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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.eflora;
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import java.net.URI;
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import java.util.HashSet;
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import java.util.List;
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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.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.api.service.ITermService;
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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.IIoObserver;
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import eu.etaxonomy.cdm.io.common.events.LoggingIoObserver;
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import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.io.eflora.floraMalesiana.FloraMalesianaTransformer;
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import eu.etaxonomy.cdm.io.markup.MarkupImportConfigurator;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.FeatureNode;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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import eu.etaxonomy.cdm.model.description.PolytomousKey;
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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 20.06.2008
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*/
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public class FloraMalesianaActivator extends EfloraActivatorBase {
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private static final Logger logger = Logger.getLogger(FloraMalesianaActivator.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 fmSource08_1 = EfloraSources.fm_08_1();
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static final URI fmSource08_2 = EfloraSources.fm_08_2();
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static final URI fmSource08_3 = EfloraSources.fm_08_3();
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static final URI fmSource10_1 = EfloraSources.fm_10_1();
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static final URI fmSource10_2 = EfloraSources.fm_10_2();
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static final URI fmSource10_3 = EfloraSources.fm_10_3();
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static final URI fmSource10_4 = EfloraSources.fm_10_4();
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static final URI fmSource11_1 = EfloraSources.fm_11_1();
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static final URI fmSource11_2 = EfloraSources.fm_11_2();
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static final URI fmSource11_3 = EfloraSources.fm_11_3();
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static final URI fmSource12_1 = EfloraSources.fm_12_1();
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static final URI fmSource12_2 = EfloraSources.fm_12_2();
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static final URI fmSource13 = EfloraSources.fm_13();
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static final URI fmSource14 = EfloraSources.fm_14();
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static final URI fmSource15 = EfloraSources.fm_15();
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static final URI fmSource16 = EfloraSources.fm_16();
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static final URI fmSource17_1 = EfloraSources.fm_17_1();
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static final URI fmSource17_2 = EfloraSources.fm_17_2();
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static final URI fmSource18 = EfloraSources.fm_18();
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static final URI fmSource19 = EfloraSources.fm_19();
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static final URI fmSource20 = EfloraSources.fm_20();
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static final URI fmSource21 = EfloraSources.fm_21();
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static final URI fmSource_Ser2_02 = EfloraSources.fm_ser2_2();
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static final URI fmSource_Ser2_03 = EfloraSources.fm_ser2_3();
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static final URI fmSource_Ser2_04 = EfloraSources.fm_ser2_4();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_preview();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_production();
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static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
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private final boolean includeBase = false;
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private final boolean includeVol08_1 = includeBase;
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private final boolean includeVol08_2 =includeBase;
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private final boolean includeVol08_3 = includeBase;
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private final boolean includeVol10_1 = includeBase;
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private final boolean includeVol10_2 = includeBase;
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private final boolean includeVol10_3 = includeBase;
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private final boolean includeVol10_4 = includeBase;
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private final boolean includeVol11_1 = includeBase;
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private final boolean includeVol11_2 = includeBase;
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private final boolean includeVol11_3 = includeBase;
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private final boolean includeVol12_1 = includeBase;
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private final boolean includeVol12_2 = includeBase;
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private final boolean includeVol13 = includeBase;
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private final boolean includeVol14 = includeBase;
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private final boolean includeVol15 = includeBase;
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private final boolean includeVol16 = includeBase;
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private final boolean includeVol17_1 = includeBase;
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private final boolean includeVol17_2 = includeBase;
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private final boolean includeVol18 = includeBase;
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private final boolean includeVol19 = includeBase;
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private final boolean includeVol20 = includeBase;
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private final boolean includeVol21 = includeBase;
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private final boolean includeVol2_2 = includeBase;
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private final boolean includeVol2_3 = includeBase;
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private final boolean includeVol2_4 = ! includeBase;
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private final boolean h2ForCheck = false;
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static final boolean reuseState = true; //when running multiple imports
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//feature tree uuid
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public static final UUID featureTreeUuid = UUID.fromString("168df0c6-6429-484c-b26f-ded1f7e44bd9");
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private static final String featureTreeTitle = "Flora Malesiana Presentation Feature Tree";
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//classification
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static final UUID classificationUuid = UUID.fromString("ca4e4bcb-a1d1-4124-a358-a3d3c41dd450");
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static final String classificationTitle = "Flora Malesiana";
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//check - import
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static CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
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static boolean doPrintKeys = false;
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//taxa
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static final boolean doTaxa = true;
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private final boolean replaceStandardKeyTitles = false;
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private final IIoObserver observer = new LoggingIoObserver();
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private final Set<IIoObserver> observerList = new HashSet<IIoObserver>();
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private void doImport(ICdmDataSource cdmDestination){
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observerList.add(observer);
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if (h2ForCheck && cdmDestination.getDatabaseType().equals(CdmDestinations.localH2().getDatabaseType())){
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check = CHECK.CHECK_ONLY;
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}
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//make Source
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// URI source = fmSource13_small;
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URI source = null;
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MarkupImportConfigurator markupConfig= MarkupImportConfigurator.NewInstance(source, cdmDestination);
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markupConfig.setClassificationUuid(classificationUuid);
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markupConfig.setClassificationName(classificationTitle);
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markupConfig.setDoTaxa(doTaxa);
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markupConfig.setCheck(check);
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markupConfig.setDoPrintKeys(doPrintKeys);
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markupConfig.setDbSchemaValidation(hbm2dll);
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markupConfig.setObservers(observerList);
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markupConfig.setReplaceStandardKeyTitles(replaceStandardKeyTitles);
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markupConfig.setReuseExistingState(reuseState);
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markupConfig.setSourceReference(getSourceReference("Flora Malesiana - Vol. 13"));
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CdmDefaultImport<MarkupImportConfigurator> myImport = new CdmDefaultImport<MarkupImportConfigurator>();
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//Vol08_1
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doSource(includeVol08_1, fmSource08_1, "Flora Malesiana - vol. 08, pt.1", markupConfig, myImport);
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//Vol08_2
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doSource(includeVol08_2, fmSource08_2, "Flora Malesiana - vol. 08, pt.2", markupConfig, myImport);
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//Vol08_3
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doSource(includeVol08_3, fmSource08_3, "Flora Malesiana - vol. 08, pt.3", markupConfig, myImport);
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//Vol10_1
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doSource(includeVol10_1, fmSource10_1, "Flora Malesiana - vol. 10, pt.1", markupConfig, myImport);
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//Vol10_2
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doSource(includeVol10_2, fmSource10_2, "Flora Malesiana - vol. 10, pt.2", markupConfig, myImport);
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//Vol10_3
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doSource(includeVol10_3, fmSource10_3, "Flora Malesiana - vol. 10, pt.3", markupConfig, myImport);
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//Vol10_4
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doSource(includeVol10_4, fmSource10_4, "Flora Malesiana - vol. 10, pt.4", markupConfig, myImport);
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//Vol11_1
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doSource(includeVol11_1, fmSource11_1, "Flora Malesiana - vol. 11, pt.1", markupConfig, myImport);
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//Vol11_2
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doSource(includeVol11_2, fmSource11_2, "Flora Malesiana - vol. 11, pt.2", markupConfig, myImport);
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//Vol11_3
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doSource(includeVol11_3, fmSource11_3, "Flora Malesiana - vol. 11, pt.3", markupConfig, myImport);
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//Vol12_1
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doSource(includeVol12_1, fmSource12_1, "Flora Malesiana - vol. 12, pt.1", markupConfig, myImport);
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//Vol12_2
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doSource(includeVol12_2, fmSource12_2, "Flora Malesiana - vol. 12, pt.2", markupConfig, myImport);
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//Vol13_large
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doSource(includeVol13, fmSource13, "Flora Malesiana - vol. 13", markupConfig, myImport);
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//Vol14
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doSource(includeVol14, fmSource14, "Flora Malesiana - vol. 14", markupConfig, myImport);
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//Vol15
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doSource(includeVol15, fmSource15, "Flora Malesiana - vol. 15", markupConfig, myImport);
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//Vol16
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doSource(includeVol16, fmSource16, "Flora Malesiana - vol. 16", markupConfig, myImport);
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//Vol17, part1
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doSource(includeVol17_1, fmSource17_1, "Flora Malesiana - vol. 17, part I", markupConfig, myImport);
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//Vol17, part2
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doSource(includeVol17_2, fmSource17_2, "Flora Malesiana - vol. 17, part II", markupConfig, myImport);
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//Vol18
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doSource(includeVol18, fmSource18, "Flora Malesiana - vol. 18", markupConfig, myImport);
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//Vol19
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doSource(includeVol19, fmSource19, "Flora Malesiana - vol. 19", markupConfig, myImport);
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//Vol20
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doSource(includeVol20, fmSource20, "Flora Malesiana - vol. 20", markupConfig, myImport);
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//Vol21
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doSource(includeVol21, fmSource21, "Flora Malesiana - vol. 21", markupConfig, myImport);
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//Vol_2_2
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doSource(includeVol2_2, fmSource_Ser2_02, "Flora Malesiana - Ser.2, vol. 2", markupConfig, myImport);
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//Vol_2_3
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doSource(includeVol2_3, fmSource_Ser2_03, "Flora Malesiana - Ser.2, vol. 3", markupConfig, myImport);
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//Vol_2_3
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doSource(includeVol2_4, fmSource_Ser2_04, "Flora Malesiana - Ser.2, vol. 4", markupConfig, myImport);
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makeAutomatedFeatureTree(myImport.getCdmAppController(), markupConfig.getState(),
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featureTreeUuid, featureTreeTitle);
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// makeGeoService();
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FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
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myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
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//check keys
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if (doPrintKeys){
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TransactionStatus tx = myImport.getCdmAppController().startTransaction();
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List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null);
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for(PolytomousKey key : keys){
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key.print(System.out);
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System.out.println();
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}
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myImport.getCdmAppController().commitTransaction(tx);
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}
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}
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private void doSource(boolean doInclude, URI source, String sourceTitle, MarkupImportConfigurator markupConfig,
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CdmDefaultImport<MarkupImportConfigurator> myImport) {
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if (doInclude){
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System.out.println("\nStart import from ("+ source.toString() + ") ...");
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markupConfig.setSource(source);
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markupConfig.setSourceReference(getSourceReference(sourceTitle));
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myImport.invoke(markupConfig);
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System.out.println("End import from ("+ source.toString() + ")...");
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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, true);
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return result;
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}
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private FeatureTree makeFeatureNode(ITermService service){
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FloraMalesianaTransformer transformer = new FloraMalesianaTransformer();
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FeatureTree result = FeatureTree.NewInstance(UUID.randomUUID());
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result.setTitleCache("Flora Malesiana Presentation Feature Tree - Old", true);
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FeatureNode root = result.getRoot();
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FeatureNode newNode;
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newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
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root.addChild(newNode);
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addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
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addFeataureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service);
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newNode = FeatureNode.NewInstance(Feature.ANATOMY());
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addFeataureNodesByStringList(anatomySubfeatureList, newNode, transformer, service);
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newNode = addFeataureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service);
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addFeataureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service);
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newNode = addFeataureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service);
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newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
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root.addChild(newNode);
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newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
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root.addChild(newNode);
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addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
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newNode = FeatureNode.NewInstance(Feature.USES());
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root.addChild(newNode);
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addFeataureNodesByStringList(chomosomesList, root, transformer, service);
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newNode = FeatureNode.NewInstance(Feature.CITATION());
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root.addChild(newNode);
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return result;
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}
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private static String [] chomosomesList = new String[]{
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"Chromosomes",
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};
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private static String [] habitatEcologyList = new String[]{
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"Habitat",
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"Habitat & Ecology"
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};
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332
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private static String [] generellDescriptionsUpToAnatomyList = new String[]{
|
|
333
|
"Fossils",
|
|
334
|
"Morphology and anatomy",
|
|
335
|
"Morphology",
|
|
336
|
"Vegetative morphology and anatomy",
|
|
337
|
};
|
|
338
|
|
|
339
|
|
|
340
|
private static String [] anatomySubfeatureList = new String[]{
|
|
341
|
"Leaf anatomy",
|
|
342
|
"Wood anatomy"
|
|
343
|
};
|
|
344
|
|
|
345
|
private static String [] generellDescriptionsFromAnatomyToPhytoChemoList = new String[]{
|
|
346
|
"Flower morphology",
|
|
347
|
"Palynology",
|
|
348
|
"Pollination",
|
|
349
|
"Pollen morphology",
|
|
350
|
"embryology",
|
|
351
|
"cytology",
|
|
352
|
"Life cycle",
|
|
353
|
"Fruits and embryology",
|
|
354
|
"Dispersal",
|
|
355
|
"Chromosome numbers",
|
|
356
|
"Phytochemistry and Chemotaxonomy",
|
|
357
|
};
|
|
358
|
|
|
359
|
|
|
360
|
private static String [] phytoChemoSubFeaturesList = new String[]{
|
|
361
|
"Alkaloids",
|
|
362
|
"Iridoid glucosides",
|
|
363
|
"Leaf phenolics",
|
|
364
|
"Storage products of seeds",
|
|
365
|
"Aluminium",
|
|
366
|
"Chemotaxonomy",
|
|
367
|
};
|
|
368
|
|
|
369
|
|
|
370
|
private static String [] generellDescriptionsFromPhytoChemoList = new String[]{
|
|
371
|
"Phytochemistry",
|
|
372
|
"Taxonomy",
|
|
373
|
"history",
|
|
374
|
"cultivation",
|
|
375
|
"Notes"
|
|
376
|
};
|
|
377
|
|
|
378
|
|
|
379
|
private static String [] descriptionFeatureList = new String[]{
|
|
380
|
"lifeform",
|
|
381
|
"Bark",
|
|
382
|
//new
|
|
383
|
"wood",
|
|
384
|
"Indumentum",
|
|
385
|
"endophytic body",
|
|
386
|
"flowering buds",
|
|
387
|
"Branchlets",
|
|
388
|
"Branches",
|
|
389
|
"Branch",
|
|
390
|
"Flowering branchlets",
|
|
391
|
"Trees",
|
|
392
|
"Twigs",
|
|
393
|
"stem",
|
|
394
|
"Stems",
|
|
395
|
"stem leaves",
|
|
396
|
"Leaves",
|
|
397
|
"flower-bearing stems",
|
|
398
|
"Petiole",
|
|
399
|
"Petiolules",
|
|
400
|
"Leaflets",
|
|
401
|
"Thyrsus",
|
|
402
|
"Thyrses",
|
|
403
|
"Inflorescences",
|
|
404
|
"Inflorescence",
|
|
405
|
"Young inflorescences",
|
|
406
|
"Male inflorescences",
|
|
407
|
"Female inflorescences",
|
|
408
|
"Bracts",
|
|
409
|
"Pedicels",
|
|
410
|
"flowering buds",
|
|
411
|
"scales",
|
|
412
|
"Buds",
|
|
413
|
"Flowers",
|
|
414
|
"Flower",
|
|
415
|
"Flowering",
|
|
416
|
"Stigma",
|
|
417
|
"perianth",
|
|
418
|
"Sepals",
|
|
419
|
"Sepal",
|
|
420
|
"Outer Sepals",
|
|
421
|
"Axillary",
|
|
422
|
"cymes",
|
|
423
|
"Calyx",
|
|
424
|
"Petal",
|
|
425
|
"Petals",
|
|
426
|
"perigone",
|
|
427
|
"perigone lobes",
|
|
428
|
"perigone tube",
|
|
429
|
"Disc",
|
|
430
|
"corolla",
|
|
431
|
"Stamens",
|
|
432
|
"Staminodes",
|
|
433
|
"Ovary",
|
|
434
|
"Anthers",
|
|
435
|
"anther",
|
|
436
|
"Pistil",
|
|
437
|
"Pistillode",
|
|
438
|
"Ovules",
|
|
439
|
"androecium",
|
|
440
|
"gynoecium",
|
|
441
|
"Filaments",
|
|
442
|
"Style",
|
|
443
|
"annulus",
|
|
444
|
"female flowers",
|
|
445
|
"Male flowers",
|
|
446
|
"Female",
|
|
447
|
"Infructescences", //order not consistent (sometimes before "Flowers")
|
|
448
|
"Fruit",
|
|
449
|
"Fruits",
|
|
450
|
"fruiting axes",
|
|
451
|
"drupes",
|
|
452
|
"Arillode",
|
|
453
|
"seed",
|
|
454
|
"Seeds",
|
|
455
|
"Seedling",
|
|
456
|
"flower tube",
|
|
457
|
"nutlets",
|
|
458
|
"pollen",
|
|
459
|
"secondary xylem",
|
|
460
|
"chromosome number",
|
|
461
|
|
|
462
|
"figure",
|
|
463
|
"fig",
|
|
464
|
"figs",
|
|
465
|
|
|
466
|
|
|
467
|
|
|
468
|
};
|
|
469
|
|
|
470
|
public FeatureNode addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
|
|
471
|
FeatureNode lastChild = null;
|
|
472
|
try {
|
|
473
|
for (String featureString : featureStringList){
|
|
474
|
UUID featureUuid;
|
|
475
|
featureUuid = transformer.getFeatureUuid(featureString);
|
|
476
|
Feature feature = (Feature)termService.find(featureUuid);
|
|
477
|
if (feature != null){
|
|
478
|
FeatureNode child = FeatureNode.NewInstance(feature);
|
|
479
|
root.addChild(child);
|
|
480
|
}
|
|
481
|
}
|
|
482
|
|
|
483
|
} catch (UndefinedTransformerMethodException e) {
|
|
484
|
logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
|
|
485
|
}
|
|
486
|
return lastChild;
|
|
487
|
}
|
|
488
|
|
|
489
|
|
|
490
|
|
|
491
|
/**
|
|
492
|
* @param args
|
|
493
|
*/
|
|
494
|
public static void main(String[] args) {
|
|
495
|
FloraMalesianaActivator me = new FloraMalesianaActivator();
|
|
496
|
me.doImport(cdmDestination);
|
|
497
|
}
|
|
498
|
|
|
499
|
}
|