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/**
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* Copyright (C) 2015 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.caryophyllales;
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import java.io.IOException;
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import java.net.URI;
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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.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.common.ImportResult;
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import eu.etaxonomy.cdm.io.tropicos.in.TropicosNameImportConfigurator;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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/**
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* @author a.mueller
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* @date 18.10.2017
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*
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*/
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public class PlumbaginaceaeTropicosActivator {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(PlumbaginaceaeTropicosActivator.class);
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//database validation status (create, update, validate ...)
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static DbSchemaValidation dbSchemaValidation = DbSchemaValidation.VALIDATE;
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// static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_test1();
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static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_caryophyllales_spp();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_caryo_spp();
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static final boolean createTaxa = true;
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static int transactionLineCount = 100;
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static boolean allowTropicosDuplicates = true;
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static boolean allowIpniDuplicates = true;
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static boolean allowWfoDuplicates = false;
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static boolean addAuthorsToReferences = true;
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static boolean reportDuplicateIdentifier = true;
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static final String classificationName = "Tropicos Plumbaginaceae";
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static final UUID parentNodeUuid = UUID.fromString("46755269-5b06-4308-9871-c55850610769");
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//check - import
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static CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
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private void doImport(ICdmDataSource cdmDestination){
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URI source = getPlumbaginaceaeTropicosUri();
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TropicosNameImportConfigurator config;
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try {
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config = TropicosNameImportConfigurator.NewInstance(source, cdmDestination);
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config.setDbSchemaValidation(dbSchemaValidation);
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config.setCheck(check);
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config.setNomenclaturalCode(NomenclaturalCode.ICNAFP);
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config.setCreateTaxa(createTaxa);
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config.setClassificationName(classificationName);
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config.setSourceReference(getSourceReference());
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config.setParentNodeUuid(parentNodeUuid);
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config.setTransactionLineCount(transactionLineCount);
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config.setAllowIpniDuplicates(allowIpniDuplicates);
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config.setAllowTropicosDuplicates(allowTropicosDuplicates);
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config.setAllowWfoDuplicates(allowWfoDuplicates);
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config.setAddAuthorsToReference(addAuthorsToReferences);
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config.setReportDuplicateIdentifier(reportDuplicateIdentifier);
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CdmDefaultImport<TropicosNameImportConfigurator> myImport = new CdmDefaultImport<>();
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ImportResult result = myImport.invoke(config);
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System.out.println(result.createReport());
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} catch (IOException e) {
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System.out.println("URI not 'found': " + source);
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}
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}
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private URI getPlumbaginaceaeTropicosUri(){
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// String fileName = "TropicosNameImportTest-input.txt";
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String fileName = "TropicosOutput2CDM-rev-output_Plumbaginaceae.txt";
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// String fileName = "TropicosOutput2CDM_Plumbaginaceae.txt";
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URI uri = URI.create("file:////BGBM-PESIHPC/Caryophyllales/" + fileName);
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return uri;
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}
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private Reference getSourceReference(){
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Reference result = ReferenceFactory.newDatabase();
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result.setTitle("Tropicos Plumbaginaceae import");
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result.setUuid(UUID.fromString("937f3a38-dbb4-4888-9ea3-2f52d47f7953"));
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return result;
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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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PlumbaginaceaeTropicosActivator me = new PlumbaginaceaeTropicosActivator();
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me.doImport(cdmDestination);
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System.exit(0);
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}
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}
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