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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.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.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.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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* Activator for Flora of the Guianas imports.
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* This class is meant for advanced use and is therefore not documented.
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* @author a.mueller
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*/
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public class FloraGuianasActivator extends EfloraActivatorBase {
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private static final Logger logger = Logger.getLogger(FloraGuianasActivator.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 fgu1 = EfloraSources.fgu_1();
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static final URI fotg03 = EfloraSources.fotg_03();
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static final URI fotg11 = EfloraSources.fotg_11();
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static final URI fotg14 = EfloraSources.fotg_14();
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static final URI fotg15 = EfloraSources.fotg_15();
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static final URI fotg16 = EfloraSources.fotg_16();
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static final URI fotg20 = EfloraSources.fotg_20();
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static final URI fotg22 = EfloraSources.fotg_22();
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static final URI fotg23 = EfloraSources.fotg_23();
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static final URI fotg24 = EfloraSources.fotg_24();
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static final URI fotg24_plus = EfloraSources.fotg_24plus();
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static final URI fotg25 = EfloraSources.fotg_25();
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static final URI fotg25_plus = EfloraSources.fotg_25plus();
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static final URI fotg26 = EfloraSources.fotg_26();
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static final URI fotg27 = EfloraSources.fotg_27();
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static final URI fotg29 = EfloraSources.fotg_29();
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static final URI fotg30 = EfloraSources.fotg_30();
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private boolean inverseInclude = false;
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private boolean includeFotg1 = false;
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private boolean includeFotg03 = true;
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private boolean includeFotg11 = false;
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private boolean includeFotg14 = false;
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private boolean includeFotg15 = false;
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private boolean includeFotg16 = false;
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private boolean includeFotg20 = false;
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private boolean includeFotg22 = false;
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private boolean includeFotg23 = false;
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private boolean includeFotg24 = false;
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private boolean includeFotg24_plus = false;
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private boolean includeFotg25 = false;
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private boolean includeFotg25_plus = false;
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private boolean includeFotg26 = false;
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private boolean includeFotg27 = false;
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private boolean includeFotg29 = false;
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private boolean includeFotg30 = false;
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_guianas_preview();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_guianas_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("2be99595-92fc-4f80-b9c4-b48d38505f5d");
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//classification
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static final UUID classificationUuid = UUID.fromString("5e3a1b07-2609-4597-bbda-7b02dfe8c2b3");
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private static final String SOURCE_REFERENCE_TITLE = "Flora of the Guianas";
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static final String classificationTitle = "Flora of the Guianas";
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private static final String FEATURE_TREE_TITLE = "Flora of the Guianas Feature Tree";
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//check - import
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private boolean h2ForCheck = true;
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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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static final boolean reuseState = true;
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private boolean replaceStandardKeyTitles = true;
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private boolean useFotGCollectionTypeOnly = true;
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// ****************** NO CHANGE *******************************************/
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private void doImport(ICdmDataSource cdmDestination){
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super.doImport(fotg22, cdmDestination,check, h2ForCheck);
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//make config
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config.setClassificationUuid(classificationUuid);
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config.setDoTaxa(doTaxa);
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config.setDoPrintKeys(doPrintKeys);
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config.setDbSchemaValidation(hbm2dll);
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config.setReplaceStandardKeyTitles(replaceStandardKeyTitles);
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config.setSourceReference(getSourceReference(SOURCE_REFERENCE_TITLE));
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config.setClassificationName(classificationTitle);
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config.setReuseExistingState(reuseState);
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config.setUseFotGSpecimenTypeCollectionAndTypeOnly(useFotGCollectionTypeOnly);
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// URI uri = config.getSource();
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// try {
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//// InputStream is = uri.toURL().openStream();
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// File file = new File(uri);
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// System.out.println(file.exists());
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// InputStream is = new FileInputStream(file);
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// System.out.println(is);
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// } catch (Exception e) {
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// e.printStackTrace();
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// }
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//Vol1-79
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executeVolume( fgu1, includeFotg1 ^ inverseInclude);
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//Vol03
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executeVolume(fotg03, includeFotg03 ^ inverseInclude);
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//Vol11
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executeVolume(fotg11, includeFotg11 ^ inverseInclude);
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//Vol14
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executeVolume(fotg14, includeFotg14 ^ inverseInclude);
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//Vol15
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executeVolume(fotg15, includeFotg15 ^ inverseInclude);
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//Vol16
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executeVolume(fotg16, includeFotg16 ^ inverseInclude);
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//Vol20
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executeVolume(fotg20, includeFotg20 ^ inverseInclude);
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//Vol22
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executeVolume(fotg22, includeFotg22 ^ inverseInclude);
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//Vol23
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executeVolume(fotg23, includeFotg23 ^ inverseInclude);
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//Vol24
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executeVolume(fotg24, includeFotg24 ^ inverseInclude);
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//Vol24+
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executeVolume(fotg24_plus, includeFotg24_plus ^ inverseInclude);
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//Vol25
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executeVolume(fotg25, includeFotg25 ^ inverseInclude);
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//Vol26
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executeVolume(fotg25_plus, includeFotg25_plus ^ inverseInclude);
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//Vol26
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executeVolume(fotg26, includeFotg26 ^ inverseInclude);
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//Vol27
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executeVolume(fotg27, includeFotg27 ^ inverseInclude);
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//Vol29
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executeVolume(fotg29, includeFotg29 ^ inverseInclude);
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//Vol30
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executeVolume(fotg30, includeFotg30 ^ inverseInclude);
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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 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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MarkupTransformer transformer = new MarkupTransformer();
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FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
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result.setTitleCache(FEATURE_TREE_TITLE, 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.COMMON_NAME());
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root.addChild(newNode);
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newNode = FeatureNode.NewInstance(Feature.PHENOLOGY());
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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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String sql = "\nSELECT feature.titleCache " +
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" FROM DescriptionElementBase deb INNER JOIN DefinedTermBase feature ON deb.feature_id = feature.id " +
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" GROUP BY feature.id " +
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" HAVING feature.id NOT IN (SELECT DISTINCT fn.feature_id " +
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" FROM FeatureNode fn " +
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" WHERE fn.feature_id IS NOT NULL) ";
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logger.warn("Check for missing features in feature tree: " + sql);
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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 [] generellDescriptionsUpToAnatomyList = 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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};
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private static String [] anatomySubfeatureList = new String[]{
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"Leaf anatomy",
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"Wood anatomy"
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};
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private static String [] generellDescriptionsFromAnatomyToPhytoChemoList = new String[]{
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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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"embryology",
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"cytology",
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"Life cycle",
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"Fruits and embryology",
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"Dispersal",
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"Chromosome numbers",
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"Phytochemistry and Chemotaxonomy",
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};
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private static String [] phytoChemoSubFeaturesList = new String[]{
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"Alkaloids",
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"Iridoid glucosides",
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"Leaf phenolics",
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"Storage products of seeds",
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"Aluminium",
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"Chemotaxonomy",
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};
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private static String [] generellDescriptionsFromPhytoChemoList = new String[]{
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"Phytochemistry",
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"Taxonomy",
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"history",
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"cultivation",
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"Notes"
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};
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private static String [] descriptionFeatureList = new String[]{
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"lifeform",
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"Juvenile parts",
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"Bark",
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//new
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"wood",
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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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"extraxylary sclerenchyma",
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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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"Lamina",
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"Veins",
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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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"Male inflorescences",
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"Female inflorescences",
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"rachises",
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"Pedicels",
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"Bracts",
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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",
|
|
371
|
"Axillary",
|
|
372
|
"cymes",
|
|
373
|
"Calyx",
|
|
374
|
"Petal",
|
|
375
|
"Petals",
|
|
376
|
"perigone",
|
|
377
|
"perigone lobes",
|
|
378
|
"perigone tube",
|
|
379
|
"Disc",
|
|
380
|
"corolla",
|
|
381
|
"Stamens",
|
|
382
|
"Staminodes",
|
|
383
|
"Ovary",
|
|
384
|
"Anthers",
|
|
385
|
"anther",
|
|
386
|
"Pistil",
|
|
387
|
"Pistillode",
|
|
388
|
"Ovules",
|
|
389
|
"androecium",
|
|
390
|
"gynoecium",
|
|
391
|
"Filaments",
|
|
392
|
"Style",
|
|
393
|
"annulus",
|
|
394
|
"female flowers",
|
|
395
|
"Male flowers",
|
|
396
|
"Female",
|
|
397
|
"Infructescences", //order not consistent (sometimes before "Flowers")
|
|
398
|
"Fruit",
|
|
399
|
"Fruits",
|
|
400
|
"fruiting axes",
|
|
401
|
"drupes",
|
|
402
|
"Arillode",
|
|
403
|
"seed",
|
|
404
|
"Seeds",
|
|
405
|
"Seedling",
|
|
406
|
"flower tube",
|
|
407
|
"nutlets",
|
|
408
|
"pollen",
|
|
409
|
"secondary xylem",
|
|
410
|
"chromosome number",
|
|
411
|
|
|
412
|
"figure",
|
|
413
|
"fig",
|
|
414
|
"figs",
|
|
415
|
|
|
416
|
|
|
417
|
|
|
418
|
};
|
|
419
|
|
|
420
|
public FeatureNode addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
|
|
421
|
FeatureNode lastChild = null;
|
|
422
|
try {
|
|
423
|
for (String featureString : featureStringList){
|
|
424
|
UUID featureUuid;
|
|
425
|
featureUuid = transformer.getFeatureUuid(featureString);
|
|
426
|
Feature feature = (Feature)termService.find(featureUuid);
|
|
427
|
if (feature != null){
|
|
428
|
FeatureNode child = FeatureNode.NewInstance(feature);
|
|
429
|
root.addChild(child);
|
|
430
|
}
|
|
431
|
}
|
|
432
|
|
|
433
|
} catch (UndefinedTransformerMethodException e) {
|
|
434
|
logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
|
|
435
|
}
|
|
436
|
return lastChild;
|
|
437
|
}
|
|
438
|
|
|
439
|
|
|
440
|
|
|
441
|
/**
|
|
442
|
* @param args
|
|
443
|
*/
|
|
444
|
public static void main(String[] args) {
|
|
445
|
FloraGuianasActivator me = new FloraGuianasActivator();
|
|
446
|
me.doImport(cdmDestination);
|
|
447
|
}
|
|
448
|
}
|