Revision 0c392a47
Added by Andreas Müller about 12 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiRelTaxonExport.java | ||
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import eu.etaxonomy.cdm.io.common.Source; |
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import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
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import eu.etaxonomy.cdm.model.common.RelationshipBase; |
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import eu.etaxonomy.cdm.model.name.NameRelationship; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| ... | ... | |
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Taxon childNodeTaxon = childNode.getTaxon(); |
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if (childNodeTaxon != null) {
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// TaxonRelationships |
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Taxon taxon = childNodeTaxon; |
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Set<TaxonRelationship> taxonRelations = taxon.getRelationsToThisTaxon(); |
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for (TaxonRelationship taxonRelationship : taxonRelations) {
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success &= saveTaxonRelationships(state, childNodeTaxon); |
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// TaxonNameRelationships |
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success &= saveNameRelationships(state, childNodeTaxon); |
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// SynonymRelationships |
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success &= saveSynonymAndSynNameRelationships(state, childNodeTaxon); |
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} |
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return success; |
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} |
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private boolean saveSynonymAndSynNameRelationships(PesiExportState state, Taxon childNodeTaxon) {
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boolean success = true; |
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for (SynonymRelationship synRel : childNodeTaxon.getSynonymRelations()) { // synonyms of accepted taxon
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Synonym synonym = synRel.getSynonym(); |
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TaxonNameBase<?,?> synonymTaxonName = synonym.getName(); |
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if (! isPesiTaxon(synonym)){
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logger.warn("Synonym " + synonym.getId() + " of synonym relation " + synRel.getId() + " is not a PESI taxon. Can't export relationship");
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continue; |
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} |
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// Store synonym data in Taxon table |
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invokeSynonyms(state, synonymTaxonName); |
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Set<SynonymRelationship> synonymRelations = synonym.getSynonymRelations(); |
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state.setCurrentFromObject(synonym); |
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for (SynonymRelationship synonymRelationship : synonymRelations) { //needed? Maybe to make sure that there are no partial synonym relations missed ??
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try {
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if (neededValuesNotNull(taxonRelationship, state)) {
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if (neededValuesNotNull(synonymRelationship, state)) {
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doCount(count++, modCount, pluralString); |
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success &= mapping.invoke(taxonRelationship); |
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success &= mapping.invoke(synonymRelationship); |
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} |
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} catch (SQLException e) {
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logger.error("TaxonRelationship could not be created for this TaxonRelation (" + taxonRelationship.getUuid() + "): " + e.getMessage());
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logger.error("SynonymRelationship (" + synonymRelationship.getUuid() + ") could not be stored : " + e.getMessage());
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} |
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} |
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// // TaxonNameRelationships |
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TaxonNameBase<?,?> childNodeTaxonName = childNodeTaxon.getName(); |
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if (childNodeTaxonName != null) {
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Set<NameRelationship> nameRelations = childNodeTaxonName.getRelationsFromThisName(); |
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for (NameRelationship nameRelation : nameRelations) {
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try {
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if (neededValuesNotNull(nameRelation, state)) {
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doCount(count++, modCount, pluralString); |
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success &= mapping.invoke(nameRelation); |
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} |
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} catch (SQLException e) {
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logger.error("NameRelationship " + nameRelation.getUuid() + " for " + nameRelation.getFromName().getTitleCache() + " and " + nameRelation.getToName().getTitleCache() + " could not be created: " + e.getMessage());
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} |
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} |
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} |
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// SynonymRelationships |
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Set<Synonym> synonyms = childNodeTaxon.getSynonyms(); // synonyms of accepted taxon |
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for (Synonym synonym : synonyms) {
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TaxonNameBase<?,?> synonymTaxonName = synonym.getName(); |
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// Store synonym data in Taxon table |
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invokeSynonyms(state, synonymTaxonName); |
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Set<SynonymRelationship> synonymRelations = synonym.getSynonymRelations(); |
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for (SynonymRelationship synonymRelationship : synonymRelations) {
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try {
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if (neededValuesNotNull(synonymRelationship, state)) {
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doCount(count++, modCount, pluralString); |
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success &= mapping.invoke(synonymRelationship); |
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} |
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} catch (SQLException e) {
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logger.error("SynonymRelationship could not be created for this SynonymRelation (" + synonymRelationship.getUuid() + "): " + e.getMessage());
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// SynonymNameRelationship |
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success &= saveNameRelationships(state, synonym); |
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} |
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return success; |
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} |
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private boolean saveNameRelationships(PesiExportState state, TaxonBase taxonBase) {
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boolean success = true; |
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TaxonNameBase<?,?> childNodeTaxonName = taxonBase.getName(); |
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//from relations |
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Set<NameRelationship> nameRelations = childNodeTaxonName.getRelationsFromThisName(); |
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state.setCurrentFromObject(taxonBase); |
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boolean isFrom = true; |
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success &= saveOneSideNameRelation(state, isFrom, nameRelations); |
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//toRelations |
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nameRelations = childNodeTaxonName.getRelationsToThisName(); |
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state.setCurrentToObject(taxonBase); |
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isFrom = false; |
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success &= saveOneSideNameRelation(state, isFrom, nameRelations); |
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return success; |
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} |
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private boolean saveOneSideNameRelation(PesiExportState state, boolean isFrom, Set<NameRelationship> nameRelations) {
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boolean success = true; |
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for (NameRelationship nameRelation : nameRelations) {
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try {
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TaxonNameBase<?,?> relatedName = isFrom ? nameRelation.getToName(): nameRelation.getFromName(); |
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if ( isPurePesiName(relatedName)){
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success &= checkAndInvokeNameRelation(state, nameRelation, relatedName, isFrom); |
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}else{
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for (TaxonBase<?> relatedTaxon : getPesiTaxa(relatedName)){
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success &= checkAndInvokeNameRelation(state, nameRelation, relatedTaxon, isFrom); |
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} |
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} |
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} catch (SQLException e) {
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logger.error("NameRelationship " + nameRelation.getUuid() + " for " + nameRelation.getFromName().getTitleCache() + " and " + nameRelation.getToName().getTitleCache() + " could not be created: " + e.getMessage());
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success = false; |
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} |
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} |
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return success; |
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} |
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// // SynonymNameRelationship |
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// Set<NameRelationship> nameRelations = synonymTaxonName.getRelationsFromThisName(); |
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// for (NameRelationship nameRelation : nameRelations) {
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// try {
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// if (neededValuesNotNull(nameRelation, state)) {
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// doCount(count++, modCount, pluralString); |
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// success &= mapping.invoke(nameRelation); |
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// } |
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// } catch (SQLException e) {
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// logger.error("NameRelationship could not be created for this NameRelation (" + nameRelation.getUuid() + "): " + e.getMessage());
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// } |
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// } |
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private boolean checkAndInvokeNameRelation(PesiExportState state, NameRelationship nameRelation, IdentifiableEntity<?> relatedObject, boolean isFrom) throws SQLException {
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boolean success = true; |
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if (isFrom){
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state.setCurrentToObject(relatedObject); |
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}else{
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state.setCurrentFromObject(relatedObject); |
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} |
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if (neededValuesNotNull(nameRelation, state)) {
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doCount(count++, modCount, pluralString); |
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success &= mapping.invoke(nameRelation); |
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} |
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return success; |
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} |
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private boolean saveTaxonRelationships(PesiExportState state, Taxon childNodeTaxon) {
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boolean success = true; |
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Taxon taxon = childNodeTaxon; |
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Set<TaxonRelationship> taxonRelations = taxon.getRelationsToThisTaxon(); |
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for (TaxonRelationship taxonRelationship : taxonRelations) {
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try {
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if (neededValuesNotNull(taxonRelationship, state)) {
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doCount(count++, modCount, pluralString); |
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success &= mapping.invoke(taxonRelationship); |
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} |
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} catch (SQLException e) {
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logger.error("TaxonRelationship could not be created for this TaxonRelation (" + taxonRelationship.getUuid() + "): " + e.getMessage());
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} |
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} |
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return success; |
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} |
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/** |
| ... | ... | |
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* @return The database key of an object in the given relationship. |
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*/ |
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private static Integer getObjectFk(RelationshipBase<?, ?, ?> relationship, PesiExportState state, boolean isFrom) {
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TaxonBase<?> taxon = null; |
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TaxonBase<?> taxonBase = null;
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if (relationship.isInstanceOf(TaxonRelationship.class)) {
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TaxonRelationship tr = (TaxonRelationship)relationship; |
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taxon = (isFrom) ? tr.getFromTaxon(): tr.getToTaxon(); |
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taxonBase = (isFrom) ? tr.getFromTaxon(): tr.getToTaxon();
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} else if (relationship.isInstanceOf(SynonymRelationship.class)) {
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SynonymRelationship sr = (SynonymRelationship)relationship; |
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taxon = (isFrom) ? sr.getSynonym() : sr.getAcceptedTaxon(); |
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taxonBase = (isFrom) ? sr.getSynonym() : sr.getAcceptedTaxon();
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} else if (relationship.isInstanceOf(NameRelationship.class)) {
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NameRelationship nr = (NameRelationship)relationship; |
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TaxonNameBase<?,?> taxonName = (isFrom) ? nr.getFromName() : nr.getToName(); |
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return state.getDbId(taxonName); |
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if (isFrom){
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return state.getDbId(state.getCurrentFromObject()); |
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}else{
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return state.getDbId(state.getCurrentToObject()); |
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} |
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} |
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if (taxon != null) {
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if (! isPesiTaxon(taxon)){
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logger.warn("Related taxon is not a PESI taxon. Taxon: " + taxon.getId() + "/" + taxon.getUuid() + "; TaxonRel: " + relationship.getId() + "(" + relationship.getType().getTitleCache() + ")");
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if (taxonBase != null) {
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if (! isPesiTaxon(taxonBase)){
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logger.warn("Related taxonBase is not a PESI taxon. Taxon: " + taxonBase.getId() + "/" + taxonBase.getUuid() + "; TaxonRel: " + relationship.getId() + "(" + relationship.getType().getTitleCache() + ")");
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| 500 | 545 |
return null; |
| 501 | 546 |
}else{
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return state.getDbId(taxon); |
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return state.getDbId(taxonBase);
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| 503 | 548 |
} |
| 504 | 549 |
|
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} |
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