Revision 9dc896c9
Added by Andreas Müller almost 7 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/in/SDDImport.java | ||
|---|---|---|
| 81 | 81 |
import eu.etaxonomy.cdm.model.name.INonViralName; |
| 82 | 82 |
import eu.etaxonomy.cdm.model.name.ITaxonNameBase; |
| 83 | 83 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 84 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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|
| 84 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 85 | 85 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
| 86 | 86 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
| 87 | 87 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 115 | 115 |
private Map<String,Reference> publications = new HashMap<>(); |
| 116 | 116 |
private Map<String,State> states = new HashMap<>(); |
| 117 | 117 |
private Map<String,TaxonDescription> taxonDescriptions = new HashMap<>(); |
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private Map<String,INonViralName> taxonNameBases = new HashMap<>();
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|
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private Map<String,INonViralName> taxonNames = new HashMap<>(); |
|
| 119 | 119 |
private Map<String,MeasurementUnit> units = new HashMap<>(); |
| 120 | 120 |
private Map<String,TaxonNode> taxonNodes = new HashMap<>(); |
| 121 | 121 |
private Map<String,NamedArea> namedAreas = new HashMap<>(); |
| ... | ... | |
| 170 | 170 |
publications = new HashMap<>(); |
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states = new HashMap<>(); |
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taxonDescriptions = new HashMap<>(); |
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taxonNameBases = new HashMap<>();
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|
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taxonNames = new HashMap<>(); |
|
| 174 | 174 |
units = new HashMap<>(); |
| 175 | 175 |
taxonNodes = new HashMap<>(); |
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namedAreas = new HashMap<>(); |
| ... | ... | |
| 490 | 490 |
Element elRepresentation, Map<Language, List<String>> langLabDet) {
|
| 491 | 491 |
List<String> labDet = null; |
| 492 | 492 |
|
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if (ie instanceof TaxonNameBase) {
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|
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if (ie instanceof TaxonName) {
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|
| 494 | 494 |
if (langLabDet.keySet().contains(getTermService().getLanguageByIso("la"))) {
|
| 495 | 495 |
labDet = langLabDet.get(getTermService().getLanguageByIso("la"));
|
| 496 | 496 |
} else if (langLabDet.keySet().contains(datasetLanguage)) {
|
| ... | ... | |
| 504 | 504 |
labDet = langLabDet.get(langLabDet.keySet().iterator().next()); |
| 505 | 505 |
} |
| 506 | 506 |
|
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//FIXME labDet is != null only for TaxonNameBase
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//FIXME labDet is != null only for TaxonName |
|
| 508 | 508 |
ie.setTitleCache(labDet.get(0), true); |
| 509 | 509 |
|
| 510 | 510 |
if (labDet.size()>1) {
|
| ... | ... | |
| 916 | 916 |
String id = elTaxonName.getAttributeValue("id");
|
| 917 | 917 |
String uri = elTaxonName.getAttributeValue("uri");
|
| 918 | 918 |
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TaxonNameBase<?,?> tnb = null;
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TaxonName tnb = null; |
|
| 920 | 920 |
if (!id.equals("")) {
|
| 921 | 921 |
tnb = TaxonNameFactory.NewNonViralInstance(defaultRank); |
| 922 | 922 |
IdentifiableSource source = null; |
| ... | ... | |
| 927 | 927 |
source = IdentifiableSource.NewDataImportInstance(id, "TaxonName"); |
| 928 | 928 |
} |
| 929 | 929 |
tnb.addSource(source); |
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taxonNameBases.put(id,tnb);
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taxonNames.put(id,tnb); |
|
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} |
| 932 | 932 |
|
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// <Representation> |
| ... | ... | |
| 1223 | 1223 |
private Taxon handleCDNoScope(Namespace sddNamespace, |
| 1224 | 1224 |
SDDImportState cdmState, Element elCodedDescription ) {
|
| 1225 | 1225 |
Taxon taxon = null; |
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TaxonNameBase<?,?> nonViralName = TaxonNameFactory.NewNonViralInstance(defaultRank);
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TaxonName nonViralName = TaxonNameFactory.NewNonViralInstance(defaultRank); |
|
| 1227 | 1227 |
String id = new String("" + taxonNamesCount);
|
| 1228 | 1228 |
IdentifiableSource source = IdentifiableSource.NewDataImportInstance(id, "TaxonName"); |
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importRepresentation(elCodedDescription, sddNamespace, nonViralName, id, cdmState); |
| ... | ... | |
| 1234 | 1234 |
|
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if(taxon != null){
|
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nonViralName = CdmBase.deproxy(taxon.getName()); |
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// taxonNameBases.put(id ,tnb);
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// taxonNames.put(id ,tnb); |
|
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// taxonNamesCount++; |
| 1239 | 1239 |
logger.info("using existing Taxon " + taxon.getTitleCache());
|
| 1240 | 1240 |
} else {
|
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nonViralName.addSource(source); |
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taxonNameBases.put(id, nonViralName);
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taxonNames.put(id, nonViralName); |
|
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taxonNamesCount++; |
| 1244 | 1244 |
logger.info("creating new Taxon from TaxonName " + nonViralName.getTitleCache());
|
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taxon = Taxon.NewInstance(nonViralName, sec); |
| ... | ... | |
| 1260 | 1260 |
Taxon taxon = null; |
| 1261 | 1261 |
Element elTaxonName = elScope.getChild("TaxonName", sddNamespace);
|
| 1262 | 1262 |
String ref = elTaxonName.getAttributeValue("ref");
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INonViralName nonViralName = taxonNameBases.get(ref);
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INonViralName nonViralName = taxonNames.get(ref); |
|
| 1264 | 1264 |
|
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if(cdmState.getConfig().isReuseExistingTaxaWhenPossible()){
|
| 1266 | 1266 |
taxon = getTaxonService().findBestMatchingTaxon(nonViralName.getTitleCache()); |
| ... | ... | |
| 1269 | 1269 |
if(taxon != null){
|
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logger.info("using existing Taxon" + taxon.getTitleCache());
|
| 1271 | 1271 |
if(!nonViralName.getUuid().equals(taxon.getName().getUuid())){
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logger.warn("TaxonNameBase entity of existing taxon does not match Name in list -> replacing Name in list");
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logger.warn("TaxonName entity of existing taxon does not match Name in list -> replacing Name in list");
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nonViralName = taxon.getName(); |
| 1274 | 1274 |
} |
| 1275 | 1275 |
} else {
|
| ... | ... | |
| 1649 | 1649 |
// rb.addMedia(me); |
| 1650 | 1650 |
// } |
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// } |
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// else if (lcb.get(k) instanceof TaxonNameBase){
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// TaxonNameBase tb = (TaxonNameBase) lcb.get(k);
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// else if (lcb.get(k) instanceof TaxonName){
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// TaxonName tb = (TaxonName) lcb.get(k);
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|
| 1654 | 1654 |
// tb.addMedia(media); |
| 1655 | 1655 |
} else {
|
| 1656 | 1656 |
logger.warn("Can't handle associated media for " + lcb.get(k).getId() + "(" + lcb.get(k).getClass().getSimpleName()+")" );
|
| ... | ... | |
| 1905 | 1905 |
if (!idN.equals("")) {
|
| 1906 | 1906 |
Element elTaxonName = elNode.getChild("TaxonName", sddNamespace);
|
| 1907 | 1907 |
String refTN = elTaxonName.getAttributeValue("ref");
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tnb = taxonNameBases.get(refTN);
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tnb = taxonNames.get(refTN); |
|
| 1909 | 1909 |
Taxon taxon = tnb.getTaxa().iterator().next() ; |
| 1910 | 1910 |
Element elParent = elNode.getChild("Parent", sddNamespace);
|
| 1911 | 1911 |
if (elParent!=null){
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Also available in: Unified diff
fix #6368 rename table and class TaxonNameBase