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package eu.etaxonomy.cdm.app.pesi.merging;
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import java.util.ArrayList;
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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.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.api.application.CdmApplicationController;
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import eu.etaxonomy.cdm.api.service.exception.ReferencedObjectUndeletableException;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.app.common.CdmDestinations;
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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.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.io.api.application.CdmIoApplicationController;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.Credit;
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import eu.etaxonomy.cdm.model.common.Extension;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.Marker;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.name.NameRelationship;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.reference.Reference;
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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.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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public class FaunaEuErmsMergeActivator extends PesiMergeBase{
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static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.localH2();
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static final int faunaEuUuid = 0;
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static final int ermsUuid = 9;
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static final int rankFaunaEu = 4;
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static final int rankErms = 13;
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private Classification faunaEuClassification;
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private Classification ermsClassification;
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private CdmApplicationController appCtrInit;
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private static final Logger logger = Logger.getLogger(FaunaEuErmsMergeActivator.class);
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//csv files starting with...
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static String sFileName = "c:\\test";
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private void initDb(ICdmDataSource db) {
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// Init source DB
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appCtrInit = CdmIoApplicationController.NewInstance(db, DbSchemaValidation.VALIDATE, false);
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}
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public static void main(String[] args) {
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FaunaEuErmsMergeActivator sc = new FaunaEuErmsMergeActivator();
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sc.initDb(faunaEuropaeaSource);
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//we also need to merge names completely identical!
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sc.mergeAuthors();
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//set the ranks of Agnatha and Gnathostomata to 50 instead of 45
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List<TaxonBase> taxaToChangeRank = new ArrayList<>();
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Pager<TaxonBase> agnatha = sc.appCtrInit.getTaxonService().findTaxaByName(TaxonBase.class, "Agnatha", null, null, null, "*", Rank.INFRAPHYLUM(), 10, 0, null);
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List<TaxonBase> agnathaList = agnatha.getRecords();
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taxaToChangeRank.addAll(agnathaList);
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Pager<TaxonBase> gnathostomata = sc.appCtrInit.getTaxonService().findTaxaByName(TaxonBase.class, "Gnathostomata", null, null, null, "*", Rank.INFRAPHYLUM(), 10, 0, null);
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List<TaxonBase> gnathostomataList = gnathostomata.getRecords();
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taxaToChangeRank.addAll(gnathostomataList);
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sc.setSpecificRank(taxaToChangeRank, Rank.SUPERCLASS());
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//ermsTaxon is accepted, faunaEu taxon is synonym
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//ermsTaxon is synonym, faunaEu is accepted
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sc.mergeDiffStatus();
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//erms is synonym, faunaEu as well
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// erms is accepted, faunaEu as well
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}
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private void mergeAuthors(){
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List<List<String>> authors = readCsvFile(sFileName + "_authors.csv");
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//authors: get firstAuthor if isFauEu = 1 otherwise get secondAuthor
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Iterator<List<String>> authorIterator = authors.iterator();
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List<TaxonBase<?>> taxaToSave = new ArrayList<>(); //TODO: needed?
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while (authorIterator.hasNext()){
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List<String> row = authorIterator.next();
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UUID uuidFaunaEu = UUID.fromString(row.get(faunaEuUuid));
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UUID uuidErms = UUID.fromString(row.get(ermsUuid));
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TaxonBase<?> taxonFaunaEu = appCtrInit.getTaxonService().find(uuidFaunaEu);
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TaxonBase<?> taxonErms = appCtrInit.getTaxonService().find(uuidErms);
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// which information should be used can be found in last row -> needs to be done manually
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if (Integer.parseInt(row.get(18)) == 1){
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//isFaunaEu = 1 -> copy the author of Fauna Europaea to Erms
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if (taxonFaunaEu.getName().getBasionymAuthorship()!= null){
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taxonErms.getName().setBasionymAuthorship(taxonFaunaEu.getName().getBasionymAuthorship());
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}
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if (taxonFaunaEu.getName().getCombinationAuthorship()!= null){
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taxonErms.getName().setCombinationAuthorship(taxonFaunaEu.getName().getCombinationAuthorship());
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}
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taxonErms.getName().generateAuthorship();
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taxaToSave.add(taxonErms);
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}else{
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if (taxonErms.getName().getBasionymAuthorship()!= null){
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taxonFaunaEu.getName().setBasionymAuthorship(taxonErms.getName().getBasionymAuthorship());
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}
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if (taxonErms.getName().getCombinationAuthorship()!= null){
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taxonFaunaEu.getName().setCombinationAuthorship(taxonErms.getName().getCombinationAuthorship());
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}
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taxonFaunaEu.getName().generateAuthorship();
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taxaToSave.add(taxonFaunaEu);
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}
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}
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}
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private void setSpecificRank(List<TaxonBase> taxa, Rank rank){
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for (TaxonBase<?> taxon: taxa){
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taxon.getName().setRank(rank);
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}
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}
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private void mergeDiffStatus(){
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List<List<String>> diffStatus = readCsvFile(sFileName + "_status.csv");
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//find all taxa accepted in erms, but synonyms in FauEu and the same rank
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List<List<String>> accErmsSynFaunaEu = new ArrayList<>();
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for (List<String> rowList: diffStatus){
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if ((rowList.get(5).equals("synonym")) && (rowList.get(rankFaunaEu).equals(rowList.get(rankErms)))){
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//both conditions are true
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accErmsSynFaunaEu.add(rowList);
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}
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}
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mergeErmsAccFaunaEuSyn(accErmsSynFaunaEu);
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//find all taxa accepted in faunaEu, but synonyms in Erms and the same rank
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List<List<String>> synErmsAccFaunaEu = new ArrayList<>();
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for (List<String> rowList: diffStatus){
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if ((rowList.get(5).equals("accepted")) && (rowList.get(rankFaunaEu).equals(rowList.get(rankErms)))){
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//both conditions are true
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synErmsAccFaunaEu.add(rowList);
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}
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}
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mergeErmsSynFaunaEuAcc(synErmsAccFaunaEu);
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}
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private void mergeSameStatus(){
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List<List<String>> sameStatus = readCsvFile(sFileName + "_names.csv");
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TaxonBase<?> taxonFaunaEu;
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TaxonBase<?> taxonErms;
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List<String> propertyPaths = new ArrayList<>();
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propertyPaths.add("taxonBases.nodes.*");
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for (List<String> row: sameStatus){
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taxonFaunaEu = appCtrInit.getTaxonService().load(UUID.fromString(row.get(faunaEuUuid)), propertyPaths);
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taxonErms = appCtrInit.getTaxonService().load(UUID.fromString(row.get(ermsUuid)), propertyPaths);
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moveAllInformationsFromFaunaEuToErms(taxonFaunaEu, taxonErms);
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if (taxonErms instanceof Taxon){
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moveFaunaEuSynonymsToErmsTaxon((Taxon)taxonFaunaEu, (Taxon)taxonErms);
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}
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}
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}
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private void mergeErmsAccFaunaEuSyn(List<List<String>> ermsAccFaEuSyn){
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// update nameRelationships -> if the nameRelationship does not exist, then create a new one with ermsAcc as relatedTo TaxonName
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updateNameRelationships(ermsAccFaEuSyn);
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//delete all synonyms of FaunaEu Syn TODO: move sources and additional informations to erms taxon
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for (List<String> rowList: ermsAccFaEuSyn){
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UUID faunaUUID = UUID.fromString(rowList.get(faunaEuUuid));
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//UUID ermsUUID = UUID.fromString(rowList.get(ermsUuid));
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Synonym syn = (Synonym)appCtrInit.getTaxonService().find(faunaUUID);
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// remove synonym from taxon then delete
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appCtrInit.getTaxonService().deleteSynonym(syn, null);
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}
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//merge the infos of
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}
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private void mergeErmsSynFaunaEuAcc (List<List<String>> ermsAccFaEuSyn){
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//occurence: connect instead of Fauna Europaea taxon the accepted taxon of the synonym with the occurrence (CDM -> distribution)
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//search distribution (via taxon of the taxon description), of which the taxon is the according Fauna Eu taxon and connect it with the accepted taxon of the ERMS syn
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for (List<String> row: ermsAccFaEuSyn){
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Taxon taxonFaunaEu = (Taxon)appCtrInit.getTaxonService().find(UUID.fromString(row.get(faunaEuUuid)));
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Synonym synErms = (Synonym)appCtrInit.getTaxonService().find(UUID.fromString(row.get(ermsUuid)));
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synErms = HibernateProxyHelper.deproxy(synErms, Synonym.class);
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Taxon taxonErms = synErms.getAcceptedTaxon();
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if (taxonErms == null){
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logger.debug("There is no accepted taxon for the synonym" + synErms.getTitleCache());
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}
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Set<Feature> features = new HashSet<>();
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features.add(Feature.DISTRIBUTION());
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List<String> propertyPaths = new ArrayList<>();
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propertyPaths.add("inDescription.Taxon.*");
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List<Distribution> distributions = appCtrInit.getDescriptionService().getDescriptionElementsForTaxon(taxonFaunaEu, features, Distribution.class, 10, 0, null);
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for(Distribution distribution: distributions){
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TaxonDescription description = (TaxonDescription)distribution.getInDescription();
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TaxonDescription newDescription = TaxonDescription.NewInstance(taxonErms);
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newDescription.addElement(distribution);
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try{
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appCtrInit.getDescriptionService().delete(description);
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}catch (Exception e){
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logger.debug("The description of" + description.getTaxon().getTitleCache() + description.getTitleCache() + "can't be deleted because it is referenced.");
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}
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}
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//Child-Parent Relationship aktualisieren -> dem Child des Fauna Europaea Taxons als parent das akzeptierte Taxon von synErms
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Set<TaxonNode> nodesErms = taxonErms.getTaxonNodes();
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Set<TaxonNode> nodesFaunaEu =taxonFaunaEu.getTaxonNodes();
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if (nodesFaunaEu.size()>1 || nodesFaunaEu.isEmpty()){
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}else{
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Iterator<TaxonNode> iteratorNodesErms = nodesErms.iterator();
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Iterator<TaxonNode> iteratorNodesFaunaEu = nodesFaunaEu.iterator();
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TaxonNode node = iteratorNodesFaunaEu.next();
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List<TaxonNode> children = node.getChildNodes();
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Iterator<TaxonNode> childrenIterator = children.iterator();
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TaxonNode childNode;
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if (iteratorNodesErms.hasNext()){
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TaxonNode ermsNode = iteratorNodesErms.next();
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while (childrenIterator.hasNext()){
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childNode = childrenIterator.next();
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ermsNode.addChildNode(childNode, childNode.getReference(), childNode.getMicroReference());
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}
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}
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}
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//the fauna eu taxon should now only contain synonyms not existing in erms
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moveFaunaEuSynonymsToErmsTaxon(taxonFaunaEu, taxonErms);
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moveAllInformationsFromFaunaEuToErms(taxonFaunaEu, taxonErms);
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moveOriginalDbToErmsTaxon(taxonFaunaEu, taxonErms);
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//neue sec Referenz an das ErmsTaxon oder an das Synonym und Taxon oder nur Synonym??
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try{
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deleteFaunaEuTaxon(taxonFaunaEu);
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}catch(ReferencedObjectUndeletableException e){
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logger.debug("The taxon " + taxonFaunaEu.getTitleCache() + " can't be deleted because it is referenced.");
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}
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}
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}
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private void updateNameRelationships(List<List<String>> ermsAccFaEuSyn){
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//search all NameRelationships of FaunaEu and Erms, where (faunaEu)relatedFrom.name.titleCache = (erms)relatedFrom.name.titleCache and replace in faunaEu relationship the relatedTo.name by the relatedTo.name of the erms-relationship
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//if this relationship does not yet exist and the type is the same!!
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//if the relatedTo name belongs to an Erms taxon and to an FaunaEu synonym
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Synonym synFaunaEu;
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Taxon taxonErms;
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for (List<String> row: ermsAccFaEuSyn){
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synFaunaEu = (Synonym)appCtrInit.getTaxonService().find(UUID.fromString(row.get(faunaEuUuid)));
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taxonErms = (Taxon)appCtrInit.getTaxonService().find(UUID.fromString(row.get(ermsUuid)));
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List<NameRelationship> relSynFaunaEu = appCtrInit.getNameService().listToNameRelationships(synFaunaEu.getName(), null, 100, 0, null, null);
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List<NameRelationship> relTaxonErms = appCtrInit.getNameService().listToNameRelationships(taxonErms.getName(), null, 100, 0, null, null);
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List<NameRelationship> deleteRel = new ArrayList<>();
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for (NameRelationship relFauEu: relSynFaunaEu){
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boolean createNewRelationship = true;
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for (NameRelationship relErms: relTaxonErms){
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if ((relErms.getFromName().getTitleCache().equals(relFauEu.getFromName().getTitleCache())) && (relErms.getToName().getTitleCache().equals(relFauEu.getFromName().getTitleCache()))){
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//delete the faunaEu relationship because there exist an analogous relationship in erms
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deleteRel.add(relFauEu);
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createNewRelationship = false;
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break;
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}
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}
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if (createNewRelationship){
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//if relationship does not exist, create a new one with erms synonym
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taxonErms.getName().addRelationshipFromName(relFauEu.getFromName(), relFauEu.getType(), relFauEu.getRuleConsidered(), null);
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}
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}
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}
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}
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private void updateSynonymRelationships(List<List<String>> ermsSynFaEuAcc){
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// -- Update queries for RelTaxon (synonym relationships - move relationships to ERMS accepted taxon if not already existent or delete if already existent)
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// UPDATE RelTaxon_1 SET RelTaxon_1.TaxonFk2 = RT.TaxonFk2
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// FROM Taxon AS ERMSSyn INNER JOIN
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// Taxon AS FaEuAcc ON ERMSSyn.RankFk = FaEuAcc.RankFk AND ERMSSyn.FullName = FaEuAcc.FullName AND
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// ERMSSyn.TaxonStatusFk <> ISNULL(FaEuAcc.TaxonStatusFk, 0) INNER JOIN
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// RelTaxon AS RT ON ERMSSyn.TaxonId = RT.TaxonFk1 INNER JOIN
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// RelTaxon AS RelTaxon_1 ON FaEuAcc.TaxonId = RelTaxon_1.TaxonFk2 INNER JOIN
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// Taxon AS FaEuSyn ON RelTaxon_1.TaxonFk1 = FaEuSyn.TaxonId LEFT OUTER JOIN
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// Taxon AS ERMSAllSyn ON RT.TaxonFk1 = ERMSAllSyn.TaxonId AND FaEuSyn.FullName <> ERMSAllSyn.FullName --(!!)
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// WHERE (ERMSSyn.OriginalDB = N'ERMS') AND (RT.RelTaxonQualifierFk > 100) AND (ERMSSyn.TaxonStatusFk <> 1) AND (ERMSSyn.KingdomFk = 2) AND
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// (FaEuAcc.OriginalDB = N'FaEu') AND (RelTaxon_1.RelTaxonQualifierFk > 100)
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Taxon taxonFaunaEu;
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Synonym synErms;
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Taxon taxonErms;
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Set<Taxon> acceptedTaxa = new HashSet<>();
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for (List<String> row: ermsSynFaEuAcc){
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taxonFaunaEu = (Taxon)appCtrInit.getTaxonService().find(UUID.fromString(row.get(faunaEuUuid)));
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synErms = (Synonym)appCtrInit.getTaxonService().find(UUID.fromString(row.get(ermsUuid)));
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acceptedTaxa.clear();
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acceptedTaxa.add( synErms.getAcceptedTaxon());
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if (!acceptedTaxa.isEmpty()){
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taxonErms = acceptedTaxa.iterator().next();
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if (acceptedTaxa.size() > 1){
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logger.debug("There are more than one accepted taxon for synonym " + synErms.getTitleCache());
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}
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}else{
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taxonErms = null;
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logger.debug("There is no accepted taxon for synonym " + synErms.getTitleCache());
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}
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if (taxonErms != null){
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Pager<Synonym> synsTaxonFaunaEuPager = appCtrInit.getTaxonService().getSynonyms(taxonFaunaEu, null, null, null, null, null);
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List<Synonym> synsTaxonFaunaEu = synsTaxonFaunaEuPager.getRecords();
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Pager<Synonym> synsTaxonErmsPager = appCtrInit.getTaxonService().getSynonyms(taxonErms, null, null, null, null, null);
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List<Synonym> synsTaxonErms = synsTaxonErmsPager.getRecords();
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List<Synonym> deleteRel = new ArrayList<>();
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for (Synonym synFauEu: synsTaxonFaunaEu){
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//TODO: wenn es noch keine SynonymRelationship gibt zu einem Synonym mit gleichem Namen,
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//dann erzeuge die SynonymRelationship vom FaunaEuSyn (des FaunaEu Taxons, das
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//identischen Namen hat) zum akzeptierten Taxon des Erms Syn
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boolean createNewRelationship = true;
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for (Synonym relErms: synsTaxonErms){
|
336
|
if (relErms.getTitleCache().equals(synFauEu.getTitleCache())){
|
337
|
//es gibt schon eine Relationship zu einem Synonym mit dem gleichen Namen wie das FaunaEu Synonym, also Relationship l�schen.
|
338
|
createNewRelationship = false;
|
339
|
break;
|
340
|
}
|
341
|
}
|
342
|
if (createNewRelationship){
|
343
|
taxonErms.addSynonym(synFauEu, synFauEu.getType());
|
344
|
}
|
345
|
deleteRel.add(synFauEu);
|
346
|
}
|
347
|
}
|
348
|
}
|
349
|
}
|
350
|
|
351
|
private void deleteFaunaEuTaxon(Taxon taxonFaunaEu) throws ReferencedObjectUndeletableException {
|
352
|
appCtrInit.getTaxonService().delete(taxonFaunaEu);
|
353
|
}
|
354
|
|
355
|
//wenn Name und Rang identisch sind und auch der Status gleich, dann alle Informationen vom Fauna Europaea Taxon/Synonym zum Erms Taxon/Synonym
|
356
|
|
357
|
private void moveAllInformationsFromFaunaEuToErms(TaxonBase<?> faunaEu, TaxonBase<?> erms){
|
358
|
Set<Annotation> annotations = faunaEu.getAnnotations();
|
359
|
Set<Extension> extensions = faunaEu.getExtensions();
|
360
|
Set<Marker> markers = faunaEu.getMarkers();
|
361
|
List<Credit> credits = faunaEu.getCredits();
|
362
|
if (faunaEu instanceof Taxon){
|
363
|
Set<TaxonDescription> descriptions = ((Taxon)faunaEu).getDescriptions();
|
364
|
Set<Taxon> misappliedNames = ((Taxon)faunaEu).getMisappliedNames(true);
|
365
|
|
366
|
if (erms instanceof Taxon){
|
367
|
Iterator<TaxonDescription> descriptionsIterator = descriptions.iterator();
|
368
|
TaxonDescription description;
|
369
|
while (descriptionsIterator.hasNext()){
|
370
|
description = descriptionsIterator.next();
|
371
|
((Taxon) erms).addDescription(description);
|
372
|
}
|
373
|
|
374
|
Iterator<Taxon> misappliedNamesIterator = misappliedNames.iterator();
|
375
|
Taxon misappliedName;
|
376
|
while (misappliedNamesIterator.hasNext()){
|
377
|
misappliedName = misappliedNamesIterator.next();
|
378
|
((Taxon) erms).addMisappliedName(misappliedName, null, null);
|
379
|
}
|
380
|
}
|
381
|
}
|
382
|
|
383
|
//move all these informations to the erms taxon
|
384
|
Iterator<Annotation> annotationsIterator = annotations.iterator();
|
385
|
Annotation annotation;
|
386
|
while (annotationsIterator.hasNext()){
|
387
|
annotation = annotationsIterator.next();
|
388
|
erms.addAnnotation(annotation);
|
389
|
}
|
390
|
|
391
|
Iterator<Extension> extensionIterator = extensions.iterator();
|
392
|
Extension extension;
|
393
|
while (extensionIterator.hasNext()){
|
394
|
extension = extensionIterator.next();
|
395
|
erms.addExtension(extension);
|
396
|
}
|
397
|
|
398
|
Iterator<Marker> markerIterator = markers.iterator();
|
399
|
Marker marker;
|
400
|
while (markerIterator.hasNext()){
|
401
|
marker = markerIterator.next();
|
402
|
erms.addMarker(marker);
|
403
|
}
|
404
|
|
405
|
for (Credit credit: credits){
|
406
|
erms.addCredit(credit);
|
407
|
}
|
408
|
//move children to erms taxon
|
409
|
if (faunaEu instanceof Taxon && ((Taxon)faunaEu).getTaxonNode(faunaEuClassification).hasChildNodes()) {
|
410
|
Taxon acceptedErmsTaxon;
|
411
|
if (erms instanceof Synonym) {
|
412
|
acceptedErmsTaxon = ((Synonym)erms).getAcceptedTaxon();
|
413
|
}else {
|
414
|
acceptedErmsTaxon = (Taxon)erms;
|
415
|
}
|
416
|
TaxonNode node = acceptedErmsTaxon.getTaxonNode(ermsClassification);
|
417
|
for (TaxonNode child:((Taxon)faunaEu).getTaxonNode(faunaEuClassification).getChildNodes()) {
|
418
|
//add pesi reference as reference??
|
419
|
node.addChildNode(child, null, null);
|
420
|
}
|
421
|
}
|
422
|
}
|
423
|
|
424
|
//if name, rank, and status (accepted) are the same, then move the synonyms of faunaEu taxon to the erms taxon
|
425
|
|
426
|
private void moveFaunaEuSynonymsToErmsTaxon(Taxon faunaEu, Taxon erms){
|
427
|
Set<Synonym> syns =faunaEu.getSynonyms();
|
428
|
Iterator<Synonym> synRelIterator = syns.iterator();
|
429
|
while (synRelIterator.hasNext()){
|
430
|
Synonym syn = synRelIterator.next();
|
431
|
faunaEu.removeSynonym(syn);
|
432
|
erms.addSynonym(syn, syn.getType());
|
433
|
}
|
434
|
}
|
435
|
|
436
|
//after merging faunaEu taxon and erms taxon, the originalSource of the faunaEu taxon has to be moved to the erms taxon
|
437
|
private void moveOriginalDbToErmsTaxon(TaxonBase<?> faunaEuTaxon, TaxonBase<?> ermsTaxon){
|
438
|
Set<IdentifiableSource> sourcesFaunaEu = faunaEuTaxon.getSources();
|
439
|
IdentifiableSource sourceFaunaEu = sourcesFaunaEu.iterator().next();
|
440
|
ermsTaxon.addSource(sourceFaunaEu);
|
441
|
}
|
442
|
|
443
|
//merged taxon should have a new sec reference
|
444
|
private void addNewSecForMergedTaxon(Taxon taxon, Reference sec){
|
445
|
taxon.setSec(sec);
|
446
|
//this does not work!!
|
447
|
//taxon.setUuid(UUID.randomUUID());
|
448
|
}
|
449
|
|
450
|
// ----------- methods for merging Erms synonyms and Fauna Europaea Taxon
|
451
|
|
452
|
}
|