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/**
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* Copyright (C) 2008 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.io.jaxb;
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import java.io.File;
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import java.net.URI;
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import java.net.URISyntaxException;
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import java.util.Collection;
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import java.util.List;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.config.Configuration;
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import eu.etaxonomy.cdm.io.common.CdmImportBase;
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import eu.etaxonomy.cdm.io.common.ICdmIO;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.common.LanguageStringBase;
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import eu.etaxonomy.cdm.model.common.User;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.model.term.FeatureNode;
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import eu.etaxonomy.cdm.model.term.FeatureTree;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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/**
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* @author a.babadshanjan
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* @since 13.11.2008
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*/
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@Component
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public class JaxbImport
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extends CdmImportBase<JaxbImportConfigurator, JaxbImportState>
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implements ICdmIO<JaxbImportState> {
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private static final long serialVersionUID = -96388140688227297L;
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private static final Logger logger = Logger.getLogger(JaxbImport.class);
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private CdmDocumentBuilder cdmDocumentBuilder = null;
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/** Reads data from an XML file and stores them into a CDM DB.
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*
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* @param config
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* @param stores (not used)
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*/
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@Override
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protected void doInvoke(JaxbImportState state) {
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JaxbImportConfigurator jaxbImpConfig = state.getConfig();
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URI uri;
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String urlFileName = jaxbImpConfig.getSource().toString();
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try {
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uri = new URI(urlFileName);
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} catch (URISyntaxException ex) {
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logger.error("File not found");
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state.setUnsuccessfull();
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return;
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}
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logger.info("Deserializing " + urlFileName + " to DB " ); //+ dbname
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DataSet dataSet = new DataSet();
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// unmarshalling XML file
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try {
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cdmDocumentBuilder = new CdmDocumentBuilder();
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logger.info("Unmarshalling " + urlFileName);
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File file = new File(uri);
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logger.debug("Absolute path: " + file.getAbsolutePath());
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dataSet = cdmDocumentBuilder.unmarshal(DataSet.class, file);
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} catch (Exception e) {
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logger.error("Unmarshalling error");
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e.printStackTrace();
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}
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// save data in DB
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logger.info("Saving data to DB... "); //+ dbname
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saveData(state, dataSet);
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return;
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}
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/** Saves data in DB */
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private void saveData (JaxbImportState state, DataSet dataSet) {
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JaxbImportConfigurator jaxbImpConfig = state.getConfig();
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boolean success = true;
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Collection<TaxonBase> taxonBases;
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List<? extends AgentBase> agents;
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List<DefinedTermBase> terms;
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List<User> users;
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List<Reference> references;
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List<TaxonName> taxonomicNames;
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List<DescriptionBase> descriptions;
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List<TypeDesignationBase<?>> typeDesignations;
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List<SpecimenOrObservationBase> occurrences;
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List<FeatureTree> featureTrees;
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List<FeatureNode> featureNodes;
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List<Media> media;
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List<LanguageStringBase> languageData;
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List<TermVocabulary<DefinedTermBase>> termVocabularies;
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List<HomotypicalGroup> homotypicalGroups;
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TransactionStatus txStatus = startTransaction();
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//TransactionStatus txStatus = null;
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// Have single transactions per service save call. Otherwise, getting
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// H2 HYT00 error (timeout locking table DEFINEDTERMBASE) when running from editor.
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try {
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if (jaxbImpConfig.isDoUser() == true) {
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/*
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* this is a crucial call, otherwise the password will not be set correctly
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* and the whole authentication will not work
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*
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* a bit preliminary, should be used only if the complete database is replaced
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*/
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authenticate(Configuration.adminLogin, Configuration.adminPassword);
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logger.info("Users: " + (users = dataSet.getUsers()).size());
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for (User user : users) {
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List<User> usersList = getUserService().listByUsername(user.getUsername(),null, null, null, null, null, null);
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if (usersList.isEmpty()){
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getUserService().save(user);
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}else{
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// User existingUser = usersList.get(0);
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// user.setId(existingUser.getId());
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// getUserService().merge(user);
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//merging does not yet work because of #4102
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}
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}
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}
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} catch (Exception ex) {
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logger.error("Error saving users");
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ex.printStackTrace();
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success = false;
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}
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if ((jaxbImpConfig.isDoTerms() == true)
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&& (terms = dataSet.getTerms()).size() > 0) {
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//txStatus = startTransaction();
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success &= saveTerms(terms);
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//commitTransaction(txStatus);
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}
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if ((jaxbImpConfig.isDoTermVocabularies() == true)
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&& (termVocabularies = dataSet.getTermVocabularies()).size() > 0) {
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//txStatus = startTransaction();
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success &= saveTermVocabularies(termVocabularies);
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}
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// TODO: Have separate data save methods
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// txStatus = startTransaction();
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// try {
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// if (jaxbImpConfig.isDoLanguageData() == true) {
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// if ((languageData = dataSet.getLanguageData()).size() > 0) {
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// logger.info("Language data: " + languageData.size());
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// getTermService().saveLanguageDataAll(languageData);
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// }
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// }
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// } catch (Exception ex) {
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// logger.error("Error saving language data");
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// ret = false;
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// }
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// commitTransaction(txStatus);
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//txStatus = startTransaction();
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try {
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if (jaxbImpConfig.isDoAuthors() == true) {
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if ((agents = dataSet.getAgents()).size() > 0) {
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logger.info("Agents: " + agents.size());
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getAgentService().saveOrUpdate((Collection)agents);
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}
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}
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} catch (Exception ex) {
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logger.error("Error saving agents");
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success = false;
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}
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//commitTransaction(txStatus);
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//txStatus = startTransaction();
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try {
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if (jaxbImpConfig.getDoReferences() != IImportConfigurator.DO_REFERENCES.NONE) {
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if ((references = dataSet.getReferences()).size() > 0) {
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logger.info("References: " + references.size());
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getReferenceService().saveOrUpdate(references);
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logger.info("ready...");
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}
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}
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} catch (Exception ex) {
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ex.printStackTrace();
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logger.error("Error saving references");
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success = false;
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}
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//commitTransaction(txStatus);
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//txStatus = startTransaction();
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try {
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if (jaxbImpConfig.isDoTaxonNames() == true) {
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if ((taxonomicNames = dataSet.getTaxonomicNames()).size() > 0) {
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logger.info("Taxonomic names: " + taxonomicNames.size());
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getNameService().saveOrUpdate(taxonomicNames);
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}
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}
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} catch (Exception ex) {
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logger.error("Error saving taxon names");
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success = false;
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}
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//commitTransaction(txStatus);
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//txStatus = startTransaction();
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try {
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if (jaxbImpConfig.isDoHomotypicalGroups() == true) {
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if ((homotypicalGroups = dataSet.getHomotypicalGroups()).size() > 0) {
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logger.info("Homotypical groups: " + homotypicalGroups.size());
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getNameService().saveAllHomotypicalGroups(homotypicalGroups);
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}
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}
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} catch (Exception ex) {
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logger.error("Error saving homotypical groups");
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success = false;
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}
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//commitTransaction(txStatus);
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//txStatus = startTransaction();
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// Need to get the taxa and the synonyms here.
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try {
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if (jaxbImpConfig.isDoTaxa() == true) {
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if ( dataSet.getTaxonBases().size() > 0) {
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List taxa = dataSet.getTaxonBases();
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dataSet.getTaxonBases();
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logger.info("Taxon bases: " + taxa.size());
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taxa.iterator();
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getTaxonService().saveOrUpdate(taxa);
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/*while (taxBases.hasNext()){
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getTaxonService().save(taxBases.next());
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}*/
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//getTaxonService().saveTaxonAll(taxonBases);
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}
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}
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} catch (Exception ex) {
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logger.error("Error saving taxa");
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ex.printStackTrace();
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success = false;
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}
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//commitTransaction(txStatus);
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//txStatus = startTransaction();
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// NomenclaturalStatus, TypeDesignations
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try {
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if (jaxbImpConfig.isDoTypeDesignations() == true) {
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if ((typeDesignations = dataSet.getTypeDesignations()).size() > 0) {
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logger.info("Type Designations: " + typeDesignations.size());
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getNameService().saveTypeDesignationAll(typeDesignations);
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}
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}
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} catch (Exception ex) {
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logger.error("Error saving type designations");
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success = false;
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}
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//commitTransaction(txStatus);
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// TODO: Implement dataSet.getDescriptions() and IDescriptionService.saveDescriptionAll()
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// if ((descriptions = dataSet.getDescriptions()) != null) {
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// logger.info("Saving " + descriptions.size() + " descriptions");
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// getDescriptionService().saveDescriptionAll(descriptions);
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// }
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//txStatus = startTransaction();
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try {
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if (jaxbImpConfig.isDoOccurrence() == true) {
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if ((occurrences = dataSet.getOccurrences()).size() > 0) {
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logger.info("Occurrences: " + occurrences.size());
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getOccurrenceService().saveOrUpdate(occurrences);
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}
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}
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} catch (Exception ex) {
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logger.error("Error saving occurrences");
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success = false;
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}
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//commitTransaction(txStatus);
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//txStatus = startTransaction();
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try {
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if (jaxbImpConfig.isDoFeatureData() == true) {
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if ((featureTrees = dataSet.getFeatureTrees()).size() > 0) {
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logger.info("Feature data: " + featureTrees.size());
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getFeatureTreeService().saveOrUpdate(featureTrees);
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}
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}
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} catch (Exception ex) {
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logger.error("Error saving feature data");
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success = false;
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}
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//commitTransaction(txStatus);
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//txStatus = startTransaction();
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try {
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if (jaxbImpConfig.isDoMedia() == true) {
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if ((media = dataSet.getMedia()).size() > 0) {
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logger.info("Media: " + media.size());
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getMediaService().saveOrUpdate(media);
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}
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}
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} catch (Exception ex) {
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logger.error("Error saving media");
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success = false;
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}
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if (jaxbImpConfig.isDoClassificationData() == true) {
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logger.info("# Classification");
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Collection<TaxonNode> nodes = dataSet.getTaxonNodes();
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Collection<Classification> classifications = dataSet.getClassifications();
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getClassificationService().saveTaxonNodeAll(nodes);
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for (Classification tree: classifications){
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getClassificationService().saveOrUpdate(tree);
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}
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}
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commitTransaction(txStatus);
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logger.info("All data saved");
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if (!success){
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state.setUnsuccessfull();
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}
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return;
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}
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private boolean saveTermVocabularies(
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List<TermVocabulary<DefinedTermBase>> termVocabularies) {
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boolean success = true;
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logger.info("Term vocabularies: " + termVocabularies.size());
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try {
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getVocabularyService().saveOrUpdate((List)termVocabularies);
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} catch (Exception ex) {
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logger.error("Error saving term vocabularies");
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success = false;
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}
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return success;
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}
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private boolean saveTerms(List<DefinedTermBase> terms) {
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boolean success = true;
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logger.info("Terms: " + terms.size());
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try {
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getTermService().save(terms);
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} catch (Exception ex) {
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logger.error("Error saving terms");
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ex.printStackTrace();
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success = false;
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}
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return success;
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}
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@Override
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protected boolean doCheck(JaxbImportState state) {
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boolean result = true;
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logger.warn("No validation implemented for Jaxb import");
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return result;
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}
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@Override
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protected boolean isIgnore(JaxbImportState state) {
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return false;
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}
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}
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