Revision ac5fb7af
Added by Andreas Müller about 7 years ago
| 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); |
Also available in: Unified diff
ref #6369 adapt existing occurrences of interface to removed generics in cdmlib-app