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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.redlist;
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import java.net.URI;
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import java.util.Arrays;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Scanner;
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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.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.io.common.CdmDefaultImport;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
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import eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportConfigurator;
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import eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences;
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import eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlTransformer;
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import eu.etaxonomy.cdm.model.metadata.CdmPreference;
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import eu.etaxonomy.cdm.model.metadata.PreferencePredicate;
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import eu.etaxonomy.cdm.model.metadata.PreferenceSubject;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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/**
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* @author a.oppermann
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* @created 16.07.2013
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*/
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public class BfnXmlImportActivator {
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private static final Logger logger = Logger.getLogger(BfnXmlImportActivator.class);
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//database validation status (create, update, validate ...)
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static DbSchemaValidation schemaValidation = DbSchemaValidation.CREATE;
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_redlist_plant_localhost();
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// static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
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static final ICdmDataSource cdmDestination = CdmDestinations.cdm_redlist_animalia_production_final();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_redlist_mammalia();
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private static final String sourceUriBase = "file:////BGBM-PESIHPC/RoteListen/RoteListenXml/";
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//nom Code
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private static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICZN;
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//check - import
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static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
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static final boolean doMetaData = true;
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static final boolean doTaxonNames = true;
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static final boolean doFeature = true;
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static final boolean doAdditionalTerms = true;
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private String filename;
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public BfnXmlImportActivator(String fileName){
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filename = fileName;
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}
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private void doImport(BfnXmlImportConfigurator config, CdmDefaultImport<BfnXmlImportConfigurator> bfnImport){
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System.out.println("Start import from " + filename + " to "+ cdmDestination.getDatabase() + " ...");
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//make Source
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URI source;
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try {
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source = URI.create(sourceUriBase + filename);
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config.setSource(source);
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//if xmllist has two lists
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config.setHasSecondList(filename.contains("BFN_Saeuger"));
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config.setNomenclaturalCode(nomenclaturalCode);
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config.setDoMetaData(doMetaData);
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config.setDoTaxonNames(doTaxonNames);
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config.setDoFeature(doFeature);
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config.setDoAdditionalTerms(doAdditionalTerms);
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config.setCheck(check);
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config.setDbSchemaValidation(schemaValidation);
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//TODO only quickfix see also MetaData import
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String classificationName;
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if (filename.startsWith("rldb")){
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classificationName = filename.replace("rldb_print_v4_0_1_0_", "")
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.split("_")[0].replace(".xml", "").replace("artenarmeWeichtiergruppen", "Artenarme Weichtiergruppen");
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}else{
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classificationName = filename.replace("RoteListe_v4_0_6_0_BFN_Saeuger_korr.xml", "Säuger");
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}
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config.setClassificationName(classificationName);
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// invoke import
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bfnImport.invoke(config);
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setVaadinPreferences(bfnImport, nomenclaturalCode);
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logger.info("End");
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System.out.println("End import from BfnXML ("+ source.toString() + ")...");
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} catch (Exception e) {
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e.printStackTrace();
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}
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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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List<String> fileNames = Arrays.asList(
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// Plants
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// //band2
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// "rldb_print_v4_0_1_0_Makroalgen_150121_syn.xml",uuidBand2_marineMakroalgen.toString(),
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//fungi
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//band6
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// "rldb_print_v4_0_1_0_Flechten_korr_verantw_syn.xml",uuidBand6_flechtenUndPilze.toString(),
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// //korrekt??
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// "rldb_print_v4_0_1_0_Saprophyten_verantw.xml",uuidBand6_flechtenUndPilze.toString(),
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// "rldb_print_v4_0_1_0_Lichenicole_verantw_syn.xml",uuidBand6_flechtenUndPilze.toString(),
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// "rldb_print_v4_0_1_0_Myxo_110708_korr_syn_neu.xml",uuidBand6_myxomyzeten.toString(),
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//
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// Animals
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// //band1
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// "rldb_print_v4_0_1_0_Brutvoegel.xml",BfnXmlImportReferences.uuidBand1_brutvoegel.toString(), //Brutvögel
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// "rldb_print_v4_0_1_0_Reptilien_1.xml",uuidBand1_kriechtiere.toString(),
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// "rldb_print_v4_0_1_0_Amphibien.xml",uuidBand1_lurche.toString(), //Kriechtiere
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// "RoteListe_v4_0_6_0_BFN_Saeuger_korr.xml",uuidBand1_saeugetiere.toString(), //Säugetiere
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// "rldb_print_v4_0_1_0_Fische.xml",uuidBand1_suessfische.toString(),
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// //
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// //band2
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// "rldb_print_v4_0_1_0_artenarmeWeichtiergruppen_121127_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
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// "rldb_print_v4_0_1_0_Asselspinnen_120907_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
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// "rldb_print_v4_0_1_0_Flohkrebse_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
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// "rldb_print_v4_0_1_0_Igelwuermer_120907_verantw.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
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// "rldb_print_v4_0_1_0_Kumazeen_120709_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
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// "rldb_print_v4_0_1_0_Asseln_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
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// "rldb_print_v4_0_1_0_Moostierchen_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
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// "rldb_print_v4_0_1_0_Muscheln_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
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// "rldb_print_v4_0_1_0_Schnecken_130206_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
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// "rldb_print_v4_0_1_0_Meeresfische_syn.xml",uuidBand2_meeresfischeUndNeunaugen.toString(),
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// "rldb_print_v4_0_1_0_Nesseltiere_130104_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
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// "rldb_print_v4_0_1_0_Schaedellose_120907_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), //Schädellose
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// "rldb_print_v4_0_1_0_Schwaemme_121127_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), //Schwämme
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// "rldb_print_v4_0_1_0_Seepocken_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
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// "rldb_print_v4_0_1_0_Seescheiden_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
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// "rldb_print_v4_0_1_0_Stachelhaeuter_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), //Stachelhäuter
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// "rldb_print_v4_0_1_0_Vielborster_130206_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
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// "rldb_print_v4_0_1_0_Wenigborster_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
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// "rldb_print_v4_0_1_0_Zehnfusskrebse_130104_verantw_syn.xml", uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
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// //
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// //band3
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// "rldb_print_v4_0_1_0_Ameisen_110609_rev120113_syn.xml", uuidBand3_ameisen.toString(), //Hymenoptera: Formicidae
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// "rldb_print_v4_0_1_0_Bienen_PWKorr_HG_120413_DF_120612_syn.xml",uuidBand3_bienen.toString(), //Hymnenoptera: Apidae
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// "rldb_print_v4_0_1_0_Binnenmollusken_0alle_120413_DF_syn.xml",uuidBand3_binnenmollusken.toString(),
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// //eulenfalter - korrekt?
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// "rldb_print_v4_0_1_0_Eulen_Korruebern_23-05-2012_KorrV_syn.xml",uuidBand3_eulenfalter.toString(), //Eulen & Korrübern
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// "rldb_print_v4_0_1_0_Thysanoptera_120413_DF_korrV_Verantw.xml",uuidBand3_fransenfluegler.toString(),
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// "rldb_print_v4_0_1_0_Heuschrecken_syn.xml",uuidBand3_heuschrecken.toString(), //Saltatoria
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// "rldb_print_v4_0_1_0_Ohrwuermer_DF_syn.xml",uuidBand3_ohrwuermer.toString(), //Dermaptera
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// "rldb_print_v4_0_1_0_Pflanzenwespen_280711_Autor_110815_HG2_120413_DF_syn.xml",uuidBand3_pflanzenwespen.toString(), //Hymenoptera: Symphata
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// "rldb_print_v4_0_1_0_Asilidae_GMH_Wolff_110314_HGxls_120413_DF_korrV_Verantw_syn.xml",uuidBand3_raubfliegen.toString(),
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// "rldb_print_v4_0_1_0_Blattoptera_140413_DF_syn.xml",uuidBand3_schaben.toString(),
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// "rldb_print_v4_0_1_0_Schwebfliegen_111103_KorrAS_120413_DF_syn.xml",uuidBand3_schwebfliegen.toString(), //Diptera: Syrphidae
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// //spanner - korrekt?
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// "rldb_print_v4_0_1_0_Eulenspinner_Spanner_13-06-2012_KorrV_syn.xml",uuidBand3_spanner.toString(), //Eulenspinner & Spanner
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// "rldb_print_v4_0_1_0_Spinner_Oktober2011_eingearbKorr_120124_Korruebern_MB_02-05-2012_KorrV_syn.xml",uuidBand3_spinner.toString(),
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// "rldb_print_v4_0_1_0_Tagfalter_06-06-2012_KorrV_syn.xml",uuidBand3_tagfalter.toString(),
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// "rldb_print_v4_0_1_0_Empidoidea_120413_DF.xml",uuidBand3_tanzfliegen.toString(), //Empidoidea
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// //wespen - fehlen ????? => siehe auch titel des Referenz Word Files
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// "rldb_print_v4_0_1_0_Pyraloidea_Februar_2012_Korruebern_MB_24-04-2012_syn.xml",uuidBand3_zuenslerfalter.toString()
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// //the 4 first lists, THESE ARE DUPLICATES
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// "RoteListe_v4_0_6_0_BFN_Saeuger_korr.xml",BfnXmlImportReferences.uuidBand1_saeugetiere.toString(),
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"rldb_print_v4_0_1_0_Amphibien.xml",BfnXmlImportReferences.uuidBand1_lurche.toString(),
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"rldb_print_v4_0_1_0_Reptilien_1.xml",BfnXmlImportReferences.uuidBand1_kriechtiere.toString(),
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"rldb_print_v4_0_1_0_Heuschrecken_syn.xml", BfnXmlImportReferences.uuidBand3_heuschrecken.toString()
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);
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CdmDefaultImport<BfnXmlImportConfigurator> bfnImport = new CdmDefaultImport<>();
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ICdmDataSource destination = cdmDestination;
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URI source = null;
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BfnXmlImportConfigurator config = BfnXmlImportConfigurator.NewInstance(source, destination);
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Iterator<String> it = fileNames.iterator();
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while(it.hasNext()){
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String fileName = it.next();
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BfnXmlImportActivator bfnXmlTestActivator = new BfnXmlImportActivator(fileName);
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String uuid = it.next();
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config.setSourceRefUuid(UUID.fromString(uuid));
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bfnXmlTestActivator.doImport(config, bfnImport);
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// pauseProg();
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schemaValidation = DbSchemaValidation.VALIDATE;
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}
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//first run
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//create DB,Metadata
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// String fileName = "rldb_print_v4_0_1_0_Ameisen_110609_rev120113_syn.xml";
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// BfnXmlTestActivator bfnXmlTestActivator = new BfnXmlTestActivator(fileName);
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// bfnXmlTestActivator.doImport();
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System.exit(0);
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}
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@SuppressWarnings("resource")
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public static void pauseProg(){
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System.out.println("Press enter to continue...");
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Scanner keyboard = new Scanner(System.in);
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keyboard.nextLine();
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}
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/**
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* @param bfnImport
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* @param nomCode
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*/
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private void setVaadinPreferences(CdmDefaultImport<BfnXmlImportConfigurator> bfnImport, NomenclaturalCode nomCode) {
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ICdmRepository app = bfnImport.getCdmAppController();
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CdmPreference statusPref = CdmPreference.NewInstance(
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PreferenceSubject.NewVaadinInstance(),
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PreferencePredicate.AvailableDistributionStatus,
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BfnXmlTransformer.uuidStatusVorkommend,
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BfnXmlTransformer.uuidStatusUnsicher,
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BfnXmlTransformer.uuidStatusAbgelehnt,
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BfnXmlTransformer.uuidStatusKeinNachweis
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);
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app.getPreferenceService().set(statusPref);
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CdmPreference areaVocPref = CdmPreference.NewInstance(
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PreferenceSubject.NewVaadinInstance(),
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PreferencePredicate.AvailableDistributionAreaVocabularies,
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BfnXmlTransformer.uuidVocGermanFederalStates);
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app.getPreferenceService().set(areaVocPref);
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CdmPreference nomCodePref = CdmPreference.NewDatabaseInstance(PreferencePredicate.NomenclaturalCode, "eu.etaxonomy.cdm.model.name.NomenclaturalCode." + nomCode.getUuid());
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app.getPreferenceService().set(nomCodePref);
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}
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}
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