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package eu.etaxonomy.cdm.app.pesi.merging;
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import java.io.File;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.OutputStreamWriter;
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import java.io.Writer;
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import java.lang.reflect.InvocationTargetException;
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import java.lang.reflect.Method;
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import java.nio.charset.StandardCharsets;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.api.application.CdmApplicationController;
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import eu.etaxonomy.cdm.app.common.CdmDestinations;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.common.StringComparator;
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import eu.etaxonomy.cdm.database.DbSchemaValidation;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.io.api.application.CdmIoApplicationController;
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import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer;
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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.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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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.persistence.dto.TaxonNodeDto;
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public class PesiFindIdenticalNamesActivator {
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private static final Logger logger = Logger.getLogger(PesiFindIdenticalNamesActivator.class);
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//static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.localH2();
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static final ICdmDataSource pesiSource = CdmDestinations.cdm_pesi2019_final();
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static final String path = System.getProperty("user.home")+File.separator+".cdmLibrary"+File.separator+"pesi"+File.separator+"pesimerge";
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private static UUID emSourceUuid = PesiTransformer.uuidSourceRefEuroMed;
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private static UUID ermsSourceUuid = PesiTransformer.uuidSourceRefErms;
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private static UUID faunaEuSourceUuid = PesiTransformer.uuidSourceRefFaunaEuropaea;
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private static UUID ifSourceUuid = PesiTransformer.uuidSourceRefIndexFungorum;
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private static List<UUID> sourceRefUuids = new ArrayList<>();
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private static Map<UUID,String> sourcesLabels = new HashMap<>();
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static {
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sourceRefUuids.addAll(Arrays.asList(new UUID[]{emSourceUuid, ermsSourceUuid, faunaEuSourceUuid, ifSourceUuid}));
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sourcesLabels.put(emSourceUuid, "E+M");
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sourcesLabels.put(ermsSourceUuid, "ERMS");
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sourcesLabels.put(faunaEuSourceUuid, "FauEu");
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sourcesLabels.put(ifSourceUuid, "IF");
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}
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private void invoke(ICdmDataSource source){
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CdmApplicationController app = CdmIoApplicationController.NewInstance(source, DbSchemaValidation.VALIDATE, false);
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List<String> propertyPaths = new ArrayList<>();
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propertyPaths.add("sources.*");
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propertyPaths.add("sources.idInSource");
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propertyPaths.add("sources.idNamespace");
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propertyPaths.add("taxonBases.*");
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propertyPaths.add("taxonBases.relationsFromThisTaxon");
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propertyPaths.add("taxonBases.taxonNodes.*");
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propertyPaths.add("taxonBases.taxonNodes.parent.*");
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propertyPaths.add("taxonBases.taxonNodes.childNodes.*");
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propertyPaths.add("taxonBases.taxonNodes.childNodes.classification.rootNode.childNodes.*");
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propertyPaths.add("taxonBases.taxonNodes.parent.taxon.name.*");
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propertyPaths.add("taxonBases.acceptedTaxon.taxonNodes.*");
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propertyPaths.add("taxonBases.acceptedTaxon.taxonNodes.childNodes.*");
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propertyPaths.add("taxonBases.acceptedTaxon.taxonNodes.childNodes.classification.rootNode.childNodes.*");
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System.out.println("Start getIdenticalNames...");
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Map<String, Map<UUID, Set<TaxonName>>> namesOfIdenticalTaxa;
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TransactionStatus tx = app.startTransaction(true);
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try {
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namesOfIdenticalTaxa = app.getTaxonService().findIdenticalTaxonNames(sourceRefUuids, propertyPaths);
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} catch (Exception e) {
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e.printStackTrace();
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return;
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}
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System.out.println("Start creating merging objects");
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List<Map<UUID, List<PesiMergeObject>>> mergingObjects = createMergeObjects(namesOfIdenticalTaxa, app);
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app.commitTransaction(tx);
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boolean resultOK = true;
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System.out.println("Start creating csv files");
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resultOK &= writeSameNamesToCsvFile(mergingObjects, path + "_namesAll.csv");
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resultOK &= writeSameNamesDifferentAuthorToCsv(mergingObjects, path + "_authors.csv");
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resultOK &= writeSameNamesDifferentStatusToCsv(mergingObjects, path + "_status.csv");
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resultOK &= writeSameNamesDifferentPhylumToCsv(mergingObjects, path + "_phylum.csv");
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resultOK &= writeSameNamesDifferentParentToCsv(mergingObjects, path + "_parent.csv");
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resultOK &= writeSameNamesDifferentRankToCsv(mergingObjects, path + "_rank.csv");
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System.out.println("End find identical names for PESI: " + resultOK + ". Results written to " + path);
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}
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private boolean writeSameNamesToCsvFile(
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List<Map<UUID,List<PesiMergeObject>>> mergingObjects, String sFileName) {
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String header = "same names (all)";
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String methodName = null;
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return writeDifference(header, methodName, mergingObjects, sFileName);
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}
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private boolean writeSameNamesDifferentPhylumToCsv(
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List<Map<UUID,List<PesiMergeObject>>> mergingObjects, String sFileName){
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String header = "same names but different phylum";
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String methodName = "getPhylum";
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return writeDifference(header, methodName, mergingObjects, sFileName);
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}
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private boolean writeSameNamesDifferentParentToCsv(
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List<Map<UUID,List<PesiMergeObject>>> mergingObjects, String sFileName){
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String header = "same names but different parent";
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String methodName = "getParentString";
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return writeDifference(header, methodName, mergingObjects, sFileName);
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}
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private boolean writeSameNamesDifferentRankToCsv(
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List<Map<UUID,List<PesiMergeObject>>> mergingObjects, String sFileName){
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String header = "same names but different rank";
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String methodName = "getRank";
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return writeDifference(header, methodName, mergingObjects, sFileName);
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}
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private boolean writeSameNamesDifferentStatusToCsv(
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List<Map<UUID,List<PesiMergeObject>>> mergingObjects, String sFileName){
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String header = "same names but different status";
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String methodName = "isStatus";
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return writeDifference(header, methodName, mergingObjects, sFileName);
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}
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private boolean writeSameNamesDifferentAuthorToCsv(
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List<Map<UUID,List<PesiMergeObject>>> mergingObjects, String sFileName){
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String header = "same names but different author";
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String methodName = "getAuthor";
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return writeDifference(header, methodName, mergingObjects, sFileName);
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}
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private boolean writeDifference(String header,
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String methodName,
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List<Map<UUID,List<PesiMergeObject>>> mergingObjects,
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String sFileName) {
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try{
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Method method = methodName == null? null : PesiMergeObject.class.getMethod(methodName);
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Writer writer = new OutputStreamWriter(new FileOutputStream(new File(sFileName)), StandardCharsets.UTF_8);
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//create Header
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createHeader(writer, header);
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//write data
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for (Map<UUID,List<PesiMergeObject>> merging : mergingObjects){
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boolean isNextNameCache = true;
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List<UUID> mySources = new ArrayList<>(merging.keySet());
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for (int i = 0; i<mySources.size()-1; i++){
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for (int j = i+1; j<mySources.size(); j++){
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boolean differenceExists = false;
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List<PesiMergeObject> mergeList1 = merging.get(mySources.get(i));
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List<PesiMergeObject> mergeList2 = merging.get(mySources.get(j));
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for (PesiMergeObject merge1 : mergeList1){
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for (PesiMergeObject merge2 : mergeList2){
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differenceExists |= isDifferent(merge1, merge2, method);
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}
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}
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if (differenceExists){
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for (PesiMergeObject merge1 : mergeList1){
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for (PesiMergeObject merge2 : mergeList2){
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writeCsvLine(writer, merge1, merge2, method, isNextNameCache);
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isNextNameCache = false;
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}
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}
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}
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}
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}
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}
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writer.flush();
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writer.close();
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return true;
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}catch(NoSuchMethodException | SecurityException | IOException e){
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logger.error(e.getMessage());
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return false;
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}
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}
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private boolean isDifferent(PesiMergeObject merge1, PesiMergeObject merge2, Method method){
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try {
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if (method == null){
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return true;
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}
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Object value1 = method.invoke(merge1);
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Object value2 = method.invoke(merge2);
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return !CdmUtils.nullSafeEqual(value1, value2);
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} catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
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e.printStackTrace();
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return true;
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}
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}
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//old method when all sources were in 1 line
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private boolean isDifferent(Map<UUID, PesiMergeObject> merging, Method method)
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throws IllegalAccessException, IllegalArgumentException, InvocationTargetException {
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if (method == null){
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return true;
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}
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Object value = null;
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boolean isFirst = true;
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for (UUID sourceUuid: merging.keySet()){
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if (isFirst){
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value = method.invoke(merging.get(sourceUuid));
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isFirst = false;
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}else{
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Object newValue = method.invoke(merging.get(sourceUuid));
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if (!CdmUtils.nullSafeEqual(newValue, value)){
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return true;
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}
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}
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}
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return false;
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}
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private void createHeader(Writer writer, String firstLine){
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try {
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writer.append(firstLine);
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writer.append('\n');
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writeHeaderPair(writer, "taxon uuid");
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writeHeaderPair(writer, "taxon id");
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writer.append("next name cache").append(";");
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writer.append("diff").append(";");
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writeHeaderPair(writer, "source");
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writeHeaderPair(writer, "name uuid");
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writeHeaderPair(writer, "idInSource");
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writeHeaderPair(writer, "nameCache");
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writeHeaderPair(writer, "author");
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writeHeaderPair(writer, "rank");
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writeHeaderPair(writer, "kingdom");
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writeHeaderPair(writer, "phylum");
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writeHeaderPair(writer, "family");
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writeHeaderPair(writer, "parentString");
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writeHeaderPair(writer, "parentRankString");
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writeHeaderPair(writer, "status");
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writer.append('\n');
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} catch (IOException e) {
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e.printStackTrace();
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}
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}
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private void writeHeaderPair(Writer writer, String header) throws IOException {
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writer.append(header+"1").append(';');
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writer.append(header+"2").append(';');
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}
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private void writeCsvLine(Writer writer,
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PesiMergeObject merge1, PesiMergeObject merge2,
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Method method, boolean isNextNameCache){
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writePair(writer, merge1, merge2, "UuidTaxon");
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writePair(writer, merge1, merge2, "IdTaxon");
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writeSingleValue(writer, isNextNameCache?"1":"0");
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boolean different = isDifferent(merge1, merge2, method);
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writeSingleValue(writer, different?"1":"0");
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writeSingleValue(writer, sourcesLabels.get(UUID.fromString(merge1.getUuidSource())));
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writeSingleValue(writer, sourcesLabels.get(UUID.fromString(merge2.getUuidSource())));
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writePair(writer, merge1, merge2, "UuidName");
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writePair(writer, merge1, merge2, "IdInSource");
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writePair(writer, merge1, merge2, "NameCache");
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writePair(writer, merge1, merge2, "Author");
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writePair(writer, merge1, merge2, "Rank");
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writePairNode(writer, merge1, merge2, "Kingdom");
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writePairNode(writer, merge1, merge2, "Phylum");
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writePairNode(writer, merge1, merge2, "Family");
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writePair(writer, merge1, merge2, "ParentString");
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writePair(writer, merge1, merge2, "ParentRankString");
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writeSingleValue(writer, merge1.isStatus()?"accepted":"synonym");
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writeSingleValue(writer, merge2.isStatus()?"accepted":"synonym");
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try {
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writer.append('\n');
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} catch (IOException e) {
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e.printStackTrace();
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}
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}
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305
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306
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private void writeSingleValue(Writer writer, String value) {
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try {
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writer.append(value).append(";");
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} catch (Exception e) {
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310
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e.printStackTrace();
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}
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}
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313
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314
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private void writePairNode(Writer writer, PesiMergeObject merge1, PesiMergeObject merge2, String methodName) {
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try {
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Method method = PesiMergeObject.class.getDeclaredMethod("get"+methodName);
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TaxonNodeDto value = (TaxonNodeDto) method.invoke(merge1);
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writer.append(value==null?"":value.getTitleCache()).append(";");
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value = (TaxonNodeDto) method.invoke(merge2);
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writer.append(value==null?"":value.getTitleCache()).append(";");
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} catch (Exception e) {
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e.printStackTrace();
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}
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324
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}
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325
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326
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private void writePair(Writer writer, PesiMergeObject merge1, PesiMergeObject merge2, String methodName) {
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try {
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328
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Method method = PesiMergeObject.class.getDeclaredMethod("get"+methodName);
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String value1 = (String) method.invoke(merge1);
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writer.append(normalize(value1)).append(";");
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String value2 = (String) method.invoke(merge2);
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writer.append(normalize(value2)).append(";");
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333
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} catch (Exception e) {
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334
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e.printStackTrace();
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335
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}
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336
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}
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337
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338
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private String normalize(String val) {
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339
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return CdmUtils.Nz(val).replace(";", "@");
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}
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341
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342
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private void writeCsvLine(Writer writer, Map<UUID,PesiMergeObject> mergeObjects, Map<UUID,String> sources) throws IOException{
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343
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344
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for (UUID uuid : sourceRefUuids){
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345
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PesiMergeObject merging = mergeObjects.get(uuid);
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346
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if(merging == null){
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347
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continue;
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348
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}
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349
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writer.append(Nz(sources.get(uuid))).append(";");
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350
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writer.append(Nz(merging.getUuidName())).append(";");
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351
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writer.append(Nz(merging.getIdInSource())).append(";");
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352
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writer.append(Nz(merging.getNameCache())).append(";");
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writer.append(Nz(merging.getAuthor())).append(";");
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writer.append(Nz(merging.getRank())).append(";");
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if (merging.isStatus()){
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writer.append("accepted").append(";");
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}else{
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writer.append("synonym").append(";");
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}
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writer.append(Nz(merging.getPhylum() != null? merging.getPhylum().getTitleCache(): "")).append(";");
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writer.append(Nz(merging.getParentString())).append(";");
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writer.append(Nz(merging.getParentRankString())).append(";");
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}
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writer.append('\n');
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}
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366
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367
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private List<Map<UUID,List<PesiMergeObject>>> createMergeObjects(
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368
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Map<String, Map<UUID, Set<TaxonName>>> identicalNames,
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369
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CdmApplicationController appCtr){
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370
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371
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List<Map<UUID,List<PesiMergeObject>>> merge = new ArrayList<>();
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372
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373
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List<String> nameCaches = new ArrayList<>(identicalNames.keySet());
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374
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nameCaches.sort(StringComparator.Instance);
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375
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for (String nameCache: nameCaches){
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376
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createSingleMergeObject(appCtr, merge, identicalNames.get(nameCache));
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377
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}
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378
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return merge;
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379
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}
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380
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381
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private void createSingleMergeObject(CdmApplicationController appCtr,
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382
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List<Map<UUID,List<PesiMergeObject>>> merge,
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383
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Map<UUID, Set<TaxonName>> identicalNames) {
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384
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|
385
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Map<UUID,List<PesiMergeObject>> mergeMap = new HashMap<>();
|
386
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|
387
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for (UUID sourceUuid : identicalNames.keySet()){
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388
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Set<TaxonName> names = identicalNames.get(sourceUuid);
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389
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List<PesiMergeObject> pmoList = new ArrayList<>();
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390
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mergeMap.put(sourceUuid, pmoList);
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391
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|
392
|
for (TaxonName name : names){
|
393
|
String nameAndIdStr = name.getTitleCache() + "; id = " + name.getId();
|
394
|
@SuppressWarnings("rawtypes")
|
395
|
Set<TaxonBase> taxonBases = name.getTaxonBases();
|
396
|
if (taxonBases.isEmpty()){
|
397
|
logger.warn("No taxonbase attached to name. This is not yet handled: " + nameAndIdStr);
|
398
|
continue;
|
399
|
}
|
400
|
for (TaxonBase<?> taxonBase : taxonBases) {
|
401
|
if (!taxonBase.isPublish()){
|
402
|
continue;
|
403
|
}
|
404
|
PesiMergeObject mergeObject = PesiMergeObject.NewInstance();
|
405
|
pmoList.add(mergeObject);
|
406
|
|
407
|
//uuid
|
408
|
mergeObject.setUuidSource(sourceUuid.toString());
|
409
|
mergeObject.setUuidName(name.getUuid().toString());
|
410
|
mergeObject.setUuidTaxon(taxonBase.getUuid().toString());
|
411
|
mergeObject.setIdTaxon(String.valueOf(taxonBase.getId()));
|
412
|
|
413
|
//nameCache
|
414
|
mergeObject.setNameCache(name.getNameCache());
|
415
|
|
416
|
//authorship
|
417
|
mergeObject.setAuthor(name.getAuthorshipCache());
|
418
|
|
419
|
//rank
|
420
|
mergeObject.setRank(name.getRank().getLabel());
|
421
|
|
422
|
//Kingdom
|
423
|
TaxonNodeDto kingdom = getHigherTaxon(appCtr, name, Rank.KINGDOM());
|
424
|
mergeObject.setKingdom(kingdom);
|
425
|
|
426
|
//Phylum/Division
|
427
|
TaxonNodeDto phylum = getHigherTaxon(appCtr, name, Rank.PHYLUM());
|
428
|
if(phylum == null){
|
429
|
phylum = getHigherTaxon(appCtr, name, Rank.DIVISION());
|
430
|
}
|
431
|
mergeObject.setPhylum(phylum);
|
432
|
|
433
|
//Family
|
434
|
TaxonNodeDto family = getHigherTaxon(appCtr, name, Rank.FAMILY());
|
435
|
mergeObject.setFamily(family);
|
436
|
|
437
|
//idInSource
|
438
|
Iterator<IdentifiableSource> sources = name.getSources().iterator();
|
439
|
//TODO idInSource - what if multiple sources exist?
|
440
|
if (sources.hasNext()){
|
441
|
IdentifiableSource source = sources.next();
|
442
|
String idInSource = source.getIdInSource();
|
443
|
mergeObject.setIdInSource(idInSource);
|
444
|
}
|
445
|
|
446
|
//status and parent
|
447
|
makeStatusAndParent(name, mergeObject);
|
448
|
}
|
449
|
}
|
450
|
}
|
451
|
|
452
|
merge.add(mergeMap);
|
453
|
|
454
|
|
455
|
//set parent informations
|
456
|
|
457
|
/*
|
458
|
Set<HybridRelationship> parentRelations = zooName.getParentRelationships();
|
459
|
Iterator parentIterator = parentRelations.iterator();
|
460
|
HybridRelationship parentRel;
|
461
|
ZoologicalName parentName;
|
462
|
while (parentIterator.hasNext()){
|
463
|
parentRel = (HybridRelationship)parentIterator.next();
|
464
|
parentName = (ZoologicalName)parentRel.getParentName();
|
465
|
mergeObject.setParentRankStringInErms(parentName.getRank().getLabel());
|
466
|
mergeObject.setParentStringInErms(parentName.getNameCache());
|
467
|
}
|
468
|
|
469
|
parentRelations = zooName2.getParentRelationships();
|
470
|
parentIterator = parentRelations.iterator();
|
471
|
|
472
|
while (parentIterator.hasNext()){
|
473
|
parentRel = (HybridRelationship)parentIterator.next();
|
474
|
parentName = (ZoologicalName)parentRel.getParentName();
|
475
|
mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel());
|
476
|
mergeObject.setParentStringInFaunaEu(parentName.getNameCache());
|
477
|
}*/
|
478
|
|
479
|
|
480
|
}
|
481
|
|
482
|
private void makeStatusAndParent(TaxonName name, PesiMergeObject mergeObject) {
|
483
|
Set<Taxon> taxa = name.getTaxa();
|
484
|
taxa = getReallyAcceptedTaxa(taxa);
|
485
|
if (!taxa.isEmpty()){
|
486
|
mergeObject.setStatus(true);
|
487
|
Iterator<Taxon> taxaIterator = taxa.iterator();
|
488
|
Taxon taxon = null;
|
489
|
while (taxaIterator.hasNext()){
|
490
|
taxon = taxaIterator.next();
|
491
|
if (!taxon.isMisapplication()){
|
492
|
break;
|
493
|
}
|
494
|
}
|
495
|
@SuppressWarnings("null")
|
496
|
Set<TaxonNode> nodes = taxon.getTaxonNodes();
|
497
|
Iterator<TaxonNode> taxonNodeIterator = nodes.iterator();
|
498
|
TaxonNode parentNode = null;
|
499
|
while (taxonNodeIterator.hasNext()){
|
500
|
TaxonNode node = taxonNodeIterator.next();
|
501
|
if (!node.isTopmostNode()){
|
502
|
parentNode = node.getParent();
|
503
|
}
|
504
|
}
|
505
|
if (parentNode != null){
|
506
|
TaxonName parentName = CdmBase.deproxy(parentNode.getTaxon().getName());
|
507
|
String parentNameCache = parentName.getNameCache();
|
508
|
mergeObject.setParentString(parentNameCache);
|
509
|
mergeObject.setParentRankString(parentName.getRank().getLabel());
|
510
|
}
|
511
|
}else{
|
512
|
mergeObject.setStatus(false);
|
513
|
TaxonNode parentNode = getAcceptedNode(name);
|
514
|
if (parentNode != null){
|
515
|
TaxonName parentName = CdmBase.deproxy(parentNode.getTaxon().getName());
|
516
|
String parentNameCache = parentName.getNameCache();
|
517
|
mergeObject.setParentString(parentNameCache);
|
518
|
mergeObject.setParentRankString(parentName.getRank().getLabel());
|
519
|
}
|
520
|
}
|
521
|
}
|
522
|
|
523
|
private TaxonNodeDto getHigherTaxon(CdmApplicationController appCtr, TaxonName name, Rank rank) {
|
524
|
if (name.getRank().equals(rank)) {
|
525
|
Taxon taxon = getAcceptedTaxon(name);
|
526
|
if (taxon != null) {
|
527
|
if (taxon.getTaxonNodes().isEmpty()){
|
528
|
return null; //probably MAN
|
529
|
}
|
530
|
if (taxon.getTaxonNodes().size()>1){
|
531
|
logger.warn("More than 1 node not yet handled for getHigherTaxon. Take arbitrary one.");
|
532
|
}
|
533
|
TaxonNode node = taxon.getTaxonNodes().iterator().next();
|
534
|
return new TaxonNodeDto(node);
|
535
|
}
|
536
|
}
|
537
|
if (name.getRank().isHigher(rank)){
|
538
|
return null;
|
539
|
}else{
|
540
|
Taxon taxon = getAcceptedTaxon(name);
|
541
|
if (taxon.getTaxonNodes().isEmpty()){
|
542
|
return null;
|
543
|
}else{
|
544
|
if (taxon.getTaxonNodes().size()>1){
|
545
|
logger.warn("More than 1 node not yet handled for getHigherTaxon. Take arbitrary one.");
|
546
|
}
|
547
|
TaxonNode node = taxon.getTaxonNodes().iterator().next();
|
548
|
List<TaxonNodeDto> higherDtos = appCtr.getTaxonNodeService().taxonNodeDtoParentRank(node.getClassification(), rank, taxon);
|
549
|
if (higherDtos.isEmpty()){
|
550
|
return null;
|
551
|
}else {
|
552
|
if (higherDtos.size() > 1){
|
553
|
logger.warn("More than 1 higher dto. This is not yet implemented: " + taxon.getTitleCache());
|
554
|
}
|
555
|
return higherDtos.get(0);
|
556
|
}
|
557
|
}
|
558
|
}
|
559
|
}
|
560
|
|
561
|
private TaxonNode getAcceptedNode(TaxonName ermsName) {
|
562
|
TaxonNode parentNode = null;
|
563
|
Set<TaxonBase> taxonBases = ermsName.getTaxonBases();
|
564
|
if (!taxonBases.isEmpty()) {
|
565
|
Taxon taxon = null;
|
566
|
TaxonBase<?> taxonBase = taxonBases.iterator().next();
|
567
|
if (taxonBase instanceof Synonym) {
|
568
|
taxon = ((Synonym)taxonBase).getAcceptedTaxon();
|
569
|
}else{
|
570
|
taxon = getAccTaxonForTaxonSynonym((Taxon)taxonBase);
|
571
|
}
|
572
|
Set<TaxonNode> nodes = taxon.getTaxonNodes();
|
573
|
if (!nodes.isEmpty()) {
|
574
|
parentNode = nodes.iterator().next();
|
575
|
}
|
576
|
}
|
577
|
|
578
|
return parentNode;
|
579
|
}
|
580
|
|
581
|
private Taxon getAcceptedTaxon(TaxonName name) {
|
582
|
Taxon taxon = null;
|
583
|
//prefer accepted taxon
|
584
|
if (name.getTaxa() != null && !name.getTaxa().isEmpty()){
|
585
|
taxon = name.getTaxa().iterator().next();
|
586
|
taxon = getAccTaxonForTaxonSynonym(taxon);
|
587
|
//else take synonym
|
588
|
}else if (name.getTaxonBases() != null && !name.getTaxonBases().isEmpty()){
|
589
|
TaxonBase<?> taxonBase = name.getTaxonBases().iterator().next();
|
590
|
if (taxonBase instanceof Synonym) {
|
591
|
Synonym syn = (Synonym)taxonBase;
|
592
|
taxon = syn.getAcceptedTaxon();
|
593
|
}
|
594
|
}
|
595
|
return taxon;
|
596
|
}
|
597
|
|
598
|
private Taxon getAccTaxonForTaxonSynonym(Taxon taxon) {
|
599
|
if (!taxon.getRelationsFromThisTaxon().isEmpty()){
|
600
|
for (TaxonRelationship rel: taxon.getRelationsFromThisTaxon()){
|
601
|
UUID uuidType = rel.getType().getUuid();
|
602
|
if (uuidType.equals(TaxonRelationshipType.uuidSynonymOfTaxonRelationship)
|
603
|
|| uuidType.equals(TaxonRelationshipType.uuidHeterotypicSynonymTaxonRelationship)
|
604
|
|| uuidType.equals(TaxonRelationshipType.uuidHomotypicSynonymTaxonRelationship)){
|
605
|
taxon = rel.getToTaxon();
|
606
|
}
|
607
|
}
|
608
|
}
|
609
|
return taxon;
|
610
|
}
|
611
|
|
612
|
/**
|
613
|
* Filters out the ERMS taxon synonyms
|
614
|
*/
|
615
|
private Set<Taxon> getReallyAcceptedTaxa(Set<Taxon> taxa) {
|
616
|
Set<Taxon> result = new HashSet<>();
|
617
|
for (Taxon taxon : taxa){
|
618
|
Taxon accTaxon = getAccTaxonForTaxonSynonym(taxon);
|
619
|
if(taxon.equals(accTaxon)) {
|
620
|
result.add(taxon);
|
621
|
}
|
622
|
}
|
623
|
return result;
|
624
|
}
|
625
|
|
626
|
private CharSequence Nz(String str) {
|
627
|
return CdmUtils.Nz(str);
|
628
|
}
|
629
|
|
630
|
public static void main(String[] args) {
|
631
|
PesiFindIdenticalNamesActivator activator = new PesiFindIdenticalNamesActivator();
|
632
|
activator.invoke(pesiSource);
|
633
|
System.exit(0);
|
634
|
}
|
635
|
}
|