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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.markup.MarkupImportConfigurator;
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import eu.etaxonomy.cdm.io.markup.MarkupTransformer;
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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 FloreGabonActivator extends EfloraActivatorBase {
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private static final Logger logger = Logger.getLogger(FloreGabonActivator.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 = EfloraSources.fdg_sample();
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static final URI fdg1 = EfloraSources.fdg_1();
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static final URI fdg2 = EfloraSources.fdg_2();
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static final URI fdg3 = EfloraSources.fdg_3();
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static final URI fdg4 = EfloraSources.fdg_4();
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static final URI fdg5 = EfloraSources.fdg_5();
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static final URI fdg5bis = EfloraSources.fdg_5bis();
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static final URI fdg6 = EfloraSources.fdg_6();
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static final URI fdg7 = EfloraSources.fdg_7();
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static final URI fdg8 = EfloraSources.fdg_8();
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static final URI fdg9 = EfloraSources.fdg_9();
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static final URI fdg10 = EfloraSources.fdg_10();
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static final URI fdg11 = EfloraSources.fdg_11();
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static final URI fdg12_17 = EfloraSources.fdg_12_17();
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static final URI fdg13 = EfloraSources.fdg_13();
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static final URI fdg14 = EfloraSources.fdg_14();
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static final URI fdg15 = EfloraSources.fdg_15();
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static final URI fdg16 = EfloraSources.fdg_16();
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static final URI fdg18 = EfloraSources.fdg_18();
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static final URI fdg19 = EfloraSources.fdg_19();
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static final URI fdg20 = EfloraSources.fdg_20();
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static final URI fdg21 = EfloraSources.fdg_21();
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static final URI fdg22 = EfloraSources.fdg_22();
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static final URI fdg23 = EfloraSources.fdg_23();
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static final URI fdg24 = EfloraSources.fdg_24();
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static final URI fdg25 = EfloraSources.fdg_25();
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static final URI fdg26 = EfloraSources.fdg_26();
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static final URI fdg27 = EfloraSources.fdg_27();
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static final URI fdg28 = EfloraSources.fdg_28();
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static final URI fdg29 = EfloraSources.fdg_29();
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static final URI fdg30 = EfloraSources.fdg_30();
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static final URI fdg31 = EfloraSources.fdg_31();
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static final URI fdg32 = EfloraSources.fdg_32();
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static final URI fdg33 = EfloraSources.fdg_33();
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static final URI fdg34 = EfloraSources.fdg_34();
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static final URI fdg35 = EfloraSources.fdg_35();
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// static final URI fdg36 = EfloraSources.fdg_36();
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// static final URI fdg37 = EfloraSources.fdg_37();
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static final URI fdg36_37 = EfloraSources.fdg_36_37();
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static final URI fdg38 = EfloraSources.fdg_38();
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static final URI fdg39 = EfloraSources.fdg_39();
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static final URI fdg40 = EfloraSources.fdg_40();
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static final URI fdg41 = EfloraSources.fdg_41();
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static final URI fdg42 = EfloraSources.fdg_42();
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static final URI fdg43 = EfloraSources.fdg_43();
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static final URI fdg44 = EfloraSources.fdg_44();
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static final URI fdg45 = EfloraSources.fdg_45();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flore_gabon_preview();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flore_gabon_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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//feature tree uuid
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public static final UUID featureTreeUuid = UUID.fromString("ee688973-2595-4d4d-b11e-6df71e96a5c2");
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private static final String featureTreeTitle = "Flore Gabon Presentation Feature Tree";
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//classification
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static final UUID classificationUuid = UUID.fromString("2f892452-ff49-48cf-834f-52ca29600719");
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static final String classificationTitle = "Flore du Gabon";
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//check - import
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private boolean h2ForCheck = false;
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static CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
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static boolean doPrintKeys = false;
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private boolean replaceStandardKeyTitles = true;
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//taxa
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static final boolean doTaxa = true;
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static final boolean reuseState = true;
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//if true, use inverse include information
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private boolean inverseInclude = true;
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private boolean includeFdg1 = true;
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private boolean includeFdg2 = true;
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private boolean includeFdg3 = true;
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private boolean includeFdg4 = true;
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private boolean includeFdg5 = true;
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private boolean includeFdg5bis = true;
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private boolean includeFdg6 = true;
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private boolean includeFdg7 = true;
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private boolean includeFdg8 = true;
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private boolean includeFdg9 = true;
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private boolean includeFdg10 = true;
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private boolean includeFdg11 = true;
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private boolean includeFdg12_17 = true;
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private boolean includeFdg13 = true;
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private boolean includeFdg14 = true;
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private boolean includeFdg15 = true;
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private boolean includeFdg16 = true;
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private boolean includeFdg18 = true;
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private boolean includeFdg19 = true;
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private boolean includeFdg20 = true;
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private boolean includeFdg21 = true;
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private boolean includeFdg22 = true;
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private boolean includeFdg23 = false;
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private boolean includeFdg24 = true;
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private boolean includeFdg25 = true;
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private boolean includeFdg26 = true;
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private boolean includeFdg27 = true;
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private boolean includeFdg28 = true;
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private boolean includeFdg29 = true;
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private boolean includeFdg30 = true;
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private boolean includeFdg31 = true;
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private boolean includeFdg32 = true;
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private boolean includeFdg33 = true;
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private boolean includeFdg34 = true;
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private boolean includeFdg35 = true;
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// private boolean includeFdg36 = true;
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// private boolean includeFdg37 = true;
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private boolean includeFdg36_37 = true;
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private boolean includeFdg38 = true;
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private boolean includeFdg39 = true;
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private boolean includeFdg40 = true;
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private boolean includeFdg41 = true;
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private boolean includeFdg42 = true;
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private boolean includeFdg43 = true;
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private boolean includeFdg44 = true;
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private boolean includeFdg45 = true;
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// **************** NO CHANGE **********************************************/
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private IIoObserver observer = new LoggingIoObserver();
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private Set<IIoObserver> observerList = new HashSet<IIoObserver>();
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private MarkupImportConfigurator config;
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private CdmDefaultImport<MarkupImportConfigurator> myImport;
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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 config
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URI source = fdg1;
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config = MarkupImportConfigurator.NewInstance(source, cdmDestination);
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config.setClassificationUuid(classificationUuid);
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config.setDoTaxa(doTaxa);
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config.setCheck(check);
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config.setDoPrintKeys(doPrintKeys);
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config.setDbSchemaValidation(hbm2dll);
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config.setObservers(observerList);
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config.setReplaceStandardKeyTitles(replaceStandardKeyTitles);
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config.setSourceReference(getSourceReference("Flore du Gabon"));
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config.setClassificationName(classificationTitle);
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config.setReuseExistingState(reuseState);
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myImport = new CdmDefaultImport<MarkupImportConfigurator>();
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//Vol1
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executeVolume( fdg1, includeFdg1 ^ inverseInclude);
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//Vol2
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executeVolume(fdg2, includeFdg2 ^ inverseInclude);
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//Vol3
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executeVolume(fdg3, includeFdg3 ^ inverseInclude);
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//Vol4
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executeVolume(fdg4, includeFdg4 ^ inverseInclude);
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//Vol5
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executeVolume(fdg5, includeFdg5 ^ inverseInclude);
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//Vol5bis
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executeVolume(fdg5bis, includeFdg5bis ^ inverseInclude);
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//Vol6
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executeVolume(fdg6, includeFdg6 ^ inverseInclude);
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//Vol7
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executeVolume(fdg7, includeFdg7 ^ inverseInclude);
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//Vol8
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executeVolume(fdg8, includeFdg8 ^ inverseInclude);
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//Vol9
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executeVolume(fdg9, includeFdg9 ^ inverseInclude);
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//Vol10
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executeVolume(fdg10, includeFdg10 ^ inverseInclude);
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//Vol11
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executeVolume(fdg11, includeFdg11 ^ inverseInclude);
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//Vol12
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executeVolume(fdg12_17, includeFdg12_17 ^ inverseInclude);
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//Vol13
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executeVolume(fdg13, includeFdg13 ^ inverseInclude);
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//Vol14
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executeVolume(fdg14, includeFdg14 ^ inverseInclude);
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//Vol15
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executeVolume(fdg15, includeFdg15 ^ inverseInclude);
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//Vol16
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executeVolume(fdg16, includeFdg16 ^ inverseInclude);
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//Vol18
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executeVolume(fdg18, includeFdg18 ^ inverseInclude);
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//Vol19
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executeVolume(fdg19, includeFdg19 ^ inverseInclude);
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//Vol20
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executeVolume(fdg20, includeFdg20 ^ inverseInclude);
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//Vol21
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executeVolume(fdg21, includeFdg21 ^ inverseInclude);
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//Vol22
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executeVolume(fdg22, includeFdg22 ^ inverseInclude);
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//Vol23
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executeVolume(fdg23, includeFdg23 ^ inverseInclude);
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//Vol24
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executeVolume(fdg24, includeFdg24 ^ inverseInclude);
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//Vol25
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executeVolume(fdg25, includeFdg25 ^ inverseInclude);
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//Vol26
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executeVolume(fdg26, includeFdg26 ^ inverseInclude);
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//Vol27
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executeVolume(fdg27, includeFdg27 ^ inverseInclude);
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//Vol28
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executeVolume(fdg28, includeFdg28 ^ inverseInclude);
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//Vol29
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executeVolume(fdg29, includeFdg29 ^ inverseInclude);
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//Vol30
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executeVolume(fdg30, includeFdg30 ^ inverseInclude);
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//Vol31
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executeVolume(fdg31, includeFdg31 ^ inverseInclude);
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//Vol32
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executeVolume(fdg32, includeFdg32 ^ inverseInclude);
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//Vol33
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executeVolume(fdg33, includeFdg33 ^ inverseInclude);
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//Vol34
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executeVolume(fdg34, includeFdg34 ^ inverseInclude);
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//Vol35
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executeVolume(fdg35, includeFdg35 ^ inverseInclude);
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// //Vol36
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// executeVolume(fdg36, includeFdg36 ^ inverseInclude);
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//
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// //Vol37
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// executeVolume(fdg37, includeFdg37 ^ inverseInclude);
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//Vol 36_37
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executeVolume(fdg36_37, includeFdg36_37 ^ inverseInclude);
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//Vol38
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executeVolume(fdg38, includeFdg38 ^ inverseInclude);
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//Vol39
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executeVolume(fdg39, includeFdg39 ^ inverseInclude);
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//Vol40
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executeVolume(fdg40, includeFdg40 ^ inverseInclude);
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//Vol41
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executeVolume(fdg41, includeFdg41 ^ inverseInclude);
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//Vol42
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executeVolume(fdg42, includeFdg42 ^ inverseInclude);
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//Vol43
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executeVolume(fdg43, includeFdg43 ^ inverseInclude);
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//Vol44
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executeVolume(fdg44, includeFdg44 ^ inverseInclude);
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//Vol45
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executeVolume(fdg45, includeFdg45 ^ inverseInclude);
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342
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FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
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myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
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makeAutomatedFeatureTree(myImport.getCdmAppController(), config.getState(),
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featureTreeUuid, featureTreeTitle);
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348
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349
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//check keys
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351
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if (doPrintKeys){
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352
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TransactionStatus tx = myImport.getCdmAppController().startTransaction();
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353
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List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null);
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354
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for(PolytomousKey key : keys){
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key.print(System.out);
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356
|
System.out.println();
|
|
357
|
}
|
|
358
|
myImport.getCdmAppController().commitTransaction(tx);
|
|
359
|
}
|
|
360
|
|
|
361
|
}
|
|
362
|
|
|
363
|
/**
|
|
364
|
* @param markupConfig
|
|
365
|
* @param myImport
|
|
366
|
*/
|
|
367
|
private void executeVolume(URI source, boolean include) {
|
|
368
|
if (include){
|
|
369
|
System.out.println("\nStart import from ("+ source.toString() + ") ...");
|
|
370
|
config.setSource(source);
|
|
371
|
myImport.invoke(config);
|
|
372
|
System.out.println("End import from ("+ source.toString() + ")...");
|
|
373
|
}
|
|
374
|
}
|
|
375
|
|
|
376
|
private Reference<?> getSourceReference(String string) {
|
|
377
|
Reference<?> result = ReferenceFactory.newGeneric();
|
|
378
|
result.setTitleCache(string, true);
|
|
379
|
return result;
|
|
380
|
}
|
|
381
|
|
|
382
|
|
|
383
|
|
|
384
|
|
|
385
|
private FeatureTree makeFeatureNode(ITermService service){
|
|
386
|
MarkupTransformer transformer = new MarkupTransformer();
|
|
387
|
|
|
388
|
FeatureTree result = FeatureTree.NewInstance();
|
|
389
|
result.setTitleCache("Old feature tree", true);
|
|
390
|
FeatureNode root = result.getRoot();
|
|
391
|
FeatureNode newNode;
|
|
392
|
|
|
393
|
newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
|
|
394
|
root.addChild(newNode);
|
|
395
|
|
|
396
|
addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
|
|
397
|
|
|
398
|
addFeataureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service);
|
|
399
|
newNode = FeatureNode.NewInstance(Feature.ANATOMY());
|
|
400
|
addFeataureNodesByStringList(anatomySubfeatureList, newNode, transformer, service);
|
|
401
|
|
|
402
|
newNode = addFeataureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service);
|
|
403
|
addFeataureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service);
|
|
404
|
|
|
405
|
newNode = addFeataureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service);
|
|
406
|
|
|
407
|
newNode = FeatureNode.NewInstance(Feature.COMMON_NAME());
|
|
408
|
root.addChild(newNode);
|
|
409
|
|
|
410
|
newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
|
|
411
|
root.addChild(newNode);
|
|
412
|
|
|
413
|
newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
|
|
414
|
root.addChild(newNode);
|
|
415
|
addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
|
|
416
|
|
|
417
|
newNode = FeatureNode.NewInstance(Feature.USES());
|
|
418
|
root.addChild(newNode);
|
|
419
|
|
|
420
|
addFeataureNodesByStringList(chomosomesList, root, transformer, service);
|
|
421
|
|
|
422
|
newNode = FeatureNode.NewInstance(Feature.CITATION());
|
|
423
|
root.addChild(newNode);
|
|
424
|
|
|
425
|
return result;
|
|
426
|
}
|
|
427
|
|
|
428
|
private static String [] chomosomesList = new String[]{
|
|
429
|
"Chromosomes",
|
|
430
|
};
|
|
431
|
|
|
432
|
|
|
433
|
private static String [] habitatEcologyList = new String[]{
|
|
434
|
"Habitat",
|
|
435
|
"Habitat & Ecology"
|
|
436
|
};
|
|
437
|
|
|
438
|
|
|
439
|
private static String [] generellDescriptionsUpToAnatomyList = new String[]{
|
|
440
|
"Fossils",
|
|
441
|
"Morphology and anatomy",
|
|
442
|
"Morphology",
|
|
443
|
"Vegetative morphology and anatomy",
|
|
444
|
};
|
|
445
|
|
|
446
|
|
|
447
|
private static String [] anatomySubfeatureList = new String[]{
|
|
448
|
"Leaf anatomy",
|
|
449
|
"Wood anatomy"
|
|
450
|
};
|
|
451
|
|
|
452
|
private static String [] generellDescriptionsFromAnatomyToPhytoChemoList = new String[]{
|
|
453
|
"Flower morphology",
|
|
454
|
"Palynology",
|
|
455
|
"Pollination",
|
|
456
|
"Pollen morphology",
|
|
457
|
"embryology",
|
|
458
|
"cytology",
|
|
459
|
"Life cycle",
|
|
460
|
"Fruits and embryology",
|
|
461
|
"Dispersal",
|
|
462
|
"Chromosome numbers",
|
|
463
|
"Phytochemistry and Chemotaxonomy",
|
|
464
|
};
|
|
465
|
|
|
466
|
|
|
467
|
private static String [] phytoChemoSubFeaturesList = new String[]{
|
|
468
|
"Alkaloids",
|
|
469
|
"Iridoid glucosides",
|
|
470
|
"Leaf phenolics",
|
|
471
|
"Storage products of seeds",
|
|
472
|
"Aluminium",
|
|
473
|
"Chemotaxonomy",
|
|
474
|
};
|
|
475
|
|
|
476
|
|
|
477
|
private static String [] generellDescriptionsFromPhytoChemoList = new String[]{
|
|
478
|
"Phytochemistry",
|
|
479
|
"Taxonomy",
|
|
480
|
"history",
|
|
481
|
"cultivation",
|
|
482
|
"Notes"
|
|
483
|
};
|
|
484
|
|
|
485
|
|
|
486
|
private static String [] descriptionFeatureList = new String[]{
|
|
487
|
"lifeform",
|
|
488
|
"Juvenile parts",
|
|
489
|
"Bark",
|
|
490
|
//new
|
|
491
|
"wood",
|
|
492
|
"Indumentum",
|
|
493
|
"endophytic body",
|
|
494
|
"apical buds",
|
|
495
|
"flowering buds",
|
|
496
|
"Branchlets",
|
|
497
|
"Branches",
|
|
498
|
"Branch",
|
|
499
|
"Flowering branchlets",
|
|
500
|
"Trees",
|
|
501
|
"Twigs",
|
|
502
|
"stem",
|
|
503
|
"Stems",
|
|
504
|
"stem leaves",
|
|
505
|
"Leaves",
|
|
506
|
"extraxylary sclerenchyma",
|
|
507
|
"flower-bearing stems",
|
|
508
|
"Petiole",
|
|
509
|
"Petiolules",
|
|
510
|
"Leaflets",
|
|
511
|
"Lamina",
|
|
512
|
"Veins",
|
|
513
|
"Lateral veins",
|
|
514
|
"secondary veins",
|
|
515
|
"Intersecondary veins",
|
|
516
|
"veinlets",
|
|
517
|
"Thyrsus",
|
|
518
|
"Thyrses",
|
|
519
|
"Inflorescences",
|
|
520
|
"Inflorescence",
|
|
521
|
"Young inflorescences",
|
|
522
|
"Male inflorescences",
|
|
523
|
"Female inflorescences",
|
|
524
|
"rachises",
|
|
525
|
"Bracts",
|
|
526
|
"Pedicels",
|
|
527
|
"flowering buds",
|
|
528
|
"scales",
|
|
529
|
"Buds",
|
|
530
|
"Flowers",
|
|
531
|
"Flower",
|
|
532
|
"Flowering",
|
|
533
|
"Stigma",
|
|
534
|
"perianth",
|
|
535
|
"Sepals",
|
|
536
|
"Sepal",
|
|
537
|
"Outer Sepals",
|
|
538
|
"Axillary",
|
|
539
|
"cymes",
|
|
540
|
"Calyx",
|
|
541
|
"Androgynophore",
|
|
542
|
"Petal",
|
|
543
|
"Petals",
|
|
544
|
"perigone",
|
|
545
|
"perigone lobes",
|
|
546
|
"perigone tube",
|
|
547
|
"Disc",
|
|
548
|
"corolla",
|
|
549
|
"Stamens",
|
|
550
|
"Staminodes",
|
|
551
|
"Ovary",
|
|
552
|
"Anthers",
|
|
553
|
"anther",
|
|
554
|
"Pistil",
|
|
555
|
"Pistillode",
|
|
556
|
"Ovules",
|
|
557
|
"androecium",
|
|
558
|
"gynoecium",
|
|
559
|
"Filaments",
|
|
560
|
"Style",
|
|
561
|
"annulus",
|
|
562
|
"female flowers",
|
|
563
|
"Male flowers",
|
|
564
|
"Androphore",
|
|
565
|
"Female",
|
|
566
|
"Infructescences", //order not consistent (sometimes before "Flowers")
|
|
567
|
"Fruit",
|
|
568
|
"Fruits",
|
|
569
|
"fruiting axes",
|
|
570
|
"drupes",
|
|
571
|
"Arillode",
|
|
572
|
"seed",
|
|
573
|
"Seeds",
|
|
574
|
"Seedling",
|
|
575
|
"flower tube",
|
|
576
|
"nutlets",
|
|
577
|
"pollen",
|
|
578
|
"secondary xylem",
|
|
579
|
"chromosome number",
|
|
580
|
|
|
581
|
"figure",
|
|
582
|
"fig",
|
|
583
|
"figs",
|
|
584
|
|
|
585
|
|
|
586
|
|
|
587
|
};
|
|
588
|
|
|
589
|
public FeatureNode addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
|
|
590
|
FeatureNode lastChild = null;
|
|
591
|
try {
|
|
592
|
for (String featureString : featureStringList){
|
|
593
|
UUID featureUuid;
|
|
594
|
featureUuid = transformer.getFeatureUuid(featureString);
|
|
595
|
Feature feature = (Feature)termService.find(featureUuid);
|
|
596
|
if (feature != null){
|
|
597
|
FeatureNode child = FeatureNode.NewInstance(feature);
|
|
598
|
root.addChild(child);
|
|
599
|
}
|
|
600
|
}
|
|
601
|
|
|
602
|
} catch (UndefinedTransformerMethodException e) {
|
|
603
|
logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
|
|
604
|
}
|
|
605
|
return lastChild;
|
|
606
|
}
|
|
607
|
|
|
608
|
|
|
609
|
|
|
610
|
/**
|
|
611
|
* @param args
|
|
612
|
*/
|
|
613
|
public static void main(String[] args) {
|
|
614
|
FloreGabonActivator me = new FloreGabonActivator();
|
|
615
|
me.doImport(cdmDestination);
|
|
616
|
}
|
|
617
|
}
|