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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.dwca;
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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.api.application.ICdmApplicationConfiguration;
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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.events.LoggingIoObserver;
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import eu.etaxonomy.cdm.io.dwca.in.DwcaDataImportConfiguratorBase.DatasetUse;
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import eu.etaxonomy.cdm.io.dwca.in.DwcaImportConfigurator;
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import eu.etaxonomy.cdm.io.dwca.in.IImportMapping.MappingType;
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import eu.etaxonomy.cdm.model.agent.Person;
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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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* @created 10.11.2011
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*/
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public class DwcaImportActivator {
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private static final Logger logger = Logger.getLogger(DwcaImportActivator.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 URI source = dwca_test_in();
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// static final URI source = dwca_test_cich_len();
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// static final URI source = dwca_test_col_sapindaceae();
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// static final URI source = dwca_test_col_cichorium();
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// static final URI source = dwca_test_scratch_test();
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// static final URI source = dwca_test_col_All();
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// static final URI source = dwca_test_col_All_Pesi2();
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static final URI source = dwca_emonocots_dioscoreaceae();
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static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_dwca();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
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// static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_pesi_test();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_pesi();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
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//classification
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static final UUID classificationUuid = UUID.fromString("29d4011f-a6dd-4081-beb8-559ba6b84a6b");
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//default nom code is ICZN as it allows adding publication year
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static final NomenclaturalCode defaultNomCode = 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 int partitionSize = 1000;
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//config
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static DatasetUse datasetUse = DatasetUse.SECUNDUM;
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static boolean scientificNameIdAsOriginalSourceId = true;
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static boolean guessNomRef = true;
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static boolean handleAllRefsAsCitation = true;
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//validate
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static boolean validateRankConsistency = false;
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//taxa
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static final boolean doTaxa = true;
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static final boolean doDistribution = false;
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//deduplicate
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static final boolean doDeduplicate = false;
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static final MappingType mappingType = MappingType.InMemoryMapping;
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private void doImport(ICdmDataSource cdmDestination){
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//make Source
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DwcaImportConfigurator config= DwcaImportConfigurator.NewInstance(source, cdmDestination);
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config.addObserver(new LoggingIoObserver());
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config.setClassificationUuid(classificationUuid);
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config.setCheck(check);
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config.setDbSchemaValidation(hbm2dll);
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config.setMappingType(mappingType);
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config.setScientificNameIdAsOriginalSourceId(scientificNameIdAsOriginalSourceId);
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config.setValidateRankConsistency(validateRankConsistency);
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config.setDefaultPartitionSize(partitionSize);
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config.setNomenclaturalCode(defaultNomCode);
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config.setDatasetUse(datasetUse);
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config.setGuessNomenclaturalReferences(guessNomRef);
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config.setHandleAllRefsAsCitation(handleAllRefsAsCitation);
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CdmDefaultImport<DwcaImportConfigurator> myImport = new CdmDefaultImport<DwcaImportConfigurator>();
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//...
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if (true){
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System.out.println("Start import from ("+ source.toString() + ") ...");
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config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
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myImport.invoke(config);
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System.out.println("End import from ("+ source.toString() + ")...");
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}
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//deduplicate
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if (doDeduplicate){
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ICdmApplicationConfiguration app = myImport.getCdmAppController();
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int count = app.getAgentService().deduplicate(Person.class, null, null);
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logger.warn("Deduplicated " + count + " persons.");
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// count = app.getAgentService().deduplicate(Team.class, null, null);
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// logger.warn("Deduplicated " + count + " teams.");
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count = app.getReferenceService().deduplicate(Reference.class, null, null);
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logger.warn("Deduplicated " + count + " references.");
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}
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}
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private Reference<?> getSourceReference(String string) {
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Reference<?> result = ReferenceFactory.newGeneric();
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result.setTitleCache(string);
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return result;
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}
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//Dwca
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public static URI dwca_test_in() {
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// URI sourceUrl = URI.create("http://dev.e-taxonomy.eu/trac/export/14463/trunk/cdmlib/cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/dwca/in/DwcaZipToStreamConverterTest-input.zip");
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URI sourceUrl = URI.create("file:///C:/Users/pesiimport/Documents/pesi_cdmlib/cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/dwca/in/DwcaZipToStreamConverterTest-input.zip");
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return sourceUrl;
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}
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//Dwca
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public static URI dwca_test_cich() {
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URI sourceUrl = URI.create("file:///E:/opt/data/dwca/20110621_1400_cichorieae_dwca.zip");
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return sourceUrl;
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}
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//Dwca
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public static URI dwca_test_cich_len() {
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URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/export/20110621_1400_cichorieae_dwca.zip");
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return sourceUrl;
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}
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//Dwca
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public static URI dwca_test_col_cichorium() {
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URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/CoL/Cichorium/archive-genus-Cichorium-bl3.zip");
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return sourceUrl;
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}
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//Dwca
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public static URI dwca_test_col_sapindaceae() {
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URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/CoL/Sapindaceae/archive-family-Sapindaceae-bl3.zip");
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return sourceUrl;
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}
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//Dwca
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public static URI dwca_emonocots_local() {
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URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/Scratchpads/dwca_dioscoreaceae_emonocots.zip");
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return sourceUrl;
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}
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//emonocots_dioscoreaceae
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public static URI dwca_emonocots_dioscoreaceae() {
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URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_dioscoreaceae.zip");
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return sourceUrl;
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}
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//emonocots_zingiberaceae
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public static URI dwca_emonocots_zingiberaceae() {
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URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_zingiberaceae.zip");
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return sourceUrl;
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}
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//emonocots_cypripedioideae
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public static URI dwca_emonocots_cypripedioideae() {
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URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_cypripedioideae.zip");
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return sourceUrl;
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}
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//CoL
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public static URI dwca_test_col_All() {
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URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/CoL/All/archive-complete.zip");
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return sourceUrl;
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}
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//CoL
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public static URI dwca_test_col_All_Pesi2() {
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URI sourceUrl = URI.create("file:///C:/opt/data/CoL/All/archive-complete.zip");
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return sourceUrl;
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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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DwcaImportActivator me = new DwcaImportActivator();
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me.doImport(cdmDestination);
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}
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}
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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.dwca;
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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.api.application.ICdmApplicationConfiguration;
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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.events.LoggingIoObserver;
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import eu.etaxonomy.cdm.io.dwca.in.DwcaDataImportConfiguratorBase.DatasetUse;
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import eu.etaxonomy.cdm.io.dwca.in.DwcaImportConfigurator;
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import eu.etaxonomy.cdm.io.dwca.in.IImportMapping.MappingType;
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import eu.etaxonomy.cdm.model.agent.Person;
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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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* @created 10.11.2011
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*/
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public class DwcaImportActivator {
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private static final Logger logger = Logger.getLogger(DwcaImportActivator.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 URI source = dwca_test_in();
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// static final URI source = dwca_test_cich_len();
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// static final URI source = dwca_test_col_sapindaceae();
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// static final URI source = dwca_test_col_cichorium();
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// static final URI source = dwca_test_scratch_test();
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// static final URI source = dwca_test_col_All();
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// static final URI source = dwca_test_col_All_Pesi2();
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static final URI source = dwca_emonocots_dioscoreaceae();
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static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_dwca();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
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// static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_pesi_test();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_pesi();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
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//classification
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static final UUID classificationUuid = UUID.fromString("29d4011f-a6dd-4081-beb8-559ba6b84a6b");
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//default nom code is ICZN as it allows adding publication year
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static final NomenclaturalCode defaultNomCode = 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 int partitionSize = 1000;
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//config
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static DatasetUse datasetUse = DatasetUse.SECUNDUM;
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static boolean scientificNameIdAsOriginalSourceId = true;
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static boolean guessNomRef = true;
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static boolean handleAllRefsAsCitation = true;
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//validate
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static boolean validateRankConsistency = false;
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//taxa
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static final boolean doTaxa = true;
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static final boolean doDistribution = false;
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//deduplicate
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static final boolean doDeduplicate = false;
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static final MappingType mappingType = MappingType.InMemoryMapping;
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private void doImport(ICdmDataSource cdmDestination){
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//make Source
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DwcaImportConfigurator config= DwcaImportConfigurator.NewInstance(source, cdmDestination);
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config.addObserver(new LoggingIoObserver());
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config.setClassificationUuid(classificationUuid);
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config.setCheck(check);
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config.setDbSchemaValidation(hbm2dll);
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config.setMappingType(mappingType);
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config.setScientificNameIdAsOriginalSourceId(scientificNameIdAsOriginalSourceId);
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config.setValidateRankConsistency(validateRankConsistency);
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config.setDefaultPartitionSize(partitionSize);
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config.setNomenclaturalCode(defaultNomCode);
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config.setDatasetUse(datasetUse);
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config.setGuessNomenclaturalReferences(guessNomRef);
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config.setHandleAllRefsAsCitation(handleAllRefsAsCitation);
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CdmDefaultImport<DwcaImportConfigurator> myImport = new CdmDefaultImport<DwcaImportConfigurator>();
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//...
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if (true){
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System.out.println("Start import from ("+ source.toString() + ") ...");
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config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
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myImport.invoke(config);
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System.out.println("End import from ("+ source.toString() + ")...");
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}
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//deduplicate
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if (doDeduplicate){
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ICdmApplicationConfiguration app = myImport.getCdmAppController();
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int count = app.getAgentService().deduplicate(Person.class, null, null);
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logger.warn("Deduplicated " + count + " persons.");
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// count = app.getAgentService().deduplicate(Team.class, null, null);
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// logger.warn("Deduplicated " + count + " teams.");
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count = app.getReferenceService().deduplicate(Reference.class, null, null);
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logger.warn("Deduplicated " + count + " references.");
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}
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}
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private Reference<?> getSourceReference(String string) {
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Reference<?> result = ReferenceFactory.newGeneric();
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result.setTitleCache(string);
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return result;
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}
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//Dwca
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public static URI dwca_test_in() {
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// URI sourceUrl = URI.create("http://dev.e-taxonomy.eu/trac/export/14463/trunk/cdmlib/cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/dwca/in/DwcaZipToStreamConverterTest-input.zip");
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URI sourceUrl = URI.create("file:///C:/Users/pesiimport/Documents/pesi_cdmlib/cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/dwca/in/DwcaZipToStreamConverterTest-input.zip");
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return sourceUrl;
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}
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//Dwca
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public static URI dwca_test_cich() {
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URI sourceUrl = URI.create("file:///E:/opt/data/dwca/20110621_1400_cichorieae_dwca.zip");
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return sourceUrl;
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}
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156 |
//Dwca
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public static URI dwca_test_cich_len() {
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URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/export/20110621_1400_cichorieae_dwca.zip");
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159 |
return sourceUrl;
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}
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162 |
//Dwca
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163 |
public static URI dwca_test_col_cichorium() {
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164 |
URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/CoL/Cichorium/archive-genus-Cichorium-bl3.zip");
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165 |
return sourceUrl;
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166 |
}
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167 |
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168 |
//Dwca
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169 |
public static URI dwca_test_col_sapindaceae() {
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URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/CoL/Sapindaceae/archive-family-Sapindaceae-bl3.zip");
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171 |
return sourceUrl;
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172 |
}
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174 |
//Dwca
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175 |
public static URI dwca_emonocots_local() {
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176 |
URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/Scratchpads/dwca_dioscoreaceae_emonocots.zip");
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177 |
return sourceUrl;
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178 |
}
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180 |
//emonocots_dioscoreaceae
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181 |
public static URI dwca_emonocots_dioscoreaceae() {
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182 |
URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_dioscoreaceae.zip");
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183 |
return sourceUrl;
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184 |
}
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186 |
//emonocots_zingiberaceae
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187 |
public static URI dwca_emonocots_zingiberaceae() {
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188 |
URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_zingiberaceae.zip");
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189 |
return sourceUrl;
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190 |
}
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191 |
//emonocots_cypripedioideae
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192 |
public static URI dwca_emonocots_cypripedioideae() {
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193 |
URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_cypripedioideae.zip");
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194 |
return sourceUrl;
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195 |
}
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196 |
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197 |
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198 |
//CoL
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|
199 |
public static URI dwca_test_col_All() {
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200 |
URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/CoL/All/archive-complete.zip");
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|
201 |
return sourceUrl;
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|
202 |
}
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203 |
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204 |
//CoL
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205 |
public static URI dwca_test_col_All_Pesi2() {
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206 |
URI sourceUrl = URI.create("file:///C:/opt/data/CoL/All/archive-complete.zip");
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|
207 |
return sourceUrl;
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|
208 |
}
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209 |
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210 |
|
|
211 |
|
|
212 |
/**
|
|
213 |
* @param args
|
|
214 |
*/
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|
215 |
public static void main(String[] args) {
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|
216 |
DwcaImportActivator me = new DwcaImportActivator();
|
|
217 |
me.doImport(cdmDestination);
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|
218 |
}
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|
219 |
|
|
220 |
}
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Adapt ColDwcaImportActivator to latest import changes