Revision 4d8fb1a4
Added by Alexander Oppermann about 9 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/bfnXml/BfnXmlImportTaxonName.java | ||
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| 10 | 10 |
package eu.etaxonomy.cdm.io.redlist.bfnXml; |
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|
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import java.util.ArrayList; |
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import java.util.Arrays; |
|
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import java.util.Collection; |
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import java.util.HashMap; |
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import java.util.LinkedHashMap; |
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import java.util.List; |
| 18 | 16 |
import java.util.Map; |
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import java.util.Set; |
|
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import java.util.UUID; |
| 21 | 18 |
|
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import org.apache.commons.lang.StringUtils; |
| 23 | 20 |
import org.apache.log4j.Logger; |
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import org.apache.poi.ss.formula.functions.T; |
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import org.hibernate.Session; |
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import org.jdom.Attribute; |
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import org.jdom.Element; |
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import org.jdom.Namespace; |
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import org.springframework.stereotype.Component; |
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import org.springframework.transaction.TransactionStatus; |
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import com.google.common.base.CharMatcher; |
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import eu.etaxonomy.cdm.api.service.IClassificationService; |
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import eu.etaxonomy.cdm.api.service.ITaxonService; |
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import eu.etaxonomy.cdm.api.service.config.MatchingTaxonConfigurator; |
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import eu.etaxonomy.cdm.api.service.pager.Pager; |
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import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge; |
|
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import eu.etaxonomy.cdm.common.ResultWrapper; |
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import eu.etaxonomy.cdm.common.XmlHelp; |
| 41 | 30 |
import eu.etaxonomy.cdm.io.common.ICdmIO; |
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import eu.etaxonomy.cdm.io.common.ImportHelper; |
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import eu.etaxonomy.cdm.io.common.MapWrapper; |
|
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
|
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import eu.etaxonomy.cdm.model.common.Language; |
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import eu.etaxonomy.cdm.model.common.RelationshipBase; |
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import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction; |
|
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import eu.etaxonomy.cdm.model.description.CategoricalData; |
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import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
|
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
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import eu.etaxonomy.cdm.model.description.Feature; |
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import eu.etaxonomy.cdm.model.description.State; |
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import eu.etaxonomy.cdm.model.description.TaxonDescription; |
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import eu.etaxonomy.cdm.model.description.TextData; |
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import eu.etaxonomy.cdm.model.location.NamedArea; |
|
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
| 58 | 44 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
| 59 | 45 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 60 | 46 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
|
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import eu.etaxonomy.cdm.model.taxon.Classification; |
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import eu.etaxonomy.cdm.model.taxon.Synonym; |
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
| ... | ... | |
| 106 | 90 |
|
| 107 | 91 |
BfnXmlImportConfigurator config = state.getConfig(); |
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Element elDataSet = getDataSetElement(config); |
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//TODO set Namespace |
|
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Namespace bfnNamespace = config.getBfnXmlNamespace(); |
| 110 | 95 |
|
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List<?> contentXML = elDataSet.getContent(); |
| ... | ... | |
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createOrUdateClassification(config, taxonService, savedTaxonMap, currentElement, state); |
| 122 | 107 |
commitTransaction(tx); |
| 123 | 108 |
}//import concept relations of taxon lists |
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else if(currentElement.getName().equalsIgnoreCase("KONZEPTBEZIEHUNGEN")){
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TransactionStatus tx = startTransaction(); |
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extractTaxonConceptRelationShips(bfnNamespace,currentElement); |
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commitTransaction(tx); |
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if(config.isHasSecondList()){
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if(currentElement.getName().equalsIgnoreCase("KONZEPTBEZIEHUNGEN")){
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TransactionStatus tx = startTransaction(); |
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extractTaxonConceptRelationShips(bfnNamespace,currentElement); |
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commitTransaction(tx); |
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} |
|
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} |
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} |
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} |
| ... | ... | |
| 248 | 235 |
Element elSynonyms = XmlHelp.getSingleChildElement(success, elTaxon, childName, bfnNamespace, obligatory); |
| 249 | 236 |
if(elSynonyms != null){
|
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childElementName = "SYNONYM"; |
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createOrUpdateSynonym(taxon, success, obligatory, bfnNamespace, childElementName,elSynonyms, taxonId, config); |
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createOrUpdateSynonym(taxon, success, obligatory, bfnNamespace, childElementName,elSynonyms, taxonId, state); |
|
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} |
|
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//for vernacular name |
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childName = "DEUTSCHENAMEN"; |
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Element elVernacularName = XmlHelp.getSingleChildElement(success, elTaxon, childName, bfnNamespace, obligatory); |
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if(elVernacularName != null){
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childElementName = "DNAME"; |
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createOrUpdateVernacularName(taxon, bfnNamespace, childElementName, elVernacularName, state); |
|
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} |
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//for each information concerning the taxon element |
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//TODO Information block |
| ... | ... | |
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} |
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|
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/** |
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* This will put the prior imported list into a classification |
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* |
| ... | ... | |
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@SuppressWarnings("rawtypes")
|
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private boolean createOrUdateClassification(BfnXmlImportConfigurator config, ITaxonService taxonService, Map<UUID, TaxonBase> savedTaxonMap, Element currentElement, BfnXmlImportState state) {
|
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boolean isNewClassification = true; |
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String classificationName = state.getFirstClassificationName(); |
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if(config.isFillSecondList()){
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classificationName = state.getSecondClassificationName(); |
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} |
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// if(classificationName == null){
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// classificationName = config.getClassificationName(); |
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// } |
|
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//TODO make classification name dynamically depending on its value in the XML. |
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Classification classification = Classification.NewInstance(config.getClassificationName()+" "+currentElement.getAttributeValue("inhalt"), state.getCurrentRef());
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Classification classification = Classification.NewInstance(classificationName+" "+currentElement.getAttributeValue("inhalt"), state.getCompleteSourceRef());
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classification.addImportSource(Integer.toString(classification.getId()), classification.getTitleCache(), state.getCompleteSourceRef(), state.getCurrentMicroRef().toString()); |
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// List<Classification> classificationList = getClassificationService().list(Classification.class, null, null, null, VOC_CLASSIFICATION_INIT_STRATEGY); |
| 298 | 302 |
// for(Classification c : classificationList){
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// if(c.getTitleCache().equalsIgnoreCase(classification.getTitleCache())){
|
| ... | ... | |
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String strAuthor = null; |
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String strSupplement = null; |
| 350 | 354 |
Taxon taxon = null; |
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Integer uniqueID = null; |
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String uniqueID = null; |
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String uriNameSpace = null; |
|
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// Long uniqueID = null; |
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for(Element elWissName:elWissNameList){
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if(elWissName.getAttributeValue("bereich", bfnNamespace).equalsIgnoreCase("Eindeutiger Code")){
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uriNameSpace = elWissName.getAttributeValue("bereich");
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String textNormalize = elWissName.getTextNormalize(); |
| 357 | 363 |
if(StringUtils.isBlank(textNormalize)){
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uniqueID = -1;
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uniqueID = "";
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}else{
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uniqueID = Integer.valueOf(textNormalize);
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uniqueID = textNormalize;
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} |
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} |
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if(elWissName.getAttributeValue("bereich", bfnNamespace).equalsIgnoreCase("Autoren")){
|
| ... | ... | |
| 397 | 403 |
// if (nameList.size()>1){
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// logger.warn("More than 1 matching taxon name found for " + nameBase.getTitleCache());
|
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// } |
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// } |
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// }CurrentMicroRef
|
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// taxon = (Taxon) taxonBase; |
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state.setCurrentRef(state.getFirstListSecRef()); |
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state.setCurrentMicroRef(state.getFirstListSecRef());
|
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if(config.isFillSecondList()){
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state.setCurrentRef(state.getSecondListSecRef()); |
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state.setCurrentMicroRef(state.getSecondListSecRef());
|
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} |
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taxon = Taxon.NewInstance(nameBase, state.getCurrentRef()); |
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taxon.addImportSource(uniqueID.toString(), config.getBfnXmlNamespace().toString(), state.getCurrentRef(), null); |
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taxon = Taxon.NewInstance(nameBase, state.getCurrentMicroRef()); |
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// logger.info("Taxon Reference" + taxon.getSec().getTitle());
|
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//set NameSpace |
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Element parentElement = elWissName.getParentElement(); |
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Element grandParentElement = parentElement.getParentElement(); |
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// Element newElement = new Element("prefix", parentElement.getName()+":"+parentElement.getAttribute("taxNr").getName());
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// Element newElement = new Element("element",grandParentElement.getName()+"-"+parentElement.getName()+"-"+elWissName.getName() , uriNameSpace);
|
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// config.setBfnXmlNamespace(newElement.getNamespace()); |
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|
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taxon.addImportSource(uniqueID, grandParentElement.getName()+":"+parentElement.getName()+":"+elWissName.getName()+":"+uriNameSpace, state.getCompleteSourceRef(), state.getCurrentMicroRef().getTitle()); |
|
| 409 | 423 |
} catch (UnknownCdmTypeException e) {
|
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success.setValue(false); |
| 411 | 425 |
} |
| ... | ... | |
| 427 | 441 |
* @param elSynonyms |
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* @param taxonId |
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* @param config |
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* @param state |
|
| 430 | 445 |
*/ |
| 431 | 446 |
|
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@SuppressWarnings({ "unchecked" })
|
| 433 | 448 |
private void createOrUpdateSynonym(Taxon taxon, ResultWrapper<Boolean> success, boolean obligatory, Namespace bfnNamespace, |
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String childElementName, Element elSynonyms, String taxonId, BfnXmlImportConfigurator config) {
|
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String childElementName, Element elSynonyms, String taxonId, BfnXmlImportState state) {
|
|
| 435 | 450 |
|
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String childName; |
| 437 | 452 |
List<Element> elSynonymList = (List<Element>)elSynonyms.getChildren(childElementName, bfnNamespace); |
| ... | ... | |
| 462 | 477 |
TaxonNameBase<?, ?> nameBase = parseNonviralNames(rank,strAuthor,strSupplement,elSynDetail); |
| 463 | 478 |
|
| 464 | 479 |
//TODO find best matching Taxa |
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Synonym synonym = Synonym.NewInstance(nameBase, config.getSourceReference());
|
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Synonym synonym = Synonym.NewInstance(nameBase, state.getCurrentMicroRef());
|
|
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taxon.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF()); |
| 467 | 482 |
|
| 468 | 483 |
} catch (UnknownCdmTypeException e) {
|
| ... | ... | |
| 476 | 491 |
} |
| 477 | 492 |
} |
| 478 | 493 |
|
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|
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/** |
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* |
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* @param taxon |
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* @param bfnNamespace |
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* @param childElementName |
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* @param elVernacularName |
|
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* @param state |
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*/ |
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private void createOrUpdateVernacularName(Taxon taxon, |
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Namespace bfnNamespace, String childElementName, |
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Element elVernacularName, BfnXmlImportState state) {
|
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|
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List<Element> elVernacularNameList = (List<Element>)elVernacularName.getChildren(childElementName, bfnNamespace); |
|
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|
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TaxonDescription taxonDescription = getTaxonDescription(taxon, false, true); |
|
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for(Element elVernacular : elVernacularNameList){
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Element child = elVernacular.getChild("TRIVIALNAME");
|
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if(child != null){
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makeCommonName(taxonDescription, child, state); |
|
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} |
|
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} |
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|
|
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} |
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|
|
| 479 | 520 |
/** |
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* |
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* @param taxon |
| ... | ... | |
| 537 | 578 |
if(elInfoDetail.getAttributeValue("standardname").equalsIgnoreCase("Kommentar zur Gefährdung")){
|
| 538 | 579 |
makeFeatures(taxonDescription, elInfoDetail, state, true); |
| 539 | 580 |
} |
| 581 |
if(elInfoDetail.getAttributeValue("standardname").equalsIgnoreCase("Sonderfälle")){
|
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makeFeatures(taxonDescription, elInfoDetail, state, false); |
|
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} |
|
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if(elInfoDetail.getAttributeValue("standardname").equalsIgnoreCase("Letzter Nachweis")){
|
|
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makeFeatures(taxonDescription, elInfoDetail, state, true); |
|
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} |
|
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if(elInfoDetail.getAttributeValue("standardname").equalsIgnoreCase("Weitere Kommentare")){
|
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makeFeatures(taxonDescription, elInfoDetail, state, true); |
|
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} |
|
| 540 | 590 |
} |
| 541 | 591 |
} |
| 542 | 592 |
} |
| 543 | 593 |
|
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|
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|
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private void makeCommonName(TaxonDescription taxonDescription, |
|
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Element child, BfnXmlImportState state) {
|
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String commonNameValue = child.getValue(); |
|
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NamedArea area = getTermService().getAreaByTdwgAbbreviation("GER");
|
|
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CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameValue, Language.GERMAN(), area); |
|
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taxonDescription.addElement(commonName); |
|
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} |
|
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|
|
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|
|
| 544 | 605 |
/** |
| 545 | 606 |
* |
| 546 | 607 |
* @param taxonDescription |
| ... | ... | |
| 553 | 614 |
Element elInfoDetail, |
| 554 | 615 |
BfnXmlImportState state, |
| 555 | 616 |
boolean isTextData) {
|
| 617 |
|
|
| 556 | 618 |
String transformedRlKatValue = null; |
| 557 | 619 |
UUID featureUUID = null; |
| 558 | 620 |
UUID stateTermUUID = null; |
| ... | ... | |
| 641 | 703 |
TaxonNameBase<?,?> taxonNameBase = null; |
| 642 | 704 |
|
| 643 | 705 |
NomenclaturalCode nomCode = BfnXmlTransformer.nomCodeString2NomCode(strNomenclaturalCode); |
| 644 |
|
|
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//Todo check author |
|
| 645 | 707 |
String strScientificName = elWissName.getTextNormalize(); |
| 646 | 708 |
if(strSupplement != null && !strSupplement.isEmpty()){
|
| 647 | 709 |
strScientificName = StringUtils.remove(strScientificName, strSupplement); |
Also available in: Unified diff
Adapted Redlist Import to new XML Schema...