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/**
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* Copyright (C) 2017 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.io.dwca.out;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.math.BigDecimal;
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import java.util.HashSet;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.junit.Assert;
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import org.junit.Before;
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import org.junit.Test;
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import org.unitils.dbunit.annotation.DataSet;
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import org.unitils.spring.annotation.SpringBeanByName;
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import org.unitils.spring.annotation.SpringBeanByType;
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import eu.etaxonomy.cdm.api.service.IClassificationService;
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import eu.etaxonomy.cdm.api.service.ITaxonNodeService;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
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import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultExport;
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import eu.etaxonomy.cdm.io.common.ExportDataWrapper;
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import eu.etaxonomy.cdm.io.common.ExportResult;
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import eu.etaxonomy.cdm.io.common.IExportConfigurator.TARGET;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.QuantitativeData;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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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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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
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import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;
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/**
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* Test for Darwin Core Archive (DwCA) export.
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*
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* @author a.mueller
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* @since 25.06.2017
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*/
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public class DwcaExportTest extends CdmTransactionalIntegrationTest{
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(DwcaExportTest.class);
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private static final UUID UUID_SUBSPEC_NODE = UUID.fromString("f8c9933a-fe3a-42ce-8a92-000e27bfdfac");
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private static final String UUID_UNPUBLISHED_TAXON = "e5cdc392-4e0b-49ad-84e9-8c4b22d1827c";
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@SpringBeanByName
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private CdmApplicationAwareDefaultExport<DwcaTaxExportConfigurator> defaultExport;
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@SpringBeanByType
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private IClassificationService classificationService;
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@SpringBeanByType
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private ITaxonNodeService taxonNodeService;
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@SpringBeanByType
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private ITermService termService;
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private static State state1;
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@Before
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public void setUp(){
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if (state1 == null){
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//FIXME #8891
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// state1 = State.NewInstance("state1 text", "state1", "st.1");
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// termService.save(state1);
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}
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}
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@Test
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDBDataSet.xml")
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public void testEmptyData(){
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File destinationFolder = null;
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DwcaTaxExportConfigurator config = DwcaTaxExportConfigurator.NewInstance(null, destinationFolder, null);
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config.setTarget(TARGET.EXPORT_DATA);
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ExportResult result = defaultExport.invoke(config);
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// System.out.println(result.createReport());
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ExportDataWrapper<?> exportData = result.getExportData();
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@SuppressWarnings("unchecked")
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Map<String, byte[]> data = (Map<String, byte[]>) exportData.getExportData();
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for (String key : data.keySet()){
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byte[] byt = data.get(key);
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// System.out.println(key + ": " + new String(byt) );
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}
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//metadata
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byte[] metadata = data.get(DwcaTaxExportFile.METADATA.getTableName());
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Assert.assertNotNull("Metadata must not be null", metadata);
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String metaDataStr = new String(metadata);
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String metaHeader = "<?xml version=\"1.0\" ?><archive xmlns=\"http://rs.tdwg.org/dwc/text/\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://rs.tdwg.org/dwc/text/ http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd\"></archive>";
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Assert.assertTrue(metaDataStr.contains(metaHeader));
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String metaCore = "<core";
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Assert.assertFalse(metaDataStr.contains(metaCore));
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metaCore = "<field";
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Assert.assertFalse(metaDataStr.contains(metaCore));
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metaCore = "<files";
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Assert.assertFalse(metaDataStr.contains(metaCore));
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//core
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byte[] core = data.get(DwcaTaxExportFile.TAXON.getTableName());
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Assert.assertNull("Core must not exist", core);
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//reference
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byte[] ref = data.get(DwcaTaxExportFile.REFERENCE.getTableName());
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Assert.assertNull("Reference must not exist", ref);
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//distribution
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byte[] distribution = data.get(DwcaTaxExportFile.DISTRIBUTION.getTableName());
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Assert.assertNull("Distribution must not exist", distribution);
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}
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@Test
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDBDataSet.xml")
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public void testSubTree(){
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createFullTestDataSet();
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File destinationFolder = null;
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DwcaTaxExportConfigurator config = DwcaTaxExportConfigurator.NewInstance(null, destinationFolder, null);
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config.setTaxonNodeFilter(TaxonNodeFilter.NewSubtreeInstance(UUID_SUBSPEC_NODE));
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config.setTarget(TARGET.EXPORT_DATA);
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ExportResult result = defaultExport.invoke(config);
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// System.out.println(result.createReport());
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ExportDataWrapper<?> exportData = result.getExportData();
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@SuppressWarnings("unchecked")
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Map<String, byte[]> data = (Map<String, byte[]>) exportData.getExportData();
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for (String key : data.keySet()){
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byte[] byt = data.get(key);
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// System.out.println(key + ": " + new String(byt) );
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}
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//metadata
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byte[] metadata = data.get(DwcaTaxExportFile.METADATA.getTableName());
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Assert.assertNotNull("Metadata must not be null", metadata);
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//further tests in fullData
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//core
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byte[] core = data.get(DwcaTaxExportFile.TAXON.getTableName());
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Assert.assertNotNull("Core must not be null", core);
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String coreStr = new String(core);
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// String notExpected = "\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"f983cc5e-4c77-4c80-8cb0-73d43df31ee9\"";
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// Assert.assertFalse("Result must not contain root taxon", coreStr.contains(notExpected));
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//
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// String expected;
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// expected = "\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"f983cc5e-4c77-4c80-8cb0-73d43df31ee9\",\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"Genus species subsp. subspec Mill.\",\"Subspecies\",\"accepted\",,\"4b6acca1-959b-4790-b76e-e474a0882990\",";
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// Assert.assertTrue(coreStr.contains(expected));
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//
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// expected = "\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"f983cc5e-4c77-4c80-8cb0-73d43df31ee9\",\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"Genus species subsp. subspec Mill.\",\"Subspecies\",\"accepted\",,\"4b6acca1-959b-4790-b76e-e474a0882990\",\"4aa0824a-1197-4143-bc63-702ebfada9d2\"";
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// Assert.assertTrue(coreStr.contains(expected));
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// expected = "\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"f983cc5e-4c77-4c80-8cb0-73d43df31ee9\",\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"Genus species subsp. subspec Mill.\",\"Subspecies\",\"accepted\",,\"4b6acca1-959b-4790-b76e-e474a0882990\",\"4aa0824a-1197-4143-bc63-702ebfada9d2\",\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\"";
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// Assert.assertTrue(coreStr.contains(expected));
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// expected = "\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"f983cc5e-4c77-4c80-8cb0-73d43df31ee9\",\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"Genus species subsp. subspec Mill.\",\"Subspecies\",\"accepted\",,\"4b6acca1-959b-4790-b76e-e474a0882990\",\"4aa0824a-1197-4143-bc63-702ebfada9d2\",\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"Genus species subsp. subspec Mill.\"";
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// Assert.assertTrue(coreStr.contains(expected));
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String expected = "\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"3483cc5e-4c77-4c80-8cb0-73d43df31ee3\",\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"Genus species subsp. subspec Mill.\",\"Subspecies\",\"accepted\",,\"4b6acca1-959b-4790-b76e-e474a0882990\",\"b8dd7f4a-0c7f-4372-bc5d-3b676363bc0f\",\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"Genus species subsp. subspec Mill.\",\"Genus species Mill. sec. My sec ref\",";
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// System.out.println(coreStr);
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Assert.assertTrue(coreStr.contains(expected));
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expected = "\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"3483cc5e-4c77-4c80-8cb0-73d43df31ee3\",\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"Genus species subsp. subspec Mill.\",\"Subspecies\",\"accepted\",,\"4b6acca1-959b-4790-b76e-e474a0882990\",\"b8dd7f4a-0c7f-4372-bc5d-3b676363bc0f\",\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"Genus species subsp. subspec Mill.\",\"Genus species Mill. sec. My sec ref\",,\"My sec ref.\",\"Mill. 1804: The book of botany 3.\",,\"Genus\",,\"species\",\"subspec\",\"subsp.\",,\"ICNAFP\",,,,,,,,,,\"DwcaExportTest Classification\",";
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Assert.assertTrue(coreStr.contains(expected));
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//distribution
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byte[] distribution = data.get(DwcaTaxExportFile.DISTRIBUTION.getTableName());
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Assert.assertNull("Distribution must not exist", distribution);
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//reference
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byte[] ref = data.get(DwcaTaxExportFile.REFERENCE.getTableName());
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Assert.assertNotNull("Reference must not be null", ref);
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String refStr = new String(ref);
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// System.out.println(refStr);
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expected = "\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",,,,,\"My sec ref.\",\"My sec ref\",,,,,,,,,";
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Assert.assertTrue(refStr.contains(expected));
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expected = "\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",,,,,\"Mill. 1804: The book of botany 3.\",,\"Mill.\",\"1804\",,,,,,,";
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Assert.assertTrue(refStr.contains(expected));
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//header
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expected = "coreid,identifier,identifier,identifier,identifier,bibliographicCitation,title,creator,date,source,description,subject,language,rights,taxonRemarks,type";
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Assert.assertTrue(refStr.contains(expected));
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}
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@Test
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDBDataSet.xml")
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public void testFullData(){
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createFullTestDataSet();
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File destinationFolder = null;
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DwcaTaxExportConfigurator config = DwcaTaxExportConfigurator.NewInstance(null, destinationFolder, null);
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config.setTarget(TARGET.EXPORT_DATA);
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config.setWithHigherClassification(true);
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ExportResult result = defaultExport.invoke(config);
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// System.out.println(result.createReport());
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ExportDataWrapper<?> exportData = result.getExportData();
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@SuppressWarnings("unchecked")
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Map<String, byte[]> data = (Map<String, byte[]>) exportData.getExportData();
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for (String key : data.keySet()){
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byte[] byt = data.get(key);
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// System.out.println(key + ": " + new String(byt) );
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}
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// System.out.println();
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//metadata
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byte[] metadata = data.get(DwcaTaxExportFile.METADATA.getTableName());
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Assert.assertNotNull("Metadata must not be null", metadata);
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String metaDataStr = new String(metadata);
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String metaHeader = "<?xml version=\"1.0\" ?><archive xmlns=\"http://rs.tdwg.org/dwc/text/\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://rs.tdwg.org/dwc/text/ http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd\">";
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Assert.assertTrue(metaDataStr.contains(metaHeader));
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String metaCore = "<core encoding=\"UTF-8\" linesTerminatedBy=\"\r\n\" fieldsEnclosedBy=\""\""
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+ " fieldsTerminatedBy=\",\" ignoreHeaderLines=\"1\" rowType=\"http://rs.tdwg.org/dwc/terms/Taxon\">"
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+ "<files><location>coreTax.txt</location></files><id index=\"0\"></id><field index=\"1\" term=\"http://rs.tdwg.org/dwc/terms/scientificNameID\"></field><field index=\"2\" term=\"http://rs.tdwg.org/dwc/terms/acceptedNameUsageID\"></field><field index=\"3\" term=\"http://rs.tdwg.org/dwc/terms/parentNameUsageID\"></field><field index=\"4\" term=\"http://rs.tdwg.org/dwc/terms/scientificName\"></field><field index=\"5\" term=\"http://rs.tdwg.org/dwc/terms/taxonRank\"></field>"
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+ "<field index=\"6\" term=\"http://rs.tdwg.org/dwc/terms/taxonomicStatus\"></field><field index=\"7\" term=\"http://rs.tdwg.org/dwc/terms/originalNameUsageID\"></field>"
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+ "<field index=\"8\" term=\"http://rs.tdwg.org/dwc/terms/nameAccordingToID\"></field>"
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+ "<field index=\"9\" term=\"http://rs.tdwg.org/dwc/terms/namePublishedInID\"></field><field index=\"10\" term=\"http://rs.tdwg.org/dwc/terms/taxonConceptID\"></field><field index=\"11\" term=\"http://rs.tdwg.org/dwc/terms/acceptedNameUsage\"></field><field index=\"12\" term=\"http://rs.tdwg.org/dwc/terms/parentNameUsage\"></field><field index=\"13\" term=\"http://rs.tdwg.org/dwc/terms/originalNameUsage\"></field><field index=\"14\" term=\"http://rs.tdwg.org/dwc/terms/nameAccordingTo\"></field>"
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+ "<field index=\"15\" term=\"http://rs.tdwg.org/dwc/terms/namePublishedIn\"></field>"
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+ "<field index=\"16\" term=\"http://rs.tdwg.org/dwc/terms/higherClassification\"></field><field index=\"17\" term=\"http://rs.tdwg.org/dwc/terms/kingdom\"></field><field index=\"18\" term=\"http://rs.tdwg.org/dwc/terms/phylum\"></field><field index=\"19\" term=\"http://rs.tdwg.org/dwc/terms/class\"></field><field index=\"20\" term=\"http://rs.tdwg.org/dwc/terms/order\"></field><field index=\"21\" term=\"http://rs.tdwg.org/dwc/terms/family\"></field><field index=\"22\" term=\"http://rs.tdwg.org/dwc/terms/genus\"></field><field index=\"23\" term=\"http://rs.tdwg.org/dwc/terms/subgenus\"></field>"
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+ "<field index=\"24\" term=\"http://rs.tdwg.org/ontology/voc/TaxonName#uninomial\"></field>"
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+ "<field index=\"25\" term=\"http://rs.tdwg.org/ontology/voc/TaxonName#genusPart\"></field><field index=\"26\" term=\"http://rs.tdwg.org/ontology/voc/TaxonName#infragenericEpithet\"></field><field index=\"27\" term=\"http://rs.tdwg.org/dwc/terms/specificEpithet\"></field><field index=\"28\" term=\"http://rs.tdwg.org/dwc/terms/infraspecificEpithet\"></field><field index=\"29\" term=\"http://rs.tdwg.org/dwc/terms/verbatimTaxonRank\"></field><field index=\"30\" term=\"http://rs.tdwg.org/dwc/terms/vernacularName\"></field>"
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+ "<field index=\"31\" term=\"http://rs.tdwg.org/dwc/terms/nomenclaturalCode\"></field><field index=\"32\" term=\"http://rs.tdwg.org/dwc/terms/nomenclaturalStatus\"></field><field index=\"33\" term=\"http://rs.tdwg.org/dwc/terms/taxonRemarks\"></field><field index=\"34\" term=\"http://purl.org/dc/terms/modified\"></field>"
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+ "<field index=\"35\" term=\"http://purl.org/dc/terms/language\"></field><field index=\"36\" term=\"http://purl.org/dc/terms/rights\"></field><field index=\"37\" term=\"http://purl.org/dc/terms/rightsHolder\"></field><field index=\"38\" term=\"http://purl.org/dc/terms/accessRights\"></field>"
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+ "<field index=\"39\" term=\"http://purl.org/dc/terms/bibliographicCitation\"></field><field index=\"40\" term=\"http://rs.tdwg.org/dwc/terms/informationWithheld\"></field><field index=\"41\" term=\"http://rs.tdwg.org/dwc/terms/datasetName\"></field><field index=\"42\" term=\"http://purl.org/dc/terms/source\"></field></core>" +
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"";
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//TODO continue
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// System.out.println(metaDataStr);
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Assert.assertTrue(metaDataStr.contains(metaCore));
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//core
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byte[] core = data.get(DwcaTaxExportFile.TAXON.getTableName());
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Assert.assertNotNull("Core must not be null", core);
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String coreStr = new String(core);
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String expected = "\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"f983cc5e-4c77-4c80-8cb0-73d43df31ee9\",\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"3f52e136-f2e1-4f9a-9010-2f35908fbd39\",\"Genus species Mill.\",\"Species\",\"accepted\"";
|
255
|
// System.out.println(coreStr);
|
256
|
Assert.assertTrue(coreStr.contains(expected));
|
257
|
String expectedClassification = "\"Family|Genus|Genus species\"";
|
258
|
Assert.assertTrue(coreStr.contains(expectedClassification));
|
259
|
Assert.assertFalse(coreStr.contains(UUID_UNPUBLISHED_TAXON));
|
260
|
|
261
|
//reference
|
262
|
byte[] ref = data.get(DwcaTaxExportFile.REFERENCE.getTableName());
|
263
|
Assert.assertNotNull("Reference must not be null", ref);
|
264
|
String refStr = new String(ref);
|
265
|
|
266
|
expected = "\"3162e136-f2e2-4f9a-9010-3f35908fbae1\",,,,,\"My sec ref.\",\"My sec ref\",,,,,,,,,";
|
267
|
// System.out.println(refStr);
|
268
|
Assert.assertTrue(refStr.contains(expected));
|
269
|
expected = "\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",,,,,\"Mill. 1804: The book of botany 3.\",,\"Mill.\",\"1804\",,,,,,,";
|
270
|
Assert.assertTrue(refStr.contains(expected));
|
271
|
|
272
|
//distribution
|
273
|
byte[] distribution = data.get(DwcaTaxExportFile.DISTRIBUTION.getTableName());
|
274
|
Assert.assertNotNull("Distribution must not be null", distribution);
|
275
|
String distributionStr = new String(distribution);
|
276
|
expected = "\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"c204c529-d8d2-458f-b939-96f0ebd2cbe8\",\"Africa\",,,\"present\",,\"uncertain\",,,,,,";
|
277
|
Assert.assertTrue(distributionStr.contains(expected));
|
278
|
|
279
|
//description
|
280
|
byte[] description = data.get(DwcaTaxExportFile.DESCRIPTION.getTableName());
|
281
|
Assert.assertNotNull("Description must not be null", distribution);
|
282
|
String descriptionStr = new String(description);
|
283
|
System.out.println(descriptionStr);
|
284
|
|
285
|
// quantitative data
|
286
|
expected = "\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"0.1-1.3 [n=2]\",\"Chromosome Numbers\"";
|
287
|
Assert.assertTrue(descriptionStr.contains(expected));
|
288
|
// textdata
|
289
|
expected = "\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"My Description\",\"Description\",,\"eng\",,,,,";
|
290
|
Assert.assertTrue(descriptionStr.contains(expected));
|
291
|
// categorical data
|
292
|
// expected = "\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"state1\",\"Ecology\""; FIXME #8891
|
293
|
expected = "\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"-no state-\",\"Ecology\"";
|
294
|
Assert.assertTrue(descriptionStr.contains(expected));
|
295
|
}
|
296
|
|
297
|
@Test
|
298
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDBDataSet.xml")
|
299
|
public void testUnpublished(){
|
300
|
createFullTestDataSet();
|
301
|
File destinationFolder = null;
|
302
|
DwcaTaxExportConfigurator config = DwcaTaxExportConfigurator.NewInstance(null, destinationFolder, null);
|
303
|
config.setTarget(TARGET.EXPORT_DATA);
|
304
|
config.getTaxonNodeFilter().setIncludeUnpublished(true);
|
305
|
ExportResult result = defaultExport.invoke(config);
|
306
|
|
307
|
//core
|
308
|
ExportDataWrapper<?> exportData = result.getExportData();
|
309
|
@SuppressWarnings("unchecked")
|
310
|
Map<String, byte[]> data = (Map<String, byte[]>) exportData.getExportData();
|
311
|
byte[] core = data.get(DwcaTaxExportFile.TAXON.getTableName());
|
312
|
Assert.assertNotNull("Core must not be null", core);
|
313
|
String coreStr = new String(core);
|
314
|
String expected = "\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\"";
|
315
|
Assert.assertTrue(coreStr.contains(expected));
|
316
|
|
317
|
Assert.assertTrue(coreStr.contains(UUID_UNPUBLISHED_TAXON));
|
318
|
}
|
319
|
|
320
|
@Test
|
321
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDBDataSet.xml")
|
322
|
public void testNoHeader(){
|
323
|
createFullTestDataSet();
|
324
|
File destinationFolder = null;
|
325
|
DwcaTaxExportConfigurator config = DwcaTaxExportConfigurator.NewInstance(null, destinationFolder, null);
|
326
|
config.setTarget(TARGET.EXPORT_DATA);
|
327
|
config.setHasHeaderLines(false);
|
328
|
ExportResult result = defaultExport.invoke(config);
|
329
|
|
330
|
//core
|
331
|
ExportDataWrapper<?> exportData = result.getExportData();
|
332
|
@SuppressWarnings("unchecked")
|
333
|
Map<String, byte[]> data = (Map<String, byte[]>) exportData.getExportData();
|
334
|
byte[] core = data.get(DwcaTaxExportFile.TAXON.getTableName());
|
335
|
Assert.assertNotNull("Core must not be null", core);
|
336
|
String coreStr = new String(core);
|
337
|
String expected = "\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\"";
|
338
|
Assert.assertTrue(coreStr.contains(expected));
|
339
|
// System.out.println(coreStr);
|
340
|
expected = "coreid,identifier,identifier,identifier,identifier,bibliographicCitation,title,creator,date,source,description,subject,language,rights,taxonRemarks,type";
|
341
|
Assert.assertFalse(coreStr.contains(expected));
|
342
|
expected = "coreid";
|
343
|
Assert.assertFalse(coreStr.startsWith(expected));
|
344
|
|
345
|
//reference
|
346
|
byte[] ref = data.get(DwcaTaxExportFile.REFERENCE.getTableName());
|
347
|
Assert.assertNotNull("Reference must not be null", ref);
|
348
|
String refStr = new String(ref);
|
349
|
expected = "\"3162e136-f2e2-4f9a-9010-3f35908fbae1\",,,,,\"My sec ref.\",\"My sec ref\",,,,,,,,,";
|
350
|
// System.out.println(refStr);
|
351
|
Assert.assertTrue(refStr.contains(expected));
|
352
|
expected = "coreid,identifier,identifier,identifier,identifier,bibliographicCitation,title,creator,date,source,description,subject,language,rights,taxonRemarks,type";
|
353
|
Assert.assertFalse(refStr.contains(expected));
|
354
|
expected = "coreid";
|
355
|
Assert.assertFalse(refStr.startsWith(expected));
|
356
|
|
357
|
}
|
358
|
|
359
|
private void createFullTestDataSet() {
|
360
|
Set<TaxonNode> nodesToSave = new HashSet<>();
|
361
|
Reference sec1 = ReferenceFactory.newGeneric();
|
362
|
setUuid(sec1, "4b6acca1-959b-4790-b76e-e474a0882990");
|
363
|
sec1.setTitle("My sec ref");
|
364
|
|
365
|
Classification classification = Classification.NewInstance("DwcaExportTest Classification");
|
366
|
setUuid(classification, "4096df99-7274-421e-8843-211b603d832e");
|
367
|
|
368
|
NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
|
369
|
|
370
|
//family
|
371
|
TaxonName familyName = parser.parseReferencedName("Family L., Sp. Pl. 3: 22. 1752",
|
372
|
NomenclaturalCode.ICNAFP, Rank.FAMILY());
|
373
|
setUuid(familyName,"e983cc5e-4c77-4c80-8cb0-73d43df31ef7");
|
374
|
setUuid(familyName.getNomenclaturalReference(), "b0dd7f4a-0c7f-4372-bc5d-3b676363bc63");
|
375
|
Taxon family = Taxon.NewInstance(familyName, sec1);
|
376
|
setUuid(family,"3162e136-f2e2-4f9a-9010-3f35908fbae1");
|
377
|
TaxonNode node1 = classification.addChildTaxon(family, sec1, "22");
|
378
|
setUuid(node1, "0fae5ad5-ffa2-4100-bcd7-8aa9dda0aebc");
|
379
|
nodesToSave.add(node1);
|
380
|
|
381
|
//genus
|
382
|
TaxonName genusName = parser.parseReferencedName("Genus Humb., The book of botany 3: 22. 1804",
|
383
|
NomenclaturalCode.ICNAFP, Rank.GENUS());
|
384
|
setUuid(genusName,"5e83cc5e-4c77-4d80-8cb0-73d63df35ee3");
|
385
|
setUuid(genusName.getNomenclaturalReference(), "5ed27f4a-6c7f-4372-bc5d-3b67636abc52");
|
386
|
Taxon genus = Taxon.NewInstance(genusName, sec1);
|
387
|
setUuid(genus,"3f52e136-f2e1-4f9a-9010-2f35908fbd39");
|
388
|
|
389
|
TaxonNode node2 = node1.addChildTaxon(genus, sec1, "33");
|
390
|
setUuid(node2, "43ca733b-fe3a-42ce-8a92-000e27badf44");
|
391
|
nodesToSave.add(node2);
|
392
|
|
393
|
//species
|
394
|
TaxonName speciesName = parser.parseReferencedName("Genus species Mill., The book of botany 3: 22. 1804",
|
395
|
NomenclaturalCode.ICNAFP, Rank.SPECIES());
|
396
|
setUuid(speciesName,"f983cc5e-4c77-4c80-8cb0-73d43df31ee9");
|
397
|
setUuid(speciesName.getNomenclaturalReference(), "a0dd7f4a-0c7f-4372-bc5d-3b676363bc0e");
|
398
|
Taxon species = Taxon.NewInstance(speciesName, sec1);
|
399
|
setUuid(species,"9182e136-f2e2-4f9a-9010-3f35908fb5e0");
|
400
|
|
401
|
TaxonNode node3 = node2.addChildTaxon(species, sec1, "33");
|
402
|
setUuid(node3, "a0c9733a-fe3a-42ce-8a92-000e27bfdfa3");
|
403
|
nodesToSave.add(node3);
|
404
|
|
405
|
//subspecies
|
406
|
TaxonName subspeciesName = parser.parseReferencedName("Genus species subsp. subspec Mill., The book of botany 3: 22. 1804",
|
407
|
NomenclaturalCode.ICNAFP, Rank.SUBSPECIES());
|
408
|
setUuid(subspeciesName,"3483cc5e-4c77-4c80-8cb0-73d43df31ee3");
|
409
|
setUuid(subspeciesName.getNomenclaturalReference(), "b8dd7f4a-0c7f-4372-bc5d-3b676363bc0f");
|
410
|
|
411
|
Taxon subspecies = Taxon.NewInstance(subspeciesName, sec1);
|
412
|
setUuid(subspecies, "b2c86698-500e-4efb-b9ae-6bb6e701d4bc");
|
413
|
TaxonNode node4 = node3.addChildTaxon(subspecies, sec1, "33");
|
414
|
node4.setUuid(UUID_SUBSPEC_NODE);
|
415
|
nodesToSave.add(node4);
|
416
|
|
417
|
//unpublished
|
418
|
TaxonName unpublishedName = parser.parseReferencedName("Genus species subsp. unpublish Mill., The book of botany 3: 22. 1804",
|
419
|
NomenclaturalCode.ICNAFP, Rank.SUBSPECIES());
|
420
|
setUuid(unpublishedName,"ebcf6bb6-6da8-46fe-9c22-127aa4cb9549");
|
421
|
setUuid(unpublishedName.getNomenclaturalReference(), "51725dbd-e4a1-43ea-8363-fe8eb1152a49");
|
422
|
|
423
|
Taxon unpublishedSpecies = Taxon.NewInstance(unpublishedName, sec1);
|
424
|
unpublishedSpecies.setPublish(false);
|
425
|
setUuid(unpublishedSpecies, UUID_UNPUBLISHED_TAXON);
|
426
|
TaxonNode nodeUnpublished = node3.addChildTaxon(unpublishedSpecies, sec1, "34");
|
427
|
setUuid(nodeUnpublished, "01368584-b626-4255-9dc4-ff011d44f493");
|
428
|
nodesToSave.add(nodeUnpublished);
|
429
|
|
430
|
classificationService.save(classification);
|
431
|
taxonNodeService.save(nodesToSave);
|
432
|
|
433
|
TaxonDescription description = TaxonDescription.NewInstance(species);
|
434
|
|
435
|
//Distribution
|
436
|
Distribution distribution = Distribution.NewInstance(NamedArea.AFRICA(), PresenceAbsenceTerm.PRESENT());
|
437
|
setUuid(distribution,"674e9e27-9102-4166-8626-8cb871a9a89b");
|
438
|
description.addElement(distribution);
|
439
|
|
440
|
//TextData
|
441
|
TextData textData = TextData.NewInstance(Feature.DESCRIPTION());
|
442
|
textData.putText(Language.DEFAULT(), "My Description");
|
443
|
setUuid(textData,"16a3f63b-c554-4479-ad36-ca9c677fbb19");
|
444
|
description.addElement(textData);
|
445
|
|
446
|
//CategoricalData
|
447
|
CategoricalData catData = CategoricalData.NewInstance(state1, Feature.ECOLOGY());
|
448
|
setUuid(catData,"84b8bfd3-d982-4b5d-8d0a-fe5d80183ec4");
|
449
|
description.addElement(catData);
|
450
|
|
451
|
//QuantitativeData
|
452
|
QuantitativeData quantData = QuantitativeData.NewMinMaxInstance(Feature.CHROMOSOME_NUMBER(), new BigDecimal("0.1"), new BigDecimal("1.3"));
|
453
|
quantData.setSampleSize(new BigDecimal("2"), null);
|
454
|
setUuid(quantData,"011264eb-d3d4-44be-86f3-e6f69a21f36b");
|
455
|
description.addElement(quantData);
|
456
|
|
457
|
commitAndStartNewTransaction(null);
|
458
|
|
459
|
}
|
460
|
|
461
|
private void setUuid(CdmBase cdmBase, String uuidStr) {
|
462
|
cdmBase.setUuid(UUID.fromString(uuidStr));
|
463
|
}
|
464
|
|
465
|
@Override
|
466
|
public void createTestDataSet() throws FileNotFoundException {}
|
467
|
}
|