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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.app.wp6.diptera;
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import java.lang.reflect.Method;
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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.ICdmRepository;
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import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources;
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import eu.etaxonomy.cdm.app.berlinModelImport.TreeCreator;
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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.database.DbSchemaValidation;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonImport.PublishMarkerChooser;
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
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import eu.etaxonomy.cdm.io.common.ImportResult;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.term.FeatureNode;
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import eu.etaxonomy.cdm.model.term.FeatureTree;
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/**
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* TODO add the following to a wiki page:
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* HINT: If you are about to import into a mysql data base running under windows and if you wish to dump and restore the resulting data bas under another operation systen
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* you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
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*
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*
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* @author a.mueller
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*
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*/
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public class DipteraActivator {
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private static final Logger logger = Logger.getLogger(DipteraActivator.class);
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//database validation status (create, update, validate ...)
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static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
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static final Source berlinModelSource = BerlinModelSources.EDIT_Diptera();
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static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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static final UUID secUuid = UUID.fromString("06fd671f-1226-4e3b-beca-1959b3b32e20");
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static final UUID treeUuid = UUID.fromString("1e3093f6-c761-4e96-8065-2c1334ddd0c1");
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static final int sourceSecId = 1000000;
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static final UUID featureTreeUuid = UUID.fromString("ae9615b8-bc60-4ed0-ad96-897f9226d568");
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static final Object[] featureKeyList = new Integer[]{1, 4, 5, 10, 11, 12, 99};
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static boolean useClassification = true;
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//editor - import
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static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
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//check - import
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static final CHECK check = CHECK.CHECK_AND_IMPORT;
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//taxon publish marker
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static final PublishMarkerChooser taxonPublish = PublishMarkerChooser.NO_MARKER;
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static final boolean doDistributionParser = true; //also run DipteraDistributionParser
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//NomenclaturalCode
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static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICZN;
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// //ignore null
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static final boolean ignoreNull = true;
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//update citations ?
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static final boolean updateCitations = true;
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//include collections and add to specimen
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static final boolean updateCollections = true;
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//authors
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static final boolean doAuthors = true;
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//references
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static final DO_REFERENCES doReferences = DO_REFERENCES.ALL;
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//names
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static final boolean doTaxonNames = true;
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static final boolean doRelNames = true;
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static final boolean doNameStatus = true;
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static final boolean doTypes = true;
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static final boolean doNameFacts = true;
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//taxa
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static final boolean doTaxa = true;
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static final boolean doRelTaxa = true;
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static final boolean doFacts = true;
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static final boolean doOccurences = false; //There are no occurrence data in diptera
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static final boolean doCommonNames = false; //no common names in diptera
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//etc.
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static final boolean doMarker = true;
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static final boolean doUser = true;
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// **************** SELECTED *********************
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// //authors
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// static final boolean doAuthors = false;
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// //references
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// static final DO_REFERENCES doReferences = DO_REFERENCES.NONE;
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// //names
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// static final boolean doTaxonNames = true;
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// static final boolean doRelNames = false;
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// static final boolean doNameStatus = false;
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// static final boolean doTypes = true;
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// static final boolean doNameFacts = false;
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//
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// //taxa
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// static final boolean doTaxa = false;
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// static final boolean doRelTaxa = false;
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// static final boolean doFacts = false;
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// static final boolean doOccurences = false;
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//
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// //etc.
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// static final boolean doMarker = false;
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// static final boolean doUser = true;
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/**
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* @param destination
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* @param args
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*/
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public ImportResult doImport(ICdmDataSource destination) {
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ImportResult success;
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System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") ...");
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//make BerlinModel Source
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Source source = berlinModelSource;
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BerlinModelImportConfigurator bmImportConfigurator = BerlinModelImportConfigurator.NewInstance(source, destination);
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bmImportConfigurator.setClassificationUuid(treeUuid);
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bmImportConfigurator.setSourceSecId(sourceSecId);
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bmImportConfigurator.setNomenclaturalCode(nomenclaturalCode);
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bmImportConfigurator.setIgnoreNull(ignoreNull);
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bmImportConfigurator.setDoAuthors(doAuthors);
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bmImportConfigurator.setDoReferences(doReferences);
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bmImportConfigurator.setDoTaxonNames(doTaxonNames);
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bmImportConfigurator.setDoRelNames(doRelNames);
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bmImportConfigurator.setDoNameStatus(doNameStatus);
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bmImportConfigurator.setDoTypes(doTypes);
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bmImportConfigurator.setDoNameFacts(doNameFacts);
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bmImportConfigurator.setUseClassification(useClassification);
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bmImportConfigurator.setDoTaxa(doTaxa);
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bmImportConfigurator.setDoRelTaxa(doRelTaxa);
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bmImportConfigurator.setDoFacts(doFacts);
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bmImportConfigurator.setDoOccurrence(doOccurences);
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bmImportConfigurator.setDoCommonNames(doCommonNames);
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bmImportConfigurator.setDoMarker(doMarker);
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bmImportConfigurator.setDoUser(doUser);
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bmImportConfigurator.setEditor(editor);
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bmImportConfigurator.setTaxonPublishMarker(taxonPublish);
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try {
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Method nameTypeDesignationStatusMethod = DipteraActivator.class.getDeclaredMethod("nameTypeDesignationStatueMethod", String.class);
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bmImportConfigurator.setNameTypeDesignationStatusMethod(nameTypeDesignationStatusMethod);
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} catch (Exception e) {
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e.printStackTrace();
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success = new ImportResult();
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success.addException(e);
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return success;
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}
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bmImportConfigurator.setDbSchemaValidation(hbm2dll);
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bmImportConfigurator.setCheck(check);
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// invoke import
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CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
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success = bmImport.invoke(bmImportConfigurator);
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if (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT) || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ){
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ICdmRepository app = bmImport.getCdmAppController();
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//parse distributions
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if (doDistributionParser){
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DipteraDistributionParser dipDist = new DipteraDistributionParser();
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dipDist.doDistribution(app);
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}
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//make feature tree
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app = bmImport.getCdmAppController();
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FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList);
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// add image
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FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
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tree.getRoot().addChild(imageNode);
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// add distribution
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FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
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tree.getRoot().addChild(distributionNode);
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app.getFeatureTreeService().saveOrUpdate(tree);
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}
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System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
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return success;
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}
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public static void main(String[] args) {
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ImportResult success;
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logger.debug("start");
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ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
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DipteraActivator me = new DipteraActivator();
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success = me.doImport(destination);
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DipteraPostImportUpdater updater = new DipteraPostImportUpdater();
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if (updateCitations){
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success = updater.updateCitations(destination);
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}
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if (updateCollections){
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success = updater.updateCollections(destination);
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}
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}
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private static NameTypeDesignationStatus nameTypeDesignationStatueMethod(String note){
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if (CdmUtils.isEmpty(note)){
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return null;
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}
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note = note.trim();
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if (note.equalsIgnoreCase("aut.") || note.equalsIgnoreCase("automatic")){
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return NameTypeDesignationStatus.AUTOMATIC();
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}else if (note.equalsIgnoreCase("subs. mon.") ){
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return NameTypeDesignationStatus.SUBSEQUENT_MONOTYPY();
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}else if (note.startsWith("mon.") ){
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return NameTypeDesignationStatus.MONOTYPY();
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}else if (note.startsWith("orig. des") ){
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return NameTypeDesignationStatus.ORIGINAL_DESIGNATION();
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}else if (note.startsWith("des") ){
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return NameTypeDesignationStatus.SUBSEQUENT_DESIGNATION();
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}else{
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logger.warn("NameTypeDesignationStatus could not be defined for: " + note);
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return null;
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}
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}
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}
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