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91138b6c
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Andreas Müller
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/**
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* Copyright (C) 2007 EDIT
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50818ab7
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Katja Luther
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* European Distributed Institute of Taxonomy
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91138b6c
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Andreas Müller
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* http://www.e-taxonomy.eu
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50818ab7
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Katja Luther
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*
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91138b6c
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Andreas Müller
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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.berlinModelImport;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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8072bd02
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Andreas Müller
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import eu.etaxonomy.cdm.api.application.ICdmRepository;
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91138b6c
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Andreas Müller
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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.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.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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50818ab7
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Katja Luther
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import eu.etaxonomy.cdm.io.common.ImportResult;
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d55d93f6
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Andreas Müller
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import eu.etaxonomy.cdm.io.common.Source;
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91138b6c
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Andreas Müller
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.FeatureNode;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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/**
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* TODO add the following to a wiki page:
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50818ab7
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Katja Luther
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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 base under another operation systen
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91138b6c
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Andreas Müller
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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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50818ab7
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Katja Luther
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*
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*
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91138b6c
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Andreas Müller
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* @author a.mueller
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*
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*/
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public class CampanulaceaeActivator {
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private static final Logger logger = Logger.getLogger(CampanulaceaeActivator.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.Campanulaceae();
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static final ICdmDataSource cdmDestination = CdmDestinations.cdm_campanulaceae_production();
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static final UUID secUuid = UUID.fromString("ed7dd0ea-fcdd-405d-9fe1-52652aa06119");
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401fe405
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Andreas Müller
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static final UUID classificationUuid = UUID.fromString("e305ddac-7200-4293-aa5d-d3426133ed9f");
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91138b6c
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Andreas Müller
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static final int sourceSecId = 100000;
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Katja Luther
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91138b6c
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Andreas Müller
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static final UUID featureTreeUuid = UUID.fromString("231809ce-ad9e-4a50-8a48-668bd336cb7e");
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50818ab7
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Katja Luther
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static final Object[] featureKeyList = new Integer[]{};
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91138b6c
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Andreas Müller
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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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Katja Luther
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91138b6c
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Andreas Müller
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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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50818ab7
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Katja Luther
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bc2e58de
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Andreas Müller
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//NomenclaturalCode
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Andreas Müller
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static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
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91138b6c
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Andreas Müller
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//ignore null
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static final boolean ignoreNull = true;
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50818ab7
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Katja Luther
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401fe405
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Andreas Müller
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static boolean useClassification = true;
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91138b6c
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Andreas Müller
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50818ab7
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Katja Luther
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static boolean includesEmCode = false;
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91138b6c
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Andreas Müller
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50818ab7
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Katja Luther
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// **************** ALL *********************
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91138b6c
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Andreas Müller
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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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50818ab7
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Katja Luther
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91138b6c
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Andreas Müller
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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; //no facts exist campanulaceae
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static final boolean doOccurences = true;
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static final boolean doCommonNames = false; //no common names exist in campanulaceae
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//etc.
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static final boolean doMarker = true;
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50818ab7
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Katja Luther
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91138b6c
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Andreas Müller
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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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50818ab7
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Katja Luther
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//
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// //taxa
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91138b6c
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Andreas Müller
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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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Katja Luther
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//
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91138b6c
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Andreas Müller
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// //etc.
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// static final boolean doMarker = false;
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Katja Luther
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private ImportResult doInvoke(ICdmDataSource destination){
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ImportResult success ;
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91138b6c
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Andreas Müller
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Source source = berlinModelSource;
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Katja Luther
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Andreas Müller
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BerlinModelImportConfigurator bmImportConfigurator = BerlinModelImportConfigurator.NewInstance(source, destination);
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Katja Luther
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401fe405
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Andreas Müller
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bmImportConfigurator.setClassificationUuid(classificationUuid);
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Andreas Müller
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bmImportConfigurator.setSourceSecId(sourceSecId);
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Katja Luther
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91138b6c
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Andreas Müller
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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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401fe405
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Andreas Müller
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bmImportConfigurator.setUseClassification(useClassification);
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50818ab7
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Katja Luther
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91138b6c
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Andreas Müller
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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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50818ab7
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Katja Luther
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91138b6c
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Andreas Müller
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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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50818ab7
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Katja Luther
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553bddfe
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Andreas Müller
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bmImportConfigurator.setIncludesEmCode(includesEmCode);
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91138b6c
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Andreas Müller
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// maximum number of name facts to import
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bmImportConfigurator.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
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50818ab7
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Katja Luther
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91138b6c
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Andreas Müller
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bmImportConfigurator.setCheck(check);
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bmImportConfigurator.setEditor(editor);
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50818ab7
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Katja Luther
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91138b6c
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Andreas Müller
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// invoke import
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CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
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Katja Luther
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success = bmImport.invoke(bmImportConfigurator);
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Andreas Müller
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if (doFacts && (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT) || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ) ){
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8072bd02
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Andreas Müller
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ICdmRepository app = bmImport.getCdmAppController();
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Katja Luther
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Andreas Müller
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//make feature tree
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FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList);
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FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
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Katja Luther
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tree.getRoot().addChild(distributionNode, 1);
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Andreas Müller
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app.getFeatureTreeService().saveOrUpdate(tree);
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}
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50818ab7
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Katja Luther
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91138b6c
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Andreas Müller
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System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
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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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Katja Luther
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Andreas Müller
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return success;
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50818ab7
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Katja Luther
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91138b6c
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Andreas Müller
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}
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50818ab7
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Katja Luther
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91138b6c
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Andreas Müller
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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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Katja Luther
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Andreas Müller
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System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + destination.getDatabase() + " ...");
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CampanulaceaeActivator me = new CampanulaceaeActivator();
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me.doInvoke(destination);
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50818ab7
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Katja Luther
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91138b6c
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Andreas Müller
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}
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}
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