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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.application.ICdmApplicationConfiguration;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor;
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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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.database.update.CdmUpdater;
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
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import eu.etaxonomy.cdm.io.common.CdmImportBase.TermMatchMode;
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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.io.specimen.excel.in.SpecimenCdmExcelImportConfigurator;
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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.common.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.common.TermType;
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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.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
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import eu.etaxonomy.cdm.model.location.NamedAreaType;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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/**
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* @author a.mueller
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* @created 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.VALIDATE;
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static final URI source = EfloraSources.ericacea_local();
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static final URI specimenSource = EfloraSources.vittaria_specimen_pesiimport3();
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static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_local();
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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_test_local_mysql();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_campanulaceae_production();
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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.uuidFrench;
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//classification
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static final UUID classificationUuid = UUID.fromString("10e5efcc-6e13-4abc-ad42-e0b46e50cbe7");
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NomenclaturalCode nc = NomenclaturalCode.ICNAFP;
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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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private boolean includeEricaceae = false;
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static final boolean doTaxa = false;
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static final boolean doDeduplicate = false;
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private boolean doNewNamedAreas = false;
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private boolean doFeatureTree = false;
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private boolean doSpecimen = true;
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private TermMatchMode specimenAreaMatchMode = TermMatchMode.UUID_ABBREVLABEL;
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private void doImport(ICdmDataSource cdmDestination){
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// CdmUpdater su = CdmUpdater.NewInstance();
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// IProgressMonitor monitor = DefaultProgressMonitor.NewInstance();
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//
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// try {
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// su.updateToCurrentVersion(cdmDestination, monitor);
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// } catch (Exception e) {
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// e.printStackTrace();
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// }
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// if (true){
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// return;
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// }
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//make Source
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CentralAfricaEricaceaeImportConfigurator config= CentralAfricaEricaceaeImportConfigurator.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.setDefaultLanguageUuid(defaultLanguageUuid);
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config.setDoPrintKeys(doPrintKeys);
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config.setDbSchemaValidation(hbm2dll);
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config.setNomenclaturalCode(nc);
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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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if (doFeatureTree){
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FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
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myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
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}
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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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//deduplicate
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if (doDeduplicate){
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ICdmApplicationConfiguration app = myImport.getCdmAppController();
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if (app == null){
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app = CdmApplicationController.NewInstance(cdmDestination, hbm2dll, false);
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}
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app.getAgentService().updateTitleCache(Team.class, null, null, null);
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return;
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// int count = app.getAgentService().deduplicate(Person.class, null, null);
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//
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// logger.warn("Deduplicated " + count + " persons.");
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//// count = app.getAgentService().deduplicate(Team.class, null, null);
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//// logger.warn("Deduplicated " + count + " teams.");
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// count = app.getReferenceService().deduplicate(Reference.class, null, null);
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// logger.warn("Deduplicated " + count + " references.");
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}
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if(doNewNamedAreas){
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newNamedAreas(myImport);
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}
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if (doSpecimen){
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logger.warn("Start specimen import");
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ICdmApplicationConfiguration app = myImport.getCdmAppController();
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SpecimenCdmExcelImportConfigurator specimenConfig= SpecimenCdmExcelImportConfigurator.NewInstance(specimenSource, cdmDestination);
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specimenConfig.setCdmAppController((CdmApplicationController)app);
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specimenConfig.setAreaMatchMode(specimenAreaMatchMode);
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specimenConfig.setNomenclaturalCode(nc);
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config.setDbSchemaValidation(DbSchemaValidation.VALIDATE);
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specimenConfig.setSourceReference(getSourceReference(specimenConfig.getSourceReferenceTitle()));
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CdmDefaultImport<SpecimenCdmExcelImportConfigurator> specimenImport = new CdmDefaultImport<SpecimenCdmExcelImportConfigurator>();
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specimenImport.setCdmAppController(app);
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specimenImport.invoke(specimenConfig);
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}
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return;
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}
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private void newNamedAreas(CdmDefaultImport<EfloraImportConfigurator> myImport) {
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ICdmApplicationConfiguration app = myImport.getCdmAppController();
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if (app == null){
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app = CdmApplicationController.NewInstance(cdmDestination, hbm2dll, false);
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}
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TransactionStatus tx = app.startTransaction();
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OrderedTermVocabulary<NamedArea> areaVoc = OrderedTermVocabulary.NewInstance(TermType.NamedArea, "Phytogeographic Regions of Central Africa", "Phytogeographic Regions of Central Africa", "FdAC regions", null);
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app.getVocabularyService().save(areaVoc);
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NamedAreaLevel level = NamedAreaLevel.NewInstance("Phytogeographic Regions of Central Africa", "Phytogeographic Regions of Central Africa", "FdAC regions");
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ITermService termService = app.getTermService();
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termService.save(level);
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NamedArea area = NamedArea.NewInstance("C\u00F4tier", "C\u00F4tier", "I");
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area.setLevel(level);
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area.setType(NamedAreaType.NATURAL_AREA());
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areaVoc.addTerm(area);
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termService.save(area);
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area = NamedArea.NewInstance("Mayumbe", "Mayumbe", "II");
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area.setLevel(level);
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area.setType(NamedAreaType.NATURAL_AREA());
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areaVoc.addTerm(area);
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termService.save(area);
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area = NamedArea.NewInstance("Bas-Congo", "Bas-Congo", "III");
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area.setLevel(level);
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area.setType(NamedAreaType.NATURAL_AREA());
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areaVoc.addTerm(area);
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termService.save(area);
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area = NamedArea.NewInstance("Kasai", "Kasai", "IV");
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area.setLevel(level);
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area.setType(NamedAreaType.NATURAL_AREA());
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areaVoc.addTerm(area);
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termService.save(area);
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area = NamedArea.NewInstance("Bas-Katanga", "Bas-Katanga", "V");
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area.setLevel(level);
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area.setType(NamedAreaType.NATURAL_AREA());
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areaVoc.addTerm(area);
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termService.save(area);
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area = NamedArea.NewInstance("Forestier Central", "Forestier Central", "VI");
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area.setLevel(level);
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area.setType(NamedAreaType.NATURAL_AREA());
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areaVoc.addTerm(area);
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termService.save(area);
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area = NamedArea.NewInstance("Ubangi-Uele", "Ubangi-Uele", "VII");
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area.setLevel(level);
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area.setType(NamedAreaType.NATURAL_AREA());
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areaVoc.addTerm(area);
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termService.save(area);
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area = NamedArea.NewInstance("Lac Albert", "Lac Albert", "VIII");
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area.setLevel(level);
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area.setType(NamedAreaType.NATURAL_AREA());
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areaVoc.addTerm(area);
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termService.save(area);
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area = NamedArea.NewInstance("Lacs \u00C9douard et Kivu", "Lacs \u00C9douard et Kivu", "IX");
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area.setLevel(level);
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area.setType(NamedAreaType.NATURAL_AREA());
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areaVoc.addTerm(area);
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termService.save(area);
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area = NamedArea.NewInstance("Rwanda-Burundi", "Rwanda-Burundi", "X");
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area.setLevel(level);
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area.setType(NamedAreaType.NATURAL_AREA());
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areaVoc.addTerm(area);
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termService.save(area);
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area = NamedArea.NewInstance("Haut-Katanga", "Haut-Katanga", "XI");
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area.setLevel(level);
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area.setType(NamedAreaType.NATURAL_AREA());
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areaVoc.addTerm(area);
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termService.save(area);
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app.getVocabularyService().save(areaVoc);
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app.commitTransaction(tx);
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}
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private Reference getSourceReference(String string) {
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Reference result = ReferenceFactory.newGeneric();
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result.setTitleCache(string);
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return result;
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}
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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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|
347
|
"Pollen morphology",
|
|
348
|
"Life cycle",
|
|
349
|
"Fruits and embryology",
|
|
350
|
"Dispersal",
|
|
351
|
"Wood anatomy",
|
|
352
|
"Leaf anatomy",
|
|
353
|
"Chromosome numbers",
|
|
354
|
"Phytochemistry and Chemotaxonomy",
|
|
355
|
"Phytochemistry",
|
|
356
|
"Taxonomy",
|
|
357
|
};
|
|
358
|
|
|
359
|
private static String [] descriptionFeatureList = new String[]{
|
|
360
|
"lifeform",
|
|
361
|
"Bark",
|
|
362
|
"Indumentum",
|
|
363
|
"endophytic body",
|
|
364
|
"flowering buds",
|
|
365
|
"Branchlets",
|
|
366
|
"Branches",
|
|
367
|
"Branch",
|
|
368
|
"Flowering branchlets",
|
|
369
|
"Trees",
|
|
370
|
"Twigs",
|
|
371
|
"stem",
|
|
372
|
"Stems",
|
|
373
|
"stem leaves",
|
|
374
|
"Leaves",
|
|
375
|
"flower-bearing stems",
|
|
376
|
"Petiole",
|
|
377
|
"Petiolules",
|
|
378
|
"Leaflets",
|
|
379
|
"Thyrsus",
|
|
380
|
"Thyrses",
|
|
381
|
"Inflorescences",
|
|
382
|
"Inflorescence",
|
|
383
|
"Young inflorescences",
|
|
384
|
"Bracts",
|
|
385
|
"Pedicels",
|
|
386
|
"flowering buds",
|
|
387
|
"scales",
|
|
388
|
"Buds",
|
|
389
|
"Flowers",
|
|
390
|
"Flower",
|
|
391
|
"Flowering",
|
|
392
|
"Stigma",
|
|
393
|
"perianth",
|
|
394
|
"Sepals",
|
|
395
|
"Sepal",
|
|
396
|
"Outer Sepals",
|
|
397
|
"Axillary",
|
|
398
|
"cymes",
|
|
399
|
"Calyx",
|
|
400
|
"Petal",
|
|
401
|
"Petals",
|
|
402
|
"perigone tube",
|
|
403
|
"Disc",
|
|
404
|
"corolla",
|
|
405
|
"Stamens",
|
|
406
|
"Staminodes",
|
|
407
|
"Ovary",
|
|
408
|
"Anthers",
|
|
409
|
"anther",
|
|
410
|
"Pistil",
|
|
411
|
"Pistillode",
|
|
412
|
"Ovules",
|
|
413
|
"androecium",
|
|
414
|
"gynoecium",
|
|
415
|
"Filaments",
|
|
416
|
"Style",
|
|
417
|
"annulus",
|
|
418
|
"female flowers",
|
|
419
|
"Male flowers",
|
|
420
|
"Female",
|
|
421
|
"Infructescences", //order not consistent (sometimes before "Flowers")
|
|
422
|
"Fruit",
|
|
423
|
"Fruits",
|
|
424
|
"fruiting axes",
|
|
425
|
"drupes",
|
|
426
|
"Arillode",
|
|
427
|
"seed",
|
|
428
|
"Seeds",
|
|
429
|
"Seedling",
|
|
430
|
"flower tube",
|
|
431
|
"nutlets",
|
|
432
|
"pollen",
|
|
433
|
"secondary xylem",
|
|
434
|
"chromosome number",
|
|
435
|
|
|
436
|
"figure",
|
|
437
|
"fig",
|
|
438
|
"figs",
|
|
439
|
|
|
440
|
|
|
441
|
|
|
442
|
|
|
443
|
};
|
|
444
|
|
|
445
|
public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
|
|
446
|
try {
|
|
447
|
for (String featureString : featureStringList){
|
|
448
|
UUID featureUuid;
|
|
449
|
featureUuid = transformer.getFeatureUuid(featureString);
|
|
450
|
Feature feature = (Feature)termService.find(featureUuid);
|
|
451
|
if (feature != null){
|
|
452
|
FeatureNode child = FeatureNode.NewInstance(feature);
|
|
453
|
root.addChild(child);
|
|
454
|
}
|
|
455
|
}
|
|
456
|
} catch (UndefinedTransformerMethodException e) {
|
|
457
|
logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
|
|
458
|
}
|
|
459
|
}
|
|
460
|
|
|
461
|
|
|
462
|
|
|
463
|
/**
|
|
464
|
* @param args
|
|
465
|
*/
|
|
466
|
public static void main(String[] args) {
|
|
467
|
CentralAfricaEricaceaeActivator me = new CentralAfricaEricaceaeActivator();
|
|
468
|
me.doImport(cdmDestination);
|
|
469
|
}
|
|
470
|
|
|
471
|
}
|