(String detail, NonViralName name) {
|
|
| 1492 |
protected String parseHomonym(String detail, TaxonNameBase name) {
|
|
| 1493 | 1493 |
String result; |
| 1494 | 1494 |
if (detail == null){
|
| 1495 | 1495 |
return detail; |
| ... | ... | |
| 1521 | 1521 |
homonymName.setSpecificEpithet(name.getSpecificEpithet()); |
| 1522 | 1522 |
homonymName.setInfraSpecificEpithet(name.getInfraSpecificEpithet()); |
| 1523 | 1523 |
Reference homonymNomRef = ReferenceFactory.newGeneric(); |
| 1524 |
homonymNomRef.setTitleCache(homonymString); |
|
| 1524 |
homonymNomRef.setTitleCache(homonymString, true);
|
|
| 1525 | 1525 |
String homonymNomRefDetail = parseReferenceYearAndDetail(homonymNomRef); |
| 1526 | 1526 |
homonymName.setNomenclaturalMicroReference(homonymNomRefDetail); |
| 1527 | 1527 |
String authorTitle = homonymNomRef.getTitleCache(); |
| ... | ... | |
| 1558 | 1558 |
* @param name |
| 1559 | 1559 |
* @param value |
| 1560 | 1560 |
*/ |
| 1561 |
protected TeamOrPersonBase handleNomenclaturalReference(NonViralName name, String value) {
|
|
| 1561 |
protected TeamOrPersonBase handleNomenclaturalReference(TaxonNameBase name, String value) {
|
|
| 1562 | 1562 |
Reference nomRef = ReferenceFactory.newGeneric(); |
| 1563 | 1563 |
nomRef.setTitleCache(value, true); |
| 1564 | 1564 |
parseNomStatus(nomRef, name); |
| ... | ... | |
| 1566 | 1566 |
name.setNomenclaturalReference(nomRef); |
| 1567 | 1567 |
microReference = parseHomonym(microReference, name); |
| 1568 | 1568 |
name.setNomenclaturalMicroReference(microReference); |
| 1569 |
TeamOrPersonBase team = name.getCombinationAuthorship();
|
|
| 1569 |
TeamOrPersonBase<?> team = name.getCombinationAuthorship();
|
|
| 1570 | 1570 |
if (team == null){
|
| 1571 | 1571 |
logger.warn("Name has nom. ref. but no author team. Name: " + name.getTitleCache() + ", Nom.Ref.: " + value);
|
| 1572 | 1572 |
}else{
|
| ... | ... | |
| 1575 | 1575 |
return team; |
| 1576 | 1576 |
} |
| 1577 | 1577 |
|
| 1578 |
private void handleInfrAuthor(EfloraImportState state, Element elAuthor, NonViralName name, boolean overwrite) {
|
|
| 1578 |
private void handleInfrAuthor(EfloraImportState state, Element elAuthor, INonViralName name, boolean overwrite) {
|
|
| 1579 | 1579 |
String strAuthor = elAuthor.getValue().trim(); |
| 1580 | 1580 |
if (strAuthor.endsWith(",")){
|
| 1581 | 1581 |
strAuthor = strAuthor.substring(0, strAuthor.length() -1); |
| ... | ... | |
| 1600 | 1600 |
* @param infraRank |
| 1601 | 1601 |
* @return |
| 1602 | 1602 |
*/ |
| 1603 |
private Rank handleInfRank(NonViralName name, List<Element> elInfraRank, Rank infraRank) {
|
|
| 1603 |
private Rank handleInfRank(INonViralName name, List<Element> elInfraRank, Rank infraRank) {
|
|
| 1604 | 1604 |
if (elInfraRank.size() == 1){
|
| 1605 | 1605 |
String strRank = elInfraRank.get(0).getTextNormalize(); |
| 1606 | 1606 |
try {
|
| ... | ... | |
| 1622 | 1622 |
} |
| 1623 | 1623 |
|
| 1624 | 1624 |
|
| 1625 |
private void handleInfrEpi(NonViralName<?> name, Rank infraRank, String value) {
|
|
| 1625 |
private void handleInfrEpi(INonViralName name, Rank infraRank, String value) {
|
|
| 1626 | 1626 |
if (infraRank != null && infraRank.isInfraSpecific()){
|
| 1627 | 1627 |
name.setInfraSpecificEpithet(value); |
| 1628 | 1628 |
if (CdmUtils.isCapital(value)){
|
| ... | ... | |
| 1647 | 1647 |
* @param isSynonym |
| 1648 | 1648 |
* @return |
| 1649 | 1649 |
*/ |
| 1650 |
private NonViralName makeName(Taxon taxon,HomotypicalGroup homotypicalGroup, boolean isSynonym) {
|
|
| 1651 |
NonViralName name;
|
|
| 1650 |
private TaxonNameBase makeName(Taxon taxon,HomotypicalGroup homotypicalGroup, boolean isSynonym) {
|
|
| 1651 |
TaxonNameBase<?,?> name;
|
|
| 1652 | 1652 |
if (isSynonym){
|
| 1653 | 1653 |
name = BotanicalName.NewInstance(Rank.SPECIES(), homotypicalGroup); |
| 1654 | 1654 |
SynonymType synonymType = SynonymType.HETEROTYPIC_SYNONYM_OF(); |
| ... | ... | |
| 1657 | 1657 |
} |
| 1658 | 1658 |
taxon.addSynonymName(name, synonymType); |
| 1659 | 1659 |
}else{
|
| 1660 |
name = (NonViralName)taxon.getName();
|
|
| 1660 |
name = taxon.getName(); |
|
| 1661 | 1661 |
} |
| 1662 | 1662 |
return name; |
| 1663 | 1663 |
} |
| ... | ... | |
| 1667 | 1667 |
* @param element |
| 1668 | 1668 |
* @param taxon |
| 1669 | 1669 |
*/ |
| 1670 |
private void handleInfraspecificEpithet(Element element, String attrValue, NonViralName<?> name) {
|
|
| 1670 |
private void handleInfraspecificEpithet(Element element, String attrValue, INonViralName name) {
|
|
| 1671 | 1671 |
String value = element.getTextNormalize(); |
| 1672 | 1672 |
if (value.indexOf("subsp.") != -1){
|
| 1673 | 1673 |
//TODO genus and species epi |
| ... | ... | |
| 1690 | 1690 |
* @param element |
| 1691 | 1691 |
* @param name |
| 1692 | 1692 |
*/ |
| 1693 |
private void handleBasionymAuthor(EfloraImportState state, Element elBasionymAuthor, NonViralName name, boolean overwrite) {
|
|
| 1693 |
private void handleBasionymAuthor(EfloraImportState state, Element elBasionymAuthor, INonViralName name, boolean overwrite) {
|
|
| 1694 | 1694 |
String strAuthor = elBasionymAuthor.getValue().trim(); |
| 1695 | 1695 |
Pattern reBasionymAuthor = Pattern.compile("^\\(.*\\)$");
|
| 1696 | 1696 |
if (reBasionymAuthor.matcher(strAuthor).matches()){
|
| ... | ... | |
| 1714 | 1714 |
* @param name |
| 1715 | 1715 |
* @param elNom |
| 1716 | 1716 |
*/ |
| 1717 |
private void handleNameAuthors(Element elAuthor, NonViralName name) {
|
|
| 1717 |
private void handleNameAuthors(Element elAuthor, INonViralName name) {
|
|
| 1718 | 1718 |
if (name.getCombinationAuthorship() != null){
|
| 1719 | 1719 |
logger.warn("Name already has a combination author. Name: " + name.getTitleCache() + ", Author: " + elAuthor.getTextNormalize());
|
| 1720 | 1720 |
} |
| ... | ... | |
| 1955 | 1955 |
* @param value |
| 1956 | 1956 |
* @param taxonNameBase |
| 1957 | 1957 |
*/ |
| 1958 |
private void handleSubGenus(String value, TaxonNameBase taxonNameBase) {
|
|
| 1958 |
private void handleSubGenus(String value, INonViralName taxonNameBase) {
|
|
| 1959 | 1959 |
String name = value.replace("Subgenus", "").trim();
|
| 1960 |
((NonViralName)taxonNameBase).setInfraGenericEpithet(name);
|
|
| 1960 |
taxonNameBase.setInfraGenericEpithet(name);
|
|
| 1961 | 1961 |
} |
| 1962 | 1962 |
|
| 1963 | 1963 |
/** |
| 1964 | 1964 |
* @param value |
| 1965 | 1965 |
* @param taxonNameBase |
| 1966 | 1966 |
*/ |
| 1967 |
private void handleSection(String value, TaxonNameBase taxonNameBase) {
|
|
| 1967 |
private void handleSection(String value, INonViralName taxonNameBase) {
|
|
| 1968 | 1968 |
String name = value.replace("Section", "").trim();
|
| 1969 |
((NonViralName)taxonNameBase).setInfraGenericEpithet(name);
|
|
| 1969 |
taxonNameBase.setInfraGenericEpithet(name);
|
|
| 1970 | 1970 |
} |
| 1971 | 1971 |
|
| 1972 | 1972 |
/** |
| ... | ... | |
| 2000 | 2000 |
* @param value |
| 2001 | 2001 |
* @param taxonNameBase |
| 2002 | 2002 |
*/ |
| 2003 |
protected void handleGenus(String value, TaxonNameBase taxonName) {
|
|
| 2003 |
protected void handleGenus(String value, INonViralName taxonName) {
|
|
| 2004 | 2004 |
Matcher matcher = rexGenusAuthor.matcher(value); |
| 2005 | 2005 |
if (matcher.find()){
|
| 2006 | 2006 |
String author = matcher.group(); |
| ... | ... | |
| 2010 | 2010 |
team.setTitleCache(author, true); |
| 2011 | 2011 |
Credit credit = Credit.NewInstance(team, null); |
| 2012 | 2012 |
taxonName.addCredit(credit); |
| 2013 |
// NonViralName nvn = (NonViralName)taxonName; |
|
| 2014 |
// nvn.setCombinationAuthorship(team); |
|
| 2015 |
// nvn.setGenusOrUninomial(genus); |
|
| 2013 |
// taxonName.setCombinationAuthorship(team); |
|
| 2014 |
// taxonName.setGenusOrUninomial(genus); |
|
| 2016 | 2015 |
}else{
|
| 2017 | 2016 |
logger.info("No Author match for " + value);
|
| 2018 | 2017 |
} |
| ... | ... | |
| 2170 | 2169 |
* @param ref |
| 2171 | 2170 |
* @param nonViralName |
| 2172 | 2171 |
*/ |
| 2173 |
protected void parseNomStatus(Reference ref, NonViralName nonViralName) {
|
|
| 2172 |
protected void parseNomStatus(Reference ref, TaxonNameBase nonViralName) {
|
|
| 2174 | 2173 |
String titleToParse = ref.getTitleCache(); |
| 2175 | 2174 |
|
| 2176 | 2175 |
String noStatusTitle = parser.parseNomStatus(titleToParse, nonViralName, true); |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ericaceae/CentralAfricaEricaceaeTaxonImport.java | ||
|---|---|---|
| 31 | 31 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 32 | 32 |
import eu.etaxonomy.cdm.model.description.TextData; |
| 33 | 33 |
import eu.etaxonomy.cdm.model.name.HomotypicalGroup; |
| 34 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
|
| 34 |
import eu.etaxonomy.cdm.model.name.INonViralName;
|
|
| 35 | 35 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 36 | 36 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 37 | 37 |
import eu.etaxonomy.cdm.model.name.TypeDesignationBase; |
| ... | ... | |
| 47 | 47 |
*/ |
| 48 | 48 |
@Component |
| 49 | 49 |
public class CentralAfricaEricaceaeTaxonImport extends EfloraTaxonImport {
|
| 50 |
private static final Logger logger = Logger.getLogger(CentralAfricaEricaceaeTaxonImport.class); |
|
| 50 |
private static final long serialVersionUID = 6442665916458420942L; |
|
| 51 |
private static final Logger logger = Logger.getLogger(CentralAfricaEricaceaeTaxonImport.class); |
|
| 51 | 52 |
|
| 52 | 53 |
|
| 53 |
|
|
| 54 |
|
|
| 55 |
/* (non-Javadoc) |
|
| 56 |
* @see eu.etaxonomy.cdm.io.eflora.EfloraTaxonImport#handleNomenclaturalReference(eu.etaxonomy.cdm.model.name.NonViralName, java.lang.String) |
|
| 57 |
*/ |
|
| 58 | 54 |
@Override |
| 59 |
protected TeamOrPersonBase handleNomenclaturalReference(NonViralName name, String value) {
|
|
| 55 |
protected TeamOrPersonBase handleNomenclaturalReference(TaxonNameBase name, String value) {
|
|
| 60 | 56 |
Reference nomRef = ReferenceFactory.newGeneric(); |
| 61 | 57 |
nomRef.setTitleCache(value, true); |
| 62 | 58 |
parseNomStatus(nomRef, name); |
| ... | ... | |
| 68 | 64 |
microReference = parseHomonym(microReference, name); |
| 69 | 65 |
name.setNomenclaturalMicroReference(microReference); |
| 70 | 66 |
|
| 71 |
TeamOrPersonBase nameTeam = CdmBase.deproxy(name.getCombinationAuthorship(), TeamOrPersonBase.class); |
|
| 72 |
TeamOrPersonBase refTeam = nomRef.getAuthorship(); |
|
| 67 |
TeamOrPersonBase<?> nameTeam = CdmBase.deproxy(name.getCombinationAuthorship(), TeamOrPersonBase.class);
|
|
| 68 |
TeamOrPersonBase<?> refTeam = nomRef.getAuthorship();
|
|
| 73 | 69 |
if (nameTeam == null ){
|
| 74 | 70 |
logger.warn("Name has nom. ref. but no author team. Name: " + name.getTitleCache() + ", Nom.Ref.: " + value);
|
| 75 | 71 |
}else if (refTeam == null ){
|
| ... | ... | |
| 167 | 163 |
* @param value |
| 168 | 164 |
*/ |
| 169 | 165 |
@Override |
| 170 |
protected TeamOrPersonBase<?> handleNameUsage(Taxon taxon, NonViralName<?> name, String referenceTitle, TeamOrPersonBase lastTeam) {
|
|
| 166 |
protected TeamOrPersonBase<?> handleNameUsage(Taxon taxon, INonViralName name, |
|
| 167 |
String referenceTitle, TeamOrPersonBase lastTeam) {
|
|
| 168 |
|
|
| 171 | 169 |
Reference ref = ReferenceFactory.newGeneric(); |
| 172 | 170 |
|
| 173 | 171 |
ref.setTitleCache(referenceTitle, true); |
| ... | ... | |
| 190 | 188 |
// parseReferenceType(ref); |
| 191 | 189 |
|
| 192 | 190 |
TextData textData = TextData.NewInstance(Feature.CITATION()); |
| 193 |
textData.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, singleRef, microReference, name, null); |
|
| 191 |
textData.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, singleRef, microReference, (TaxonNameBase) name, null);
|
|
| 194 | 192 |
description.addElement(textData); |
| 195 | 193 |
} |
| 196 | 194 |
return team; |
| ... | ... | |
| 229 | 227 |
|
| 230 | 228 |
} |
| 231 | 229 |
|
| 232 |
protected TeamOrPersonBase getReferenceAuthor (Reference ref, NonViralName name) {
|
|
| 230 |
protected TeamOrPersonBase getReferenceAuthor (Reference ref, INonViralName name) {
|
|
| 233 | 231 |
String titleString = ref.getTitleCache(); |
| 234 | 232 |
String re = "\\(.*\\)"; |
| 235 | 233 |
Pattern pattern = Pattern.compile(re); |
| ... | ... | |
| 248 | 246 |
|
| 249 | 247 |
} |
| 250 | 248 |
|
| 251 |
private TeamOrPersonBase getAuthorTeam(String authorString, NonViralName name) {
|
|
| 249 |
private TeamOrPersonBase getAuthorTeam(String authorString, INonViralName name) {
|
|
| 252 | 250 |
//TODO atomize |
| 253 | 251 |
// TeamOrPersonBase nameTeam = CdmBase.deproxy(name.getCombinationAuthorship(), TeamOrPersonBase.class); |
| 254 | 252 |
// String nameTeamTitle = nameTeam == null ? "" : nameTeam.getNomenclaturalTitle(); |
| ... | ... | |
| 367 | 365 |
} |
| 368 | 366 |
|
| 369 | 367 |
@Override |
| 370 |
protected void handleGenus(String value, TaxonNameBase taxonName) {
|
|
| 368 |
protected void handleGenus(String value, INonViralName taxonName) {
|
|
| 371 | 369 |
// do nothing |
| 372 | 370 |
} |
| 373 | 371 |
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonImport.java | ||
|---|---|---|
| 45 | 45 |
import eu.etaxonomy.cdm.model.common.ExtensionType; |
| 46 | 46 |
import eu.etaxonomy.cdm.model.common.TimePeriod; |
| 47 | 47 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 48 |
import eu.etaxonomy.cdm.model.name.INonViralName; |
|
| 48 | 49 |
import eu.etaxonomy.cdm.model.name.NameTypeDesignation; |
| 49 | 50 |
import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus; |
| 50 | 51 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 51 | 52 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
| 52 | 53 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
| 53 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
|
| 54 | 54 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 55 | 55 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 56 | 56 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| ... | ... | |
| 647 | 647 |
if (StringUtils.isNotBlank(referenceString) || StringUtils.isNotBlank(volume) || |
| 648 | 648 |
StringUtils.isNotBlank(pages) || StringUtils.isNotBlank(illustrations) || |
| 649 | 649 |
StringUtils.isNotBlank(datePublishedString) || StringUtils.isNotBlank(paperTitle)){
|
| 650 |
NonViralName<?> name = CdmBase.deproxy(taxonBase.getName(), NonViralName.class);
|
|
| 650 |
INonViralName name = taxonBase.getName();
|
|
| 651 | 651 |
Reference reference = ReferenceFactory.newGeneric(); |
| 652 | 652 |
reference.setAuthorship(name.getCombinationAuthorship()); |
| 653 | 653 |
reference.setTitle(referenceString); |
| 654 | 654 |
reference.setVolume(volume); |
| 655 | 655 |
reference.setEdition(part); |
| 656 |
Reference inrefernce = null; |
|
| 656 |
Reference inreference = null;
|
|
| 657 | 657 |
//TODO parser |
| 658 | 658 |
TimePeriod datePublished = TimePeriodParser.parseString(datePublishedString); |
| 659 | 659 |
reference.setDatePublished(datePublished); |
| ... | ... | |
| 697 | 697 |
|
| 698 | 698 |
TaxonBase<?> taxonBase = state.getRelatedObject(state.CURRENT_OBJECT_NAMESPACE, state.CURRENT_OBJECT_ID, TaxonBase.class); |
| 699 | 699 |
if (StringUtils.isNotBlank(nomRemarksString)){
|
| 700 |
NonViralName name = CdmBase.deproxy(taxonBase.getName(), NonViralName.class);
|
|
| 700 |
INonViralName name = taxonBase.getName();
|
|
| 701 | 701 |
parseNomRemark(state, name, nomRemarksString.trim(),taxonStatus, taxonNumber); |
| 702 | 702 |
} |
| 703 | 703 |
return taxonBase; |
| ... | ... | |
| 707 | 707 |
} |
| 708 | 708 |
|
| 709 | 709 |
|
| 710 |
private void parseNomRemark(CentralAfricaFernsImportState state, NonViralName name, String nomRemarksString, String taxonStatus, String taxonNumber) {
|
|
| 710 |
private void parseNomRemark(CentralAfricaFernsImportState state, INonViralName name, String nomRemarksString, String taxonStatus, String taxonNumber) {
|
|
| 711 | 711 |
|
| 712 | 712 |
if (nomRemarksString.equalsIgnoreCase("comb. illeg.")){
|
| 713 | 713 |
name.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.COMBINATION_ILLEGITIMATE())); |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonRelationImport.java | ||
|---|---|---|
| 48 | 48 |
import eu.etaxonomy.cdm.model.location.NamedAreaLevel; |
| 49 | 49 |
import eu.etaxonomy.cdm.model.location.NamedAreaType; |
| 50 | 50 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 51 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
|
| 51 |
import eu.etaxonomy.cdm.model.name.INonViralName;
|
|
| 52 | 52 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 53 | 53 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 54 | 54 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 142 | 142 |
|
| 143 | 143 |
List<Taxon> taxonList = getTaxonService().list(Taxon.class, null, null, null, propPath ); |
| 144 | 144 |
for (Taxon taxon : taxonList){
|
| 145 |
NonViralName<?> nvn = CdmBase.deproxy(taxon.getName(), NonViralName.class);
|
|
| 145 |
INonViralName nvn = taxon.getName();
|
|
| 146 | 146 |
UUID uuid = taxon.getUuid(); |
| 147 | 147 |
String nameCache = nvn.getNameCache(); |
| 148 | 148 |
String titleCache = nvn.getTitleCache(); |
| ... | ... | |
| 401 | 401 |
* @param constructedHigherTaxon |
| 402 | 402 |
*/ |
| 403 | 403 |
private Taxon mergeExistingAndConstructedTaxon(CentralAfricaFernsImportState state, Taxon existingTaxon, Taxon constructedTaxon) {
|
| 404 |
NonViralName<?> constructedName = CdmBase.deproxy(constructedTaxon.getName(), NonViralName.class);
|
|
| 405 |
NonViralName<?> existingName = CdmBase.deproxy(existingTaxon.getName(), NonViralName.class);
|
|
| 404 |
INonViralName constructedName = constructedTaxon.getName();
|
|
| 405 |
INonViralName existingName = existingTaxon.getName();
|
|
| 406 | 406 |
if (constructedName.hasAuthors()){
|
| 407 | 407 |
if (! existingName.hasAuthors()){
|
| 408 | 408 |
logger.warn(state.getTaxonNumber() + " - Constrcucted name ("+constructedName.getTitleCache()+") has authors but existing name ("+existingName.getTitleCache()+") has no authors");
|
| ... | ... | |
| 574 | 574 |
* @param name2 |
| 575 | 575 |
* @return |
| 576 | 576 |
*/ |
| 577 |
private boolean authorsMatch(NonViralName<?> name1, NonViralName<?> name2) {
|
|
| 577 |
private boolean authorsMatch(INonViralName name1, INonViralName name2) {
|
|
| 578 | 578 |
String combinationAuthor1 = name1.computeCombinationAuthorNomenclaturalTitle(); |
| 579 | 579 |
String combinationAuthor2 = name2.computeCombinationAuthorNomenclaturalTitle(); |
| 580 | 580 |
String basionymAuthor1 = name1.computeBasionymAuthorNomenclaturalTitle(); |
| ... | ... | |
| 1187 | 1187 |
* @param existingHigherTaxon |
| 1188 | 1188 |
*/ |
| 1189 | 1189 |
private boolean mergeAuthors_old(Taxon higherTaxon, Taxon existingHigherTaxon) {
|
| 1190 |
NonViralName<?> existingName = CdmBase.deproxy(higherTaxon.getName(), NonViralName.class);
|
|
| 1191 |
NonViralName<?> newName = CdmBase.deproxy(existingHigherTaxon.getName(), NonViralName.class);
|
|
| 1190 |
INonViralName existingName = higherTaxon.getName();
|
|
| 1191 |
INonViralName newName = existingHigherTaxon.getName();
|
|
| 1192 | 1192 |
if (existingName == newName){
|
| 1193 | 1193 |
return true; |
| 1194 | 1194 |
} |
Also available in: Unified diff
ref #6369 adapt existing occurrences of interface to removed generics in cdmlib-app