Revision ac5020e6
Added by Andreas Müller about 8 years ago
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/jaxb/JaxbExport.java | ||
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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.ByteArrayOutputStream; |
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import java.io.File; |
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import java.io.FileNotFoundException; |
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import java.io.FileOutputStream; |
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import java.io.OutputStreamWriter; |
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import java.io.PrintWriter; |
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import java.io.UnsupportedEncodingException; |
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import java.net.URI; |
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import java.util.ArrayList; |
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import java.util.List; |
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import javax.xml.transform.stream.StreamResult; |
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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.hibernate.HibernateProxyHelper; |
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import eu.etaxonomy.cdm.io.common.CdmExportBase; |
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import eu.etaxonomy.cdm.io.common.ICdmExport; |
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import eu.etaxonomy.cdm.io.common.IExportConfigurator; |
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import eu.etaxonomy.cdm.io.common.mapping.out.IExportTransformer; |
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import eu.etaxonomy.cdm.model.agent.AgentBase; |
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import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
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import eu.etaxonomy.cdm.model.common.User; |
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import eu.etaxonomy.cdm.model.description.FeatureTree; |
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import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
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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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/** |
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* @author a.babadshanjan |
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* @created 25.09.2008 |
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* @version 1.0 |
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*/ |
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@Component |
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public class JaxbExport extends CdmExportBase<JaxbExportConfigurator, JaxbExportState, IExportTransformer> implements ICdmExport<JaxbExportConfigurator, JaxbExportState> { |
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private static final Logger logger = Logger.getLogger(JaxbExport.class); |
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private DataSet dataSet; |
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// /** |
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// * |
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// */ |
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// public JaxbExport() { |
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// super(); |
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// this.ioName = this.getClass().getSimpleName(); |
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// } |
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/** Retrieves data from a CDM DB and serializes them CDM to XML. |
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* Starts with root taxa and traverses the classification to retrieve children taxa, synonyms and relationships. |
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* Taxa that are not part of the classification are not found. |
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* |
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* @param exImpConfig |
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* @param dbname |
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* @param filename |
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*/ |
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// @Override |
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// protected boolean doInvoke(IExportConfigurator config, |
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// Map<String, MapWrapper<? extends CdmBase>> stores) { |
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@Override |
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protected void doInvoke(JaxbExportState state) { |
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JaxbExportConfigurator jaxbExpConfig = (JaxbExportConfigurator)state.getConfig(); |
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// String dbname = jaxbExpConfig.getSource().getName(); |
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URI uri = jaxbExpConfig.getDestination(); |
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// logger.info("Serializing DB " + dbname + " to file " + fileName); |
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// logger.debug("DbSchemaValidation = " + jaxbExpConfig.getDbSchemaValidation()); |
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TransactionStatus txStatus = null; |
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txStatus = startTransaction(true); |
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dataSet = new DataSet(); |
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// get data from DB |
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try { |
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logger.info("Retrieving data from DB"); |
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retrieveData(jaxbExpConfig, dataSet); |
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} catch (Exception e) { |
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logger.error("Error retrieving data"); |
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e.printStackTrace(); |
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} |
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logger.info("All data retrieved"); |
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try { |
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switch(jaxbExpConfig.getTarget()) { |
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case FILE: |
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writeToFile(new File(uri), dataSet); |
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break; |
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case EXPORT_DATA: |
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CdmDocumentBuilder cdmDocumentBuilder = new CdmDocumentBuilder(); |
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exportStream = new ByteArrayOutputStream(); |
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cdmDocumentBuilder.marshal(dataSet, new StreamResult(exportStream)); |
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break; |
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default: |
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break; |
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} |
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} catch (Exception e) { |
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logger.error("Marshalling error"); |
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e.printStackTrace(); |
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} |
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commitTransaction(txStatus); |
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return; |
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} |
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public static void writeToFile(File file, DataSet dataSet) throws UnsupportedEncodingException, FileNotFoundException { |
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CdmDocumentBuilder cdmDocumentBuilder = new CdmDocumentBuilder(); |
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PrintWriter writer = new PrintWriter(new OutputStreamWriter(new FileOutputStream(file), "UTF8"), true); |
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cdmDocumentBuilder.marshal(dataSet, writer); |
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// TODO: Split into one file per data set member to see whether performance improves? |
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logger.info("XML file written"); |
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logger.info("Filename is: " + file.getAbsolutePath()); |
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} |
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private void retrieveData (IExportConfigurator config, DataSet dataSet) { |
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JaxbExportConfigurator jaxbExpConfig = (JaxbExportConfigurator)config; |
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final int MAX_ROWS = 50000; |
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int numberOfRows = jaxbExpConfig.getMaxRows(); |
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int agentRows = numberOfRows; |
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int definedTermBaseRows = numberOfRows; |
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int referenceBaseRows = numberOfRows; |
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int taxonNameBaseRows = numberOfRows; |
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int taxonBaseRows = numberOfRows; |
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int taxonNodeRows = numberOfRows; |
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int relationshipRows = numberOfRows; |
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int occurrencesRows = numberOfRows; |
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int mediaRows = numberOfRows; |
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int featureDataRows = numberOfRows; |
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int classificationDataRows = numberOfRows; |
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int languageDataRows = numberOfRows; |
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int termVocabularyRows = numberOfRows; |
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int homotypicalGroupRows = numberOfRows; |
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int UserRows= numberOfRows; |
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if (jaxbExpConfig.isDoUsers() == true) { |
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if (UserRows == 0) { UserRows = MAX_ROWS; } |
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logger.info("# User"); |
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List<User> users = getUserService().list(null, UserRows, 0, null, null); |
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for (User user: users){ |
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dataSet.addUser( (User)HibernateProxyHelper.deproxy(user)); |
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} |
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} |
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if (jaxbExpConfig.isDoTermVocabularies() == true) { |
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if (termVocabularyRows == 0) { termVocabularyRows = MAX_ROWS; } |
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logger.info("# TermVocabulary"); |
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dataSet.setTermVocabularies((List)getVocabularyService().list(null,termVocabularyRows, 0, null, null)); |
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} |
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// if (jaxbExpConfig.isDoLanguageData() == true) { |
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// if (languageDataRows == 0) { languageDataRows = MAX_ROWS; } |
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// logger.info("# Representation, Language String"); |
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// dataSet.setLanguageData(getTermService().getAllRepresentations(MAX_ROWS, 0)); |
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//TODO!!! |
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dataSet.setLanguageStrings(getTermService().getAllLanguageStrings(MAX_ROWS, 0)); |
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// } |
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if (jaxbExpConfig.isDoTerms() == true) { |
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if (definedTermBaseRows == 0) { definedTermBaseRows = getTermService().count(DefinedTermBase.class); } |
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logger.info("# DefinedTermBase: " + definedTermBaseRows); |
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dataSet.setTerms(getTermService().list(null,definedTermBaseRows, 0,null,null)); |
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} |
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if (jaxbExpConfig.isDoAuthors() == true) { |
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if (agentRows == 0) { agentRows = getAgentService().count(AgentBase.class); } |
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logger.info("# Agents: " + agentRows); |
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//logger.info(" # Team: " + appCtr.getAgentService().count(Team.class)); |
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dataSet.setAgents(getAgentService().list(null,agentRows, 0,null,null)); |
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} |
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if (jaxbExpConfig.getDoReferences() != IExportConfigurator.DO_REFERENCES.NONE) { |
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if (referenceBaseRows == 0) { referenceBaseRows = getReferenceService().count(Reference.class); } |
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logger.info("# Reference: " + referenceBaseRows); |
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dataSet.setReferences(getReferenceService().list(null,referenceBaseRows, 0,null,null)); |
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} |
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if (jaxbExpConfig.isDoHomotypicalGroups() == true) { |
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if (homotypicalGroupRows == 0) { homotypicalGroupRows = MAX_ROWS; } |
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logger.info("# Homotypical Groups"); |
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dataSet.setHomotypicalGroups(getNameService().getAllHomotypicalGroups(homotypicalGroupRows, 0)); |
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} |
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if (jaxbExpConfig.isDoTaxonNames() == true) { |
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if (taxonNameBaseRows == 0) { taxonNameBaseRows = getNameService().count(TaxonNameBase.class); } |
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logger.info("# TaxonNameBase: " + taxonNameBaseRows); |
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//logger.info(" # Taxon: " + getNameService().count(BotanicalName.class)); |
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dataSet.setTaxonomicNames(getNameService().list(null,taxonNameBaseRows, 0,null,null)); |
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} |
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if (jaxbExpConfig.isDoTaxa() == true) { |
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if (taxonBaseRows == 0) { taxonBaseRows = getTaxonService().count(TaxonBase.class); } |
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logger.info("# TaxonBase: " + taxonBaseRows); |
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// dataSet.setTaxa(new ArrayList<Taxon>()); |
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// dataSet.setSynonyms(new ArrayList<Synonym>()); |
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List<TaxonBase> tb = getTaxonService().list(null,taxonBaseRows, 0,null,null); |
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for (TaxonBase taxonBase : tb) { |
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dataSet.addTaxonBase((TaxonBase)HibernateProxyHelper.deproxy(taxonBase)); |
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} |
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} |
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// TODO: |
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// retrieve taxa and synonyms separately |
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// need correct count for taxa and synonyms |
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// if (taxonBaseRows == 0) { taxonBaseRows = getTaxonService().count(TaxonBase.class); } |
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// logger.info("# Synonym: " + taxonBaseRows); |
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// dataSet.setSynonyms(new ArrayList<Synonym>()); |
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// dataSet.setSynonyms(getTaxonService().getAllSynonyms(taxonBaseRows, 0)); |
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// if (jaxbExpConfig.isDoRelTaxa() == true) { |
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// if (relationshipRows == 0) { relationshipRows = MAX_ROWS; } |
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// logger.info("# Relationships"); |
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// List<RelationshipBase> relationList = getTaxonService().getAllRelationships(relationshipRows, 0); |
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// Set<RelationshipBase> relationSet = new HashSet<RelationshipBase>(relationList); |
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// dataSet.setRelationships(relationSet); |
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// } |
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if (jaxbExpConfig.isDoOccurrence() == true) { |
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if (occurrencesRows == 0) { occurrencesRows = getOccurrenceService().count(SpecimenOrObservationBase.class); } |
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logger.info("# SpecimenOrObservationBase: " + occurrencesRows); |
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List<SpecimenOrObservationBase> occurrenceList = getOccurrenceService().list(null,occurrencesRows, 0,null,null); |
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/*List<SpecimenOrObservationBase> noProxyList = new ArrayList<SpecimenOrObservationBase>(); |
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for (SpecimenOrObservationBase specimen : occurrenceList){ |
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specimen = (SpecimenOrObservationBase)HibernateProxyHelper.deproxy(specimen); |
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noProxyList.add(specimen); |
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}*/ |
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dataSet.setOccurrences(occurrenceList); |
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} |
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if (jaxbExpConfig.isDoTypeDesignations() == true) { |
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logger.info("# TypeDesignations"); |
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dataSet.addTypeDesignations(getNameService().getAllTypeDesignations(MAX_ROWS, 0)); |
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} |
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if (jaxbExpConfig.isDoMedia() == true) { |
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if (mediaRows == 0) { mediaRows = MAX_ROWS; } |
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logger.info("# Media"); |
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dataSet.setMedia(getMediaService().list(null,mediaRows, 0,null,null)); |
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// dataSet.addMedia(getMediaService().getAllMediaRepresentations(mediaRows, 0)); |
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// dataSet.addMedia(getMediaService().getAllMediaRepresentationParts(mediaRows, 0)); |
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} |
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if (jaxbExpConfig.isDoFeatureData() == true) { |
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if (featureDataRows == 0) { featureDataRows = MAX_ROWS; } |
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logger.info("# Feature Tree, Feature Node"); |
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List<FeatureTree> featureTrees = new ArrayList<FeatureTree>(); |
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featureTrees= getFeatureTreeService().list(null,featureDataRows, 0, null, null); |
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List<FeatureTree> taxTreesdeproxy = new ArrayList<FeatureTree>(); |
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for (FeatureTree featureTree : featureTrees){ |
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HibernateProxyHelper.deproxy(featureTree); |
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taxTreesdeproxy.add(featureTree); |
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} |
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dataSet.setFeatureTrees(getFeatureTreeService().list(null,null,null,null,null)); |
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} |
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if (jaxbExpConfig.isDoClassificationData() == true) { |
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if (classificationDataRows == 0) { classificationDataRows = MAX_ROWS; } |
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logger.info("# Classification"); |
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List<Classification> taxTrees = new ArrayList<Classification>(); |
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taxTrees= getClassificationService().list(null,classificationDataRows, 0, null, null); |
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List<Classification> taxTreesdeproxy = new ArrayList<Classification>(); |
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for (Classification taxTree : taxTrees){ |
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HibernateProxyHelper.deproxy(taxTree); |
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taxTreesdeproxy.add(taxTree); |
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} |
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List<TaxonNode> taxNodes = new ArrayList<TaxonNode>(); |
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taxNodes= getClassificationService().getAllNodes(); |
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List<TaxonNode> taxNodesdeproxy = new ArrayList<TaxonNode>(); |
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for (TaxonNode taxNode : taxNodes){ |
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HibernateProxyHelper.deproxy(taxNode); |
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taxNodesdeproxy.add(taxNode); |
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} |
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dataSet.setTaxonNodes(taxNodesdeproxy); |
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dataSet.setClassifications(taxTreesdeproxy ); |
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} |
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//TODO: FIXME!!!!! |
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dataSet.setLanguageStrings(null); |
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} |
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@Override |
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protected boolean doCheck(JaxbExportState state) { |
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boolean result = true; |
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logger.warn("No check implemented for Jaxb export"); |
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return result; |
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} |
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@Override |
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protected boolean isIgnore(JaxbExportState state) { |
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return false; |
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} |
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} |
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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.ByteArrayOutputStream; |
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import java.io.File; |
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import java.io.FileNotFoundException; |
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import java.io.FileOutputStream; |
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import java.io.OutputStreamWriter; |
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import java.io.PrintWriter; |
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import java.io.UnsupportedEncodingException; |
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import java.net.URI; |
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import java.util.ArrayList; |
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import java.util.List; |
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import javax.xml.transform.stream.StreamResult; |
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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.hibernate.HibernateProxyHelper; |
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import eu.etaxonomy.cdm.io.common.CdmExportBase; |
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import eu.etaxonomy.cdm.io.common.ICdmExport; |
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import eu.etaxonomy.cdm.io.common.IExportConfigurator; |
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import eu.etaxonomy.cdm.io.common.mapping.out.IExportTransformer; |
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import eu.etaxonomy.cdm.model.agent.AgentBase; |
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import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
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import eu.etaxonomy.cdm.model.common.User; |
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import eu.etaxonomy.cdm.model.description.FeatureTree; |
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import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
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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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|
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/** |
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* @author a.babadshanjan |
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* @created 25.09.2008 |
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* @version 1.0 |
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*/ |
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@Component |
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public class JaxbExport extends CdmExportBase<JaxbExportConfigurator, JaxbExportState, IExportTransformer> implements ICdmExport<JaxbExportConfigurator, JaxbExportState> { |
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private static final Logger logger = Logger.getLogger(JaxbExport.class); |
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private DataSet dataSet; |
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// /** |
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// * |
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// */ |
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// public JaxbExport() { |
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// super(); |
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// this.ioName = this.getClass().getSimpleName(); |
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// } |
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/** Retrieves data from a CDM DB and serializes them CDM to XML. |
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* Starts with root taxa and traverses the classification to retrieve children taxa, synonyms and relationships. |
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* Taxa that are not part of the classification are not found. |
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* |
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* @param exImpConfig |
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* @param dbname |
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* @param filename |
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*/ |
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// @Override |
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// protected boolean doInvoke(IExportConfigurator config, |
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// Map<String, MapWrapper<? extends CdmBase>> stores) { |
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@Override |
|
78 |
protected void doInvoke(JaxbExportState state) { |
|
79 |
|
|
80 |
JaxbExportConfigurator jaxbExpConfig = (JaxbExportConfigurator)state.getConfig(); |
|
81 |
// String dbname = jaxbExpConfig.getSource().getName(); |
|
82 |
URI uri = jaxbExpConfig.getDestination(); |
|
83 |
// logger.info("Serializing DB " + dbname + " to file " + fileName); |
|
84 |
// logger.debug("DbSchemaValidation = " + jaxbExpConfig.getDbSchemaValidation()); |
|
85 |
|
|
86 |
TransactionStatus txStatus = null; |
|
87 |
|
|
88 |
txStatus = startTransaction(true); |
|
89 |
|
|
90 |
dataSet = new DataSet(); |
|
91 |
|
|
92 |
// get data from DB |
|
93 |
|
|
94 |
try { |
|
95 |
logger.info("Retrieving data from DB"); |
|
96 |
|
|
97 |
retrieveData(jaxbExpConfig, dataSet); |
|
98 |
|
|
99 |
} catch (Exception e) { |
|
100 |
logger.error("Error retrieving data"); |
|
101 |
e.printStackTrace(); |
|
102 |
} |
|
103 |
|
|
104 |
logger.info("All data retrieved"); |
|
105 |
|
|
106 |
try { |
|
107 |
switch(jaxbExpConfig.getTarget()) { |
|
108 |
case FILE: |
|
109 |
writeToFile(new File(uri), dataSet); |
|
110 |
break; |
|
111 |
case EXPORT_DATA: |
|
112 |
CdmDocumentBuilder cdmDocumentBuilder = new CdmDocumentBuilder(); |
|
113 |
exportStream = new ByteArrayOutputStream(); |
|
114 |
cdmDocumentBuilder.marshal(dataSet, new StreamResult(exportStream)); |
|
115 |
break; |
|
116 |
default: |
|
117 |
break; |
|
118 |
} |
|
119 |
} catch (Exception e) { |
|
120 |
logger.error("Marshalling error"); |
|
121 |
e.printStackTrace(); |
|
122 |
} |
|
123 |
|
|
124 |
commitTransaction(txStatus); |
|
125 |
|
|
126 |
return; |
|
127 |
|
|
128 |
} |
|
129 |
|
|
130 |
public static void writeToFile(File file, DataSet dataSet) throws UnsupportedEncodingException, FileNotFoundException { |
|
131 |
CdmDocumentBuilder cdmDocumentBuilder = new CdmDocumentBuilder(); |
|
132 |
PrintWriter writer = new PrintWriter(new OutputStreamWriter(new FileOutputStream(file), "UTF8"), true); |
|
133 |
cdmDocumentBuilder.marshal(dataSet, writer); |
|
134 |
|
|
135 |
// TODO: Split into one file per data set member to see whether performance improves? |
|
136 |
|
|
137 |
logger.info("XML file written"); |
|
138 |
logger.info("Filename is: " + file.getAbsolutePath()); |
|
139 |
} |
|
140 |
|
|
141 |
private void retrieveData (IExportConfigurator config, DataSet dataSet) { |
|
142 |
|
|
143 |
JaxbExportConfigurator jaxbExpConfig = (JaxbExportConfigurator)config; |
|
144 |
final int MAX_ROWS = 50000; |
|
145 |
int numberOfRows = jaxbExpConfig.getMaxRows(); |
|
146 |
|
|
147 |
int agentRows = numberOfRows; |
|
148 |
int definedTermBaseRows = numberOfRows; |
|
149 |
int referenceBaseRows = numberOfRows; |
|
150 |
int taxonNameBaseRows = numberOfRows; |
|
151 |
int taxonBaseRows = numberOfRows; |
|
152 |
int taxonNodeRows = numberOfRows; |
|
153 |
int relationshipRows = numberOfRows; |
|
154 |
int occurrencesRows = numberOfRows; |
|
155 |
int mediaRows = numberOfRows; |
|
156 |
int featureDataRows = numberOfRows; |
|
157 |
int classificationDataRows = numberOfRows; |
|
158 |
int languageDataRows = numberOfRows; |
|
159 |
int termVocabularyRows = numberOfRows; |
|
160 |
int homotypicalGroupRows = numberOfRows; |
|
161 |
int UserRows= numberOfRows; |
|
162 |
|
|
163 |
if (jaxbExpConfig.isDoUsers() == true) { |
|
164 |
|
|
165 |
if (UserRows == 0) { UserRows = MAX_ROWS; } |
|
166 |
logger.info("# User"); |
|
167 |
List<User> users = getUserService().list(null, UserRows, 0, null, null); |
|
168 |
|
|
169 |
|
|
170 |
for (User user: users){ |
|
171 |
dataSet.addUser(HibernateProxyHelper.deproxy(user)); |
|
172 |
} |
|
173 |
|
|
174 |
} |
|
175 |
if (jaxbExpConfig.isDoTermVocabularies() == true) { |
|
176 |
if (termVocabularyRows == 0) { termVocabularyRows = MAX_ROWS; } |
|
177 |
logger.info("# TermVocabulary"); |
|
178 |
dataSet.setTermVocabularies((List)getVocabularyService().list(null,termVocabularyRows, 0, null, null)); |
|
179 |
} |
|
180 |
|
|
181 |
|
|
182 |
|
|
183 |
// if (jaxbExpConfig.isDoLanguageData() == true) { |
|
184 |
// if (languageDataRows == 0) { languageDataRows = MAX_ROWS; } |
|
185 |
// logger.info("# Representation, Language String"); |
|
186 |
// dataSet.setLanguageData(getTermService().getAllRepresentations(MAX_ROWS, 0)); |
|
187 |
//TODO!!! |
|
188 |
dataSet.setLanguageStrings(getTermService().getAllLanguageStrings(MAX_ROWS, 0)); |
|
189 |
// } |
|
190 |
|
|
191 |
if (jaxbExpConfig.isDoTerms() == true) { |
|
192 |
if (definedTermBaseRows == 0) { definedTermBaseRows = getTermService().count(DefinedTermBase.class); } |
|
193 |
logger.info("# DefinedTermBase: " + definedTermBaseRows); |
|
194 |
dataSet.setTerms(getTermService().list(null,definedTermBaseRows, 0,null,null)); |
|
195 |
} |
|
196 |
|
|
197 |
if (jaxbExpConfig.isDoAuthors() == true) { |
|
198 |
if (agentRows == 0) { agentRows = getAgentService().count(AgentBase.class); } |
|
199 |
logger.info("# Agents: " + agentRows); |
|
200 |
//logger.info(" # Team: " + appCtr.getAgentService().count(Team.class)); |
|
201 |
dataSet.setAgents(getAgentService().list(null,agentRows, 0,null,null)); |
|
202 |
} |
|
203 |
|
|
204 |
|
|
205 |
|
|
206 |
if (jaxbExpConfig.getDoReferences() != IExportConfigurator.DO_REFERENCES.NONE) { |
|
207 |
if (referenceBaseRows == 0) { referenceBaseRows = getReferenceService().count(Reference.class); } |
|
208 |
logger.info("# Reference: " + referenceBaseRows); |
|
209 |
dataSet.setReferences(getReferenceService().list(null,referenceBaseRows, 0,null,null)); |
|
210 |
} |
|
211 |
|
|
212 |
if (jaxbExpConfig.isDoHomotypicalGroups() == true) { |
|
213 |
if (homotypicalGroupRows == 0) { homotypicalGroupRows = MAX_ROWS; } |
|
214 |
logger.info("# Homotypical Groups"); |
|
215 |
dataSet.setHomotypicalGroups(getNameService().getAllHomotypicalGroups(homotypicalGroupRows, 0)); |
|
216 |
} |
|
217 |
|
|
218 |
if (jaxbExpConfig.isDoTaxonNames() == true) { |
|
219 |
if (taxonNameBaseRows == 0) { taxonNameBaseRows = getNameService().count(TaxonNameBase.class); } |
|
220 |
logger.info("# TaxonNameBase: " + taxonNameBaseRows); |
|
221 |
//logger.info(" # Taxon: " + getNameService().count(BotanicalName.class)); |
|
222 |
dataSet.setTaxonomicNames(getNameService().list(null,taxonNameBaseRows, 0,null,null)); |
|
223 |
} |
|
224 |
|
|
225 |
|
|
226 |
|
|
227 |
if (jaxbExpConfig.isDoTaxa() == true) { |
|
228 |
if (taxonBaseRows == 0) { taxonBaseRows = getTaxonService().count(TaxonBase.class); } |
|
229 |
logger.info("# TaxonBase: " + taxonBaseRows); |
|
230 |
// dataSet.setTaxa(new ArrayList<Taxon>()); |
|
231 |
// dataSet.setSynonyms(new ArrayList<Synonym>()); |
|
232 |
List<TaxonBase> tb = getTaxonService().list(null,taxonBaseRows, 0,null,null); |
|
233 |
for (TaxonBase taxonBase : tb) { |
|
234 |
dataSet.addTaxonBase(HibernateProxyHelper.deproxy(taxonBase)); |
|
235 |
} |
|
236 |
} |
|
237 |
|
|
238 |
// TODO: |
|
239 |
// retrieve taxa and synonyms separately |
|
240 |
// need correct count for taxa and synonyms |
|
241 |
// if (taxonBaseRows == 0) { taxonBaseRows = getTaxonService().count(TaxonBase.class); } |
|
242 |
// logger.info("# Synonym: " + taxonBaseRows); |
|
243 |
// dataSet.setSynonyms(new ArrayList<Synonym>()); |
|
244 |
// dataSet.setSynonyms(getTaxonService().getAllSynonyms(taxonBaseRows, 0)); |
|
245 |
|
|
246 |
// if (jaxbExpConfig.isDoRelTaxa() == true) { |
|
247 |
// if (relationshipRows == 0) { relationshipRows = MAX_ROWS; } |
|
248 |
// logger.info("# Relationships"); |
|
249 |
// List<RelationshipBase> relationList = getTaxonService().getAllRelationships(relationshipRows, 0); |
|
250 |
// Set<RelationshipBase> relationSet = new HashSet<RelationshipBase>(relationList); |
|
251 |
// dataSet.setRelationships(relationSet); |
|
252 |
// } |
|
253 |
if (jaxbExpConfig.isDoOccurrence() == true) { |
|
254 |
if (occurrencesRows == 0) { occurrencesRows = getOccurrenceService().count(SpecimenOrObservationBase.class); } |
|
255 |
logger.info("# SpecimenOrObservationBase: " + occurrencesRows); |
|
256 |
List<SpecimenOrObservationBase> occurrenceList = getOccurrenceService().list(null,occurrencesRows, 0,null,null); |
|
257 |
/*List<SpecimenOrObservationBase> noProxyList = new ArrayList<SpecimenOrObservationBase>(); |
|
258 |
for (SpecimenOrObservationBase specimen : occurrenceList){ |
|
259 |
specimen = (SpecimenOrObservationBase)HibernateProxyHelper.deproxy(specimen); |
|
260 |
noProxyList.add(specimen); |
|
261 |
}*/ |
|
262 |
dataSet.setOccurrences(occurrenceList); |
|
263 |
} |
|
264 |
|
|
265 |
if (jaxbExpConfig.isDoTypeDesignations() == true) { |
|
266 |
logger.info("# TypeDesignations"); |
|
267 |
dataSet.addTypeDesignations(getNameService().getAllTypeDesignations(MAX_ROWS, 0)); |
|
268 |
} |
|
269 |
|
|
270 |
|
|
271 |
|
|
272 |
if (jaxbExpConfig.isDoMedia() == true) { |
|
273 |
if (mediaRows == 0) { mediaRows = MAX_ROWS; } |
|
274 |
logger.info("# Media"); |
|
275 |
dataSet.setMedia(getMediaService().list(null,mediaRows, 0,null,null)); |
|
276 |
// dataSet.addMedia(getMediaService().getAllMediaRepresentations(mediaRows, 0)); |
|
277 |
// dataSet.addMedia(getMediaService().getAllMediaRepresentationParts(mediaRows, 0)); |
|
278 |
} |
|
279 |
|
|
280 |
if (jaxbExpConfig.isDoFeatureData() == true) { |
|
281 |
if (featureDataRows == 0) { featureDataRows = MAX_ROWS; } |
|
282 |
logger.info("# Feature Tree, Feature Node"); |
|
283 |
List<FeatureTree> featureTrees = new ArrayList<FeatureTree>(); |
|
284 |
featureTrees= getFeatureTreeService().list(null,featureDataRows, 0, null, null); |
|
285 |
List<FeatureTree> taxTreesdeproxy = new ArrayList<FeatureTree>(); |
|
286 |
for (FeatureTree featureTree : featureTrees){ |
|
287 |
HibernateProxyHelper.deproxy(featureTree); |
|
288 |
taxTreesdeproxy.add(featureTree); |
|
289 |
} |
|
290 |
|
|
291 |
dataSet.setFeatureTrees(getFeatureTreeService().list(null,null,null,null,null)); |
|
292 |
} |
|
293 |
if (jaxbExpConfig.isDoClassificationData() == true) { |
|
294 |
if (classificationDataRows == 0) { classificationDataRows = MAX_ROWS; } |
|
295 |
logger.info("# Classification"); |
|
296 |
|
|
297 |
|
|
298 |
List<Classification> taxTrees = new ArrayList<Classification>(); |
|
299 |
taxTrees= getClassificationService().list(null,classificationDataRows, 0, null, null); |
|
300 |
|
|
301 |
List<Classification> taxTreesdeproxy = new ArrayList<Classification>(); |
|
302 |
for (Classification taxTree : taxTrees){ |
|
303 |
HibernateProxyHelper.deproxy(taxTree); |
|
304 |
taxTreesdeproxy.add(taxTree); |
|
305 |
} |
|
306 |
List<TaxonNode> taxNodes = new ArrayList<TaxonNode>(); |
|
307 |
taxNodes= getClassificationService().getAllNodes(); |
|
308 |
List<TaxonNode> taxNodesdeproxy = new ArrayList<TaxonNode>(); |
|
309 |
for (TaxonNode taxNode : taxNodes){ |
|
310 |
HibernateProxyHelper.deproxy(taxNode); |
|
311 |
taxNodesdeproxy.add(taxNode); |
|
312 |
} |
|
313 |
|
|
314 |
dataSet.setTaxonNodes(taxNodesdeproxy); |
|
315 |
dataSet.setClassifications(taxTreesdeproxy ); |
|
316 |
} |
|
317 |
//TODO: FIXME!!!!! |
|
318 |
dataSet.setLanguageStrings(null); |
|
319 |
} |
|
320 |
|
|
321 |
|
|
322 |
@Override |
|
323 |
protected boolean doCheck(JaxbExportState state) { |
|
324 |
boolean result = true; |
|
325 |
logger.warn("No check implemented for Jaxb export"); |
|
326 |
return result; |
|
327 |
} |
|
328 |
|
|
329 |
|
|
330 |
@Override |
|
331 |
protected boolean isIgnore(JaxbExportState state) { |
|
332 |
return false; |
|
333 |
} |
|
334 |
|
|
335 |
} |
Also available in: Unified diff
Fix CCE in DefinedTermDaoImpl.getPartOf (#5556) and make deproxy more
generic