Revision 72f1cc5a
Added by Andreas Müller almost 9 years ago
app-import/src/main/java/eu/etaxonomy/cdm/app/dwca/DwcaImportActivator.java | ||
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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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//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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178 |
} |
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179 |
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//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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185 |
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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; |
|
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"); |
|
201 |
return sourceUrl; |
|
202 |
} |
|
203 |
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|
204 |
//CoL |
|
205 |
public static URI dwca_test_col_All_Pesi2() { |
|
206 |
URI sourceUrl = URI.create("file:///C:/opt/data/CoL/All/archive-complete.zip"); |
|
207 |
return sourceUrl; |
|
208 |
} |
|
209 |
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|
210 |
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|
211 |
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|
212 |
/** |
|
213 |
* @param args |
|
214 |
*/ |
|
215 |
public static void main(String[] args) { |
|
216 |
DwcaImportActivator me = new DwcaImportActivator(); |
|
217 |
me.doImport(cdmDestination); |
|
218 |
} |
|
219 |
|
|
220 |
} |
Also available in: Unified diff
Adapt ColDwcaImportActivator to latest import changes