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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.cichorieae;
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import java.io.File;
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import java.net.URI;
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import java.net.URISyntaxException;
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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.app.images.ImageImportConfigurator;
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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.common.CdmDefaultImport;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator;
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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.io.wp6.CichorieaeImageImport;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.ISourceable;
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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 CichorieaeActivator {
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private static final Logger logger = Logger.getLogger(CichorieaeActivator.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_CICHORIEAE();
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static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
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static final UUID secUuid = UUID.fromString("6924c75d-e0d0-4a6d-afb7-3dd8c71195ca");
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static final UUID classificationUuid = UUID.fromString("534e190f-3339-49ba-95d9-fa27d5493e3e");
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// static final UUID treeUuid = UUID.fromString("00db28a7-50e1-4abc-86ec-b2a8ce870de9");
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static final int sourceSecId = 7800000;
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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, 43, 31, 4, 12, 98, 41};
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/* --------- MEDIA recources ------------ */
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static final boolean stopOnMediaErrors = false;
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static final String protologueUrlString = "http://wp5.e-taxonomy.eu/dataportal/cichorieae/media/protolog/";
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//Mac
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//static final File protologuePath = new File("/Volumes/protolog/protolog/");
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//Windows
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public static final String imageFolderString = "//media/editwp6/photos";
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static final File protologuePath = new File("//media/editwp6/protolog");
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// public static final File imageFolder = new File("/media/photos");
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// static final File protologuePath = new File("/media/protolog");
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/* -------------------------------------- */
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// set to zero for unlimited nameFacts
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static final int maximumNumberOfNameFacts = 0;
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static final int recordsPerTransaction = 2000;
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//should the other imports run as well?
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static final boolean includeTaraxacum = true;
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static final boolean includeImages = false;
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//check - import
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static final CHECK check = CHECK.CHECK_AND_IMPORT;
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//editor - import
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static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
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//NomenclaturalCode
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static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
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//ignore null
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static final boolean ignoreNull = true;
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static boolean useClassification = true;
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// **************** ALL *********************
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static final boolean doUser = 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 = false;
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static final boolean doOccurences = false;
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static final boolean doCommonNames = true;
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//etc.
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static final boolean doMarker = false;
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// **************** SELECTED *********************
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//
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// static final boolean doUser = false;
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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 = false;
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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 = false;
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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 doCommonNames = 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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private ImportResult doInvoke(ICdmDataSource destination){
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ImportResult success = new ImportResult();
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Source source = berlinModelSource;
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BerlinModelImportConfigurator bmImportConfigurator = BerlinModelImportConfigurator.NewInstance(source, destination);
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bmImportConfigurator.setClassificationUuid(classificationUuid);
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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.setDbSchemaValidation(hbm2dll);
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bmImportConfigurator.setRecordsPerTransaction(recordsPerTransaction);
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// protologueResourceLocations
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if ( protologuePath.exists() && protologuePath.isDirectory()){
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bmImportConfigurator.setMediaUrl(protologueUrlString);
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bmImportConfigurator.setMediaPath(protologuePath);
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}else{
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if(stopOnMediaErrors){
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logger.error("Could not configure protologue ResourceLocations -> will quit.");
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System.exit(-1);
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}
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logger.error("Could not configure protologue ResourceLocations");
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}
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File imageFolder = new File(imageFolderString);
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// also check the image source folder
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if ( !imageFolder.exists() || !imageFolder.isDirectory()){
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if(stopOnMediaErrors){
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logger.error("Could not configure imageFolder -> will quit.");
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System.exit(-1);
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}
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logger.error("Could not configure imageFolder");
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}
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// maximum number of name facts to import
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bmImportConfigurator.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
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bmImportConfigurator.setCheck(check);
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bmImportConfigurator.setEditor(editor);
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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 (doFacts && (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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ISourceable obj = app.getCommonService().getSourcedObjectByIdInSource(TaxonName.class, "1000027", null);
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logger.info(obj);
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//make feature tree
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FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList);
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FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
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tree.getRoot().addChild(imageNode);
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FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
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tree.getRoot().addChild(distributionNode, 2);
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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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try {
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if (includeTaraxacum) {
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System.out.println("Start Taraxacum import from BerlinModel ...");
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TaraxacumActivator taraxacumActivator = new TaraxacumActivator();
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ImportResult successTaraxacum = taraxacumActivator.doImport(destination, DbSchemaValidation.UPDATE);
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success.merge(successTaraxacum);
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logger.warn("Taraxacum import still needs to be tested");
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System.out.println("End Taraxacum import from BerlinModel ...");
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}
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} catch (Exception e) {
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success.addException(e);
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logger.error("Exception occurred during Taraxacum import.");
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e.printStackTrace();
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}
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if (includeImages) {
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System.out.println("Start importing images ...");
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CdmDefaultImport<IImportConfigurator> imageImporter = new CdmDefaultImport<IImportConfigurator>();
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URI imageFolderCichorieae;
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try {
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imageFolderCichorieae = new URI(CichorieaeActivator.imageFolderString);
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ImageImportConfigurator imageConfigurator = ImageImportConfigurator.NewInstance(
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imageFolderCichorieae, destination, CichorieaeImageImport.class);
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imageConfigurator.setSecUuid(secUuid);
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imageConfigurator.setClassificationUuid(classificationUuid);
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ImportResult resultImageImport = imageImporter.invoke(imageConfigurator);
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success.merge(resultImageImport);
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} catch (URISyntaxException e) {
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e.printStackTrace();
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}
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System.out.println("End importing images ...");
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}
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logger.warn("!!!! NOTE: RefDetail notes and RelPTaxon notes are not imported automatically. Please check for these notes and import them manually.");
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return success;
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}
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/**
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* @param args
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*/
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public static void main(String[] args) {
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ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
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System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + destination.getDatabase() + " ...");
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CichorieaeActivator me = new CichorieaeActivator();
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me.doInvoke(destination);
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}
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}
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