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// $Id$
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/**
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* Copyright (C) 2009 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.sdd;
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import java.io.File;
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import java.net.MalformedURLException;
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import java.sql.SQLException;
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import junit.framework.Assert;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.database.CdmDataSource;
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import eu.etaxonomy.cdm.database.CdmPersistentDataSource;
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import eu.etaxonomy.cdm.database.DataSourceNotFoundException;
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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.CdmDefaultExport;
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import eu.etaxonomy.cdm.io.common.IExportConfigurator.DO_REFERENCES;
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import eu.etaxonomy.cdm.io.sdd.out.SDDExportConfigurator;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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/**
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* @author l.morris
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* @date 29 Nov 2012
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*
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*/
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public class SDDExportActivator {
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/* SerializeFrom DB **/
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private static final String sourceDbName = "cdm";
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//private static final String destinationFileName = "ViolaFromCDM.xml";
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//private static final String destinationFolder = "/Developer/exports SDD";
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//private static final String destinationFolder = "C:/tmp/viola/exports_SDD";
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/** NUMBER_ROWS_TO_RETRIEVE = 0 is the default case to retrieve all rows.
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* For testing purposes: If NUMBER_ROWS_TO_RETRIEVE >0 then retrieve
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* as many rows as specified for agents, references, etc.
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* Only root taxa and no synonyms and relationships are retrieved. */
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private static final int NUMBER_ROWS_TO_RETRIEVE = 0;
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private static final String server = "134.157.190.207";
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private static final String username = "sa";
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public static ICdmDataSource CDM_DB(String dbname) {
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logger.info("Setting DB " + dbname);
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ICdmDataSource datasource = CdmDataSource.NewH2EmbeddedInstance(dbname, username, "");
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return datasource;
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}
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private static ICdmDataSource customDataSource() {
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CdmPersistentDataSource loadedDataSource = null;
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//ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("192.168.2.10", "cdm_test_niels2", 3306, "edit", password, code);
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String dataSourceName = CdmUtils.readInputLine("Database name: ");
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String username = CdmUtils.readInputLine("Username: ");
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String password = CdmUtils.readInputLine("Password: ");
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dataSourceName = (dataSourceName.equals("")) ? "cdm_test3" : dataSourceName;
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username = (username.equals("")) ? "ljm" : username;
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//ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("127.0.0.1", "cdm_test3", 3306, "ljm", password, NomenclaturalCode.ICBN);
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ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("127.0.0.1", dataSourceName, 3306, username, password, NomenclaturalCode.ICBN);
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//ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("127.0.0.1", "cdm_edit_cichorieae", 3306, "ljm", password, NomenclaturalCode.ICBN);
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//ICdmDataSource dataSource =
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CdmDataSource.NewMySqlInstance("160.45.63.201", "cdm_edit_cichorieae", 3306, "edit", password, NomenclaturalCode.ICBN);
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boolean connectionAvailable;
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try {
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connectionAvailable = dataSource.testConnection();
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System.out.println("LORNA connection available " + connectionAvailable);
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Assert.assertTrue("Testdatabase is not available", connectionAvailable);
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} catch (ClassNotFoundException e1) {
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// TODO Auto-generated catch block
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e1.printStackTrace();
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} catch (SQLException e1) {
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// TODO Auto-generated catch block
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e1.printStackTrace();
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}
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CdmPersistentDataSource.save(dataSourceName, dataSource);
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try {
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loadedDataSource = CdmPersistentDataSource.NewInstance(dataSourceName);
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// CdmApplicationController.NewInstance(loadedDataSource, DbSchemaValidation.CREATE);
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NomenclaturalCode loadedCode = loadedDataSource.getNomenclaturalCode();
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Assert.assertEquals(NomenclaturalCode.ICBN, loadedCode);
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} catch (DataSourceNotFoundException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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}
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//return loadedDataSource;
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return dataSource;
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}
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private static final Logger logger = Logger.getLogger(ViolaExportActivator.class);
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//private static final ICdmDataSource sourceDb = ViolaExportActivator.CDM_DB(sourceDbName);
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private static final ICdmDataSource sourceDb = customDataSource();
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//private static final File destinationFile = new File(destinationFolder + File.separator + destinationFileName);
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private static boolean doAgents = true;
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private static boolean doAgentData = true;
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private static boolean doLanguageData = true;
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private static boolean doFeatureData = true;
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private static boolean doDescriptions = true;
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private static boolean doMedia = true;
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private static boolean doOccurrences = true;
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//private static boolean doReferences = true;
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private static final DO_REFERENCES doReferences = DO_REFERENCES.ALL;
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private static boolean doReferencedEntities = true;
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private static boolean doRelationships = false; //causes org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [eu.etaxonomy.cdm.model.taxon.Taxon#24563] in cichoriae
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private static boolean doSynonyms = true;
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private static boolean doTaxonNames = true;
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private static boolean doTaxa = true;
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private static boolean doTerms = true;
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private static boolean doTermVocabularies = true;
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private static boolean doHomotypicalGroups = true;//try export again
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private void invokeExport() {
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// export data
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//String exporturlStr = "/sdd/SDDImportExportTest.sdd.xml";
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String exporturlStr = "SDDImportExportTest.sdd.xml";
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File f = new File(exporturlStr);
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try {
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exporturlStr = f.toURI().toURL().toString();
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} catch (MalformedURLException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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}
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//lorna//SDDExportConfigurator sddExportConfigurator =
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//SDDExportConfigurator.NewInstance(sourceDb, destinationFileName, destinationFolder);
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SDDExportConfigurator sddExportConfigurator =
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SDDExportConfigurator.NewInstance(sourceDb, exporturlStr);
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CdmDefaultExport<SDDExportConfigurator> sddExport =
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new CdmDefaultExport<SDDExportConfigurator>();
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sddExportConfigurator.setSource(sourceDb);
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//lorna//sddExportConfigurator.setDestination(destinationFile);
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sddExportConfigurator.setDbSchemaValidation(DbSchemaValidation.VALIDATE);
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sddExportConfigurator.setMaxRows(NUMBER_ROWS_TO_RETRIEVE);
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sddExportConfigurator.setDoAuthors(doAgents);
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sddExportConfigurator.setDoAgentData(doAgentData);
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sddExportConfigurator.setDoLanguageData(doLanguageData);
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sddExportConfigurator.setDoFeatureData(doFeatureData);
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sddExportConfigurator.setDoDescriptions(doDescriptions);
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sddExportConfigurator.setDoMedia(doMedia);
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sddExportConfigurator.setDoOccurrence(doOccurrences);
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sddExportConfigurator.setDoReferences(doReferences);
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sddExportConfigurator.setDoReferencedEntities(doReferencedEntities);
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sddExportConfigurator.setDoRelTaxa(doRelationships);
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sddExportConfigurator.setDoSynonyms(doSynonyms);
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sddExportConfigurator.setDoTaxonNames(doTaxonNames);
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sddExportConfigurator.setDoTaxa(doTaxa);
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sddExportConfigurator.setDoTerms(doTerms);
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sddExportConfigurator.setDoTermVocabularies(doTermVocabularies);
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sddExportConfigurator.setDoHomotypicalGroups(doHomotypicalGroups);
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// invoke export
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logger.debug("Invoking SDD export");
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sddExport.invoke(sddExportConfigurator);
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}
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/**
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* @param args
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*/
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public static void main(String[] args) {
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SDDExportActivator sddex = new SDDExportActivator();
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sddex.invokeExport();
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}
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}
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