Revision 3cbea5bb
Added by Andreas Müller over 3 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonRelationImport.java | ||
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import org.springframework.stereotype.Component; |
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import org.springframework.transaction.TransactionStatus; |
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import eu.etaxonomy.cdm.common.CdmUtils; |
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import eu.etaxonomy.cdm.common.ResultWrapper; |
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import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer; |
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import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelTaxonRelationImportValidator; |
| ... | ... | |
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import eu.etaxonomy.cdm.model.common.AnnotatableEntity; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
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import eu.etaxonomy.cdm.model.name.NameRelationshipType; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
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import eu.etaxonomy.cdm.model.name.TaxonName; |
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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.SynonymType; |
| ... | ... | |
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship; |
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; |
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; |
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
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import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser; |
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/** |
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* @author a.mueller |
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private static final Logger logger = Logger.getLogger(BerlinModelTaxonRelationImport.class); |
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public static final String TREE_NAMESPACE = "PTRefFk"; |
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private static final Integer AUCT_REF_ID = 5959; |
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private static int modCount = 30000; |
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private static final String pluralString = "taxon relations"; |
| ... | ... | |
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int relPTaxonId = rs.getInt("RelPTaxonId");
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Integer taxon1Id = nullSafeInt(rs, "taxon1Id"); |
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Integer taxon2Id = nullSafeInt(rs, "taxon2Id"); |
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Integer ptRefFk1 = nullSafeInt(rs, "PTRefFk1"); |
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int relQualifierFk = -1; |
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try {
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Integer relRefFk = nullSafeInt(rs,"relRefFk"); |
| ... | ... | |
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if (relQualifierFk == TAX_REL_IS_INCLUDED_IN){
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taxonRelationship = makeTaxonomicallyIncluded(state, classificationMap, treeRefFk, fromTaxon, toTaxon, citation, microcitation); |
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}else if (relQualifierFk == TAX_REL_IS_MISAPPLIED_NAME_OF){
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taxonRelationship = toTaxon.addMisappliedName(fromTaxon, citation, microcitation); |
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boolean isProParte = "p.p.".equals(notes); |
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if (isProParte){
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notes = null; |
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} |
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boolean isDoubtful = "?".equals(notes); |
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if (isDoubtful){
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notes = null; |
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} |
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if (notes!= null && notes.startsWith("{non ") && notes.endsWith("}")){
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notes = notes.substring(1, notes.length() - 1); |
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} |
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//handle auct. author |
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if (fromTaxon.getSec() == null || fromTaxon.getSec().getTitleCache().startsWith("auct.")){
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String existingSecTitle = fromTaxon.getSec() == null ? null : fromTaxon.getSec().getTitleCache().trim(); |
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String existingAppendedPhrase = fromTaxon.getAppendedPhrase(); |
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if (fromTaxon.getSec() == null && isBlank(existingAppendedPhrase)){
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existingAppendedPhrase = "auct."; |
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} |
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fromTaxon.setSec(null); |
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if (isNotBlank(existingAppendedPhrase) && isNotBlank(notes)){
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logger.warn("Misapplied name has >1 MA relation with a note, RelId: " + relPTaxonId);
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} |
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String newAppendedPhrase = CdmUtils.concat(", ", existingSecTitle, notes);
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fromTaxon.setAppendedPhrase(CdmUtils.concat("; ", existingAppendedPhrase, newAppendedPhrase));
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if (isBlank(fromTaxon.getAppendedPhrase())){
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logger.warn("Appended phrase is empty. This is probably not correct. RelID: " + relPTaxonId);
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}else if ("auct.".equals(fromTaxon.getAppendedPhrase())){
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fromTaxon.setAppendedPhrase(null); |
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} |
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notes = null; |
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}else if (notes != null && notes.startsWith("non ")){
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fromTaxon.setAppendedPhrase(CdmUtils.concat(", ", fromTaxon.getAppendedPhrase(), notes));
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notes = null; |
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} |
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if (isProParte){
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taxonRelationship = toTaxon.addProParteMisappliedName(fromTaxon, citation, microcitation); |
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}else{
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taxonRelationship = toTaxon.addMisappliedName(fromTaxon, citation, microcitation); |
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} |
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if (isDoubtful){
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((TaxonRelationship)taxonRelationship).setDoubtful(true); |
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} |
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}else if (relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF || |
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//TODO homo/hetero |
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relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF || |
| ... | ... | |
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success = false; |
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logger.warn("Synonym relationship type not yet implemented: " + relQualifierFk);
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} |
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// |
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notes = handleSynonymNotes(state, toTaxon, synonym, notes, relPTaxonId); |
|
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}else if (isConceptRelationship){
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ResultWrapper<Boolean> isInverse = ResultWrapper.NewInstance(false); |
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ResultWrapper<Boolean> isDoubtful = ResultWrapper.NewInstance(false); |
| ... | ... | |
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success = false; |
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} |
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if (taxonRelationship != null){
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if (taxonRelationship != null && isNotBlank(notes)){
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doNotes(taxonRelationship, notes); |
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}else if (isNotBlank(notes)){
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logger.warn("Notes for synonym relationship or unknown taxon relationship not handled. RelID: " + relPTaxonId + ". Note: " + notes);
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} |
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if (isNotBlank(notes)){
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logger.warn("Notes in RelPTaxon should all be handled explicitly and should not exist as notes anymore. RelID: " + relPTaxonId + ". Note: " + notes);
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} |
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taxaToSave.add(taxon2); |
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|
| ... | ... | |
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} |
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private void handleAllRelatedTaxa(BerlinModelImportState state, Taxon taxon, Map<Integer, Classification> classificationMap, Integer secRefFk) {
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/** |
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* @param toTaxon |
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* @param synonym |
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* @param notes |
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* @return |
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*/ |
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private String handleSynonymNotes(BerlinModelImportState state, Taxon toTaxon, Synonym synonym, String notes, int relId) {
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if (state.getConfig().isEuroMed() && isNotBlank(notes)){
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notes = notes.trim(); |
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if (notes.startsWith("[non ") && notes.endsWith("]")){
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notes = notes.substring(5, notes.length()-1).trim(); |
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String[] splits = notes.split(", nec ");
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for (String split : splits){
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String nameStr = split.replace("<i>", "").replace("</i>", "");
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NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance(); |
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TaxonName name; |
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NomenclaturalStatusType status = null; |
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if (nameStr.endsWith(", nom. rej.") || nameStr.endsWith(", nom. cons.")||nameStr.endsWith(", nom. illeg.")){
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String statusStr = nameStr.endsWith(", nom. rej.")? ", nom. rej.":
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nameStr.endsWith(", nom. cons.")? ", nom. cons.":
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", nom. illeg."; |
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nameStr = nameStr.replace(statusStr, ""); |
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statusStr = statusStr.replace(", ", "");
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try {
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status = NomenclaturalStatusType.getNomenclaturalStatusTypeByAbbreviation(statusStr, null); |
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} catch (UnknownCdmTypeException e) {
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logger.warn("NomStatusType not recognized: "+ statusStr + ", RelId: " + relId);
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} |
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} |
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if (nameStr.contains(",") || nameStr.contains(" in ") ){
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name = parser.parseReferencedName(nameStr, state.getConfig().getNomenclaturalCode(), null); |
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}else if (nameStr.matches(".*\\s\\d{4}")){
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String nameStr2 = nameStr.substring(0, nameStr.length() - 5).trim(); |
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String yearStr = nameStr.substring(nameStr.length()-4); |
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name = (TaxonName)parser.parseFullName(nameStr2, state.getConfig().getNomenclaturalCode(), null); |
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Reference nomRef = name.getNomenclaturalReference(); |
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if (nomRef == null){
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nomRef = ReferenceFactory.newGeneric(); |
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name.setNomenclaturalReference(nomRef); |
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} |
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nomRef.setDatePublished(TimePeriodParser.parseStringVerbatim(yearStr)); |
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}else if (nameStr.endsWith(" 1831-1832")){
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String nameStr2 = nameStr.substring(0, nameStr.length() - 10).trim(); |
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name = (TaxonName)parser.parseFullName(nameStr2, state.getConfig().getNomenclaturalCode(), null); |
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Reference nomRef = name.getNomenclaturalReference(); |
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if (nomRef == null){
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nomRef = ReferenceFactory.newGeneric(); |
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name.setNomenclaturalReference(nomRef); |
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} |
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nomRef.setDatePublished(TimePeriodParser.parseStringVerbatim("1831-1832"));
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}else{
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name = parser.parseReferencedName(nameStr, state.getConfig().getNomenclaturalCode(), null); |
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} |
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if (name.isProtectedTitleCache() || name.isProtectedNameCache() |
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|| name.getNomenclaturalReference() != null && (name.getNomenclaturalReference().isProtectedAbbrevTitleCache()|| name.getNomenclaturalReference().isProtectedTitleCache() )){
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logger.warn("Blocking name for synonym relation could not be parsed: " + nameStr + ", RelId: "+ relId);
|
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} |
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if (status != null){
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name.addStatus(NomenclaturalStatus.NewInstance(status)); |
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} |
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synonym.getName().addRelationshipFromName(name, NameRelationshipType.BLOCKING_NAME_FOR(), null, null, null); |
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|
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getNameService().saveOrUpdate(name); |
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} |
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return null; |
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}else{
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return notes; |
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} |
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}else{
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return notes; |
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} |
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} |
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|
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private void handleAllRelatedTaxa(BerlinModelImportState state, Taxon taxon, |
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Map<Integer, Classification> classificationMap, Integer secRefFk) {
|
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if (taxon.getTaxonNodes().size() > 0){
|
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return; |
| 402 | 535 |
}else{
|
Also available in: Unified diff
E+M latest changes to taxon relations import