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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.List;
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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.application.CdmApplicationController;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.app.common.CdmDestinations;
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import eu.etaxonomy.cdm.database.DbSchemaValidation;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
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import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.io.eflora.EfloraImportConfigurator;
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import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeImportConfigurator;
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import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeTransformer;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.common.Language;
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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.ReferenceBase;
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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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* @version 1.0
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*/
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public class CentralAfricaEricaceaeActivator {
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private static final Logger logger = Logger.getLogger(CentralAfricaEricaceaeActivator.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.ericacea_local();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production();
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// static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest();
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//feature tree uuid
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public static final UUID featureTreeUuid = UUID.fromString("051d35ee-22f1-42d8-be07-9e9bfec5bcf7");
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public static UUID defaultLanguageUuid = Language.uuidEnglish;
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//classification
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static final UUID classificationUuid = UUID.fromString("10e5efcc-6e13-4abc-ad42-e0b46e50cbe7");
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//check - import
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static final 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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static final boolean doDeduplicate = false;
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private boolean includeEricaceae = true;
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private void doImport(ICdmDataSource cdmDestination){
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//make Source
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CentralAfricaEricaceaeImportConfigurator config= CentralAfricaEricaceaeImportConfigurator.NewInstance(source, cdmDestination);
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config.setTaxonomicTreeUuid(classificationUuid);
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config.setDoTaxa(doTaxa);
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config.setCheck(check);
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config.setDefaultLanguageUuid(defaultLanguageUuid);
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config.setDoPrintKeys(doPrintKeys);
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config.setDbSchemaValidation(hbm2dll);
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CdmDefaultImport<EfloraImportConfigurator> myImport = new CdmDefaultImport<EfloraImportConfigurator>();
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//Ericaceae
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if (includeEricaceae){
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System.out.println("Start import from ("+ source.toString() + ") ...");
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config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
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myImport.invoke(config);
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System.out.println("End import from ("+ source.toString() + ")...");
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}
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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<FeatureTree> keys = myImport.getCdmAppController().getFeatureTreeService().list(PolytomousKey.class, null, null, null, null);
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for(FeatureTree key : keys){
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((PolytomousKey)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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//deduplicate
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if (doDeduplicate){
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CdmApplicationController app = myImport.getCdmAppController();
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int count = app.getAgentService().deduplicate(Person.class, null, null);
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logger.warn("Deduplicated " + count + " persons.");
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count = app.getAgentService().deduplicate(Team.class, null, null);
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logger.warn("Deduplicated " + count + " teams.");
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count = app.getReferenceService().deduplicate(ReferenceBase.class, null, null);
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logger.warn("Deduplicated " + count + " references.");
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}
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}
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private ReferenceBase getSourceReference(String string) {
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ReferenceBase result = ReferenceFactory.newGeneric();
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result.setTitleCache(string);
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return result;
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}
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private FeatureTree makeFeatureNode(ITermService service){
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CentralAfricaEricaceaeTransformer transformer = new CentralAfricaEricaceaeTransformer();
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FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
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result.setTitleCache("Central Africa Ericaceae Feature Tree");
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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(generellDescriptionsList, 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.COMMON_NAME());
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root.addChild(newNode);
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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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private static String [] generellDescriptionsList = new String[]{
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"Fossils",
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"Morphology and anatomy",
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"Morphology",
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"Vegetative morphology and anatomy",
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"Flower morphology",
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"Palynology",
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"Pollination",
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"Pollen morphology",
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"Life cycle",
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"Fruits and embryology",
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"Dispersal",
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"Wood anatomy",
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"Leaf anatomy",
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"Chromosome numbers",
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"Phytochemistry and Chemotaxonomy",
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"Phytochemistry",
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"Taxonomy",
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};
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private static String [] descriptionFeatureList = new String[]{
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"lifeform",
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"Bark",
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"Indumentum",
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"endophytic body",
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"flowering buds",
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"Branchlets",
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"Branches",
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"Branch",
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"Flowering branchlets",
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"Trees",
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"Twigs",
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"stem",
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"Stems",
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"stem leaves",
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"Leaves",
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"flower-bearing stems",
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"Petiole",
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"Petiolules",
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"Leaflets",
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"Thyrsus",
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"Thyrses",
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"Inflorescences",
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"Inflorescence",
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"Young inflorescences",
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"Bracts",
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"Pedicels",
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"flowering buds",
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"scales",
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"Buds",
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"Flowers",
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"Flower",
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"Flowering",
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"Stigma",
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"perianth",
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"Sepals",
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"Sepal",
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"Outer Sepals",
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"Axillary",
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"cymes",
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"Calyx",
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"Petal",
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"Petals",
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"perigone tube",
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"Disc",
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"corolla",
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"Stamens",
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"Staminodes",
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"Ovary",
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"Anthers",
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"anther",
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"Pistil",
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"Pistillode",
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"Ovules",
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"androecium",
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"gynoecium",
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"Filaments",
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"Style",
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"annulus",
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"female flowers",
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"Male flowers",
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"Female",
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"Infructescences", //order not consistent (sometimes before "Flowers")
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"Fruit",
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"Fruits",
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"fruiting axes",
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"drupes",
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"Arillode",
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"seed",
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"Seeds",
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"Seedling",
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"flower tube",
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"nutlets",
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"pollen",
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"secondary xylem",
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"chromosome number",
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"figure",
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"fig",
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"figs",
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};
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public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
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try {
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for (String featureString : featureStringList){
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UUID featureUuid;
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featureUuid = transformer.getFeatureUuid(featureString);
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Feature feature = (Feature)termService.find(featureUuid);
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if (feature != null){
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FeatureNode child = FeatureNode.NewInstance(feature);
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root.addChild(child);
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}
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}
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} catch (UndefinedTransformerMethodException e) {
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logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
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}
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}
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/**
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* @param args
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*/
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public static void main(String[] args) {
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CentralAfricaEricaceaeActivator me = new CentralAfricaEricaceaeActivator();
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me.doImport(cdmDestination);
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}
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}
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