EDIT

app-import/src/main/java/eu/etaxonomy/cdm/app/sdd/SDDExportActivator.java -text

// $Id$

/**

* Copyright (C) 2009 EDIT

* European Distributed Institute of Taxonomy 

* http://www.e-taxonomy.eu

* 

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.app.sdd;

import java.io.File;

import java.net.MalformedURLException;

import java.sql.SQLException;

import junit.framework.Assert;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.database.CdmDataSource;

import eu.etaxonomy.cdm.database.CdmPersistentDataSource;

import eu.etaxonomy.cdm.database.DataSourceNotFoundException;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.io.common.CdmDefaultExport;

import eu.etaxonomy.cdm.io.common.IExportConfigurator.DO_REFERENCES;

import eu.etaxonomy.cdm.io.sdd.out.SDDExportConfigurator;

import eu.etaxonomy.cdm.model.name.NomenclaturalCode;

/**

 * @author l.morris

 * @date 29 Nov 2012

 *

 */

public class SDDExportActivator {

	/* SerializeFrom DB **/

	private static final String sourceDbName = "cdm";

	//private static final String destinationFileName = "ViolaFromCDM.xml";

	//private static final String destinationFolder = "/Developer/exports SDD";

	//private static final String destinationFolder = "C:/tmp/viola/exports_SDD";

	/** NUMBER_ROWS_TO_RETRIEVE = 0 is the default case to retrieve all rows.

	 * For testing purposes: If NUMBER_ROWS_TO_RETRIEVE >0 then retrieve 

	 *  as many rows as specified for agents, references, etc. 

	 *  Only root taxa and no synonyms and relationships are retrieved. */

	private static final int NUMBER_ROWS_TO_RETRIEVE = 0;

	private static final String server = "134.157.190.207";

	private static final String username = "sa";

	public static ICdmDataSource CDM_DB(String dbname) {

		logger.info("Setting DB " + dbname);

		ICdmDataSource datasource = CdmDataSource.NewH2EmbeddedInstance(dbname, username, "");

		return datasource;

	}

    private static ICdmDataSource customDataSource() {

        CdmPersistentDataSource loadedDataSource = null;

       //ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("192.168.2.10", "cdm_test_niels2", 3306, "edit", password, code);

       String dataSourceName = CdmUtils.readInputLine("Database name: ");

       String username = CdmUtils.readInputLine("Username: ");

       String password = CdmUtils.readInputLine("Password: ");

       dataSourceName = (dataSourceName.equals("")) ? "cdm_test3" : dataSourceName;

       username = (username.equals("")) ? "ljm" : username;

       //ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("127.0.0.1", "cdm_test3", 3306, "ljm", password, NomenclaturalCode.ICBN);

       ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("127.0.0.1", dataSourceName, 3306, username, password, NomenclaturalCode.ICBN);

       //ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("127.0.0.1", "cdm_edit_cichorieae", 3306, "ljm", password, NomenclaturalCode.ICBN);

       //ICdmDataSource dataSource = 

       CdmDataSource.NewMySqlInstance("160.45.63.201", "cdm_edit_cichorieae", 3306, "edit", password, NomenclaturalCode.ICBN);

       boolean connectionAvailable;

       try {

           connectionAvailable = dataSource.testConnection();

           System.out.println("LORNA connection available " + connectionAvailable);

           Assert.assertTrue("Testdatabase is not available", connectionAvailable);

       } catch (ClassNotFoundException e1) {

           // TODO Auto-generated catch block

           e1.printStackTrace();

       } catch (SQLException e1) {

           // TODO Auto-generated catch block

           e1.printStackTrace();

       }

       CdmPersistentDataSource.save(dataSourceName, dataSource);

       try {

           loadedDataSource = CdmPersistentDataSource.NewInstance(dataSourceName);

//			CdmApplicationController.NewInstance(loadedDataSource, DbSchemaValidation.CREATE);

           NomenclaturalCode loadedCode = loadedDataSource.getNomenclaturalCode();

           Assert.assertEquals(NomenclaturalCode.ICBN, loadedCode);

       } catch (DataSourceNotFoundException e) {

           // TODO Auto-generated catch block

           e.printStackTrace();

       }

       //return loadedDataSource;

       return dataSource;

   }

	private static final Logger logger = Logger.getLogger(ViolaExportActivator.class);

	//private static final ICdmDataSource sourceDb = ViolaExportActivator.CDM_DB(sourceDbName);

	private static final ICdmDataSource sourceDb = customDataSource();

	//private static final File destinationFile = new File(destinationFolder + File.separator + destinationFileName);

	private static boolean doAgents = true;

	private static boolean doAgentData = true;

	private static boolean doLanguageData = true;

	private static boolean doFeatureData = true;

	private static boolean doDescriptions = true;

	private static boolean doMedia = true;

	private static boolean doOccurrences = true;

	//private static boolean doReferences = true;

	private static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;

    private static boolean doReferencedEntities = true;

	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

	private static boolean doSynonyms = true;

	private static boolean doTaxonNames = true;

	private static boolean doTaxa = true;

	private static boolean doTerms = true;

	private static boolean doTermVocabularies = true;

	private static boolean doHomotypicalGroups = true;//try export again

	private void invokeExport() {

        // export data

        //String exporturlStr = "/sdd/SDDImportExportTest.sdd.xml";

        String exporturlStr = "SDDImportExportTest.sdd.xml";

        File f = new File(exporturlStr);

        try {

			exporturlStr = f.toURI().toURL().toString();

		} catch (MalformedURLException e) {

			// TODO Auto-generated catch block

			e.printStackTrace();

		}

		//lorna//SDDExportConfigurator sddExportConfigurator = 

			//SDDExportConfigurator.NewInstance(sourceDb, destinationFileName, destinationFolder);

		SDDExportConfigurator sddExportConfigurator = 

				SDDExportConfigurator.NewInstance(sourceDb, exporturlStr);

		CdmDefaultExport<SDDExportConfigurator> sddExport = 

			new CdmDefaultExport<SDDExportConfigurator>();

		sddExportConfigurator.setSource(sourceDb);

		//lorna//sddExportConfigurator.setDestination(destinationFile);

		sddExportConfigurator.setDbSchemaValidation(DbSchemaValidation.VALIDATE);

		sddExportConfigurator.setMaxRows(NUMBER_ROWS_TO_RETRIEVE);

		sddExportConfigurator.setDoAuthors(doAgents);

		sddExportConfigurator.setDoAgentData(doAgentData);

		sddExportConfigurator.setDoLanguageData(doLanguageData);

		sddExportConfigurator.setDoFeatureData(doFeatureData);

		sddExportConfigurator.setDoDescriptions(doDescriptions);

		sddExportConfigurator.setDoMedia(doMedia);

		sddExportConfigurator.setDoOccurrence(doOccurrences);

		sddExportConfigurator.setDoReferences(doReferences);

		sddExportConfigurator.setDoReferencedEntities(doReferencedEntities);

		sddExportConfigurator.setDoRelTaxa(doRelationships);

		sddExportConfigurator.setDoSynonyms(doSynonyms);

		sddExportConfigurator.setDoTaxonNames(doTaxonNames);

		sddExportConfigurator.setDoTaxa(doTaxa);

		sddExportConfigurator.setDoTerms(doTerms);

		sddExportConfigurator.setDoTermVocabularies(doTermVocabularies);

		sddExportConfigurator.setDoHomotypicalGroups(doHomotypicalGroups);

		// invoke export

		logger.debug("Invoking SDD export");

		sddExport.invoke(sddExportConfigurator);

	}

	/**

	 * @param args

	 */

	public static void main(String[] args) {

		SDDExportActivator sddex = new SDDExportActivator();

		sddex.invokeExport();

	}

}

import java.net.URL;

import java.sql.SQLException;

import junit.framework.Assert;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.database.CdmDataSource;

import eu.etaxonomy.cdm.database.CdmPersistentDataSource;

import eu.etaxonomy.cdm.database.DataSourceNotFoundException;

import eu.etaxonomy.cdm.model.name.NomenclaturalCode;

 * @author l.morris

    private static ICdmDataSource customDataSource() {

        CdmPersistentDataSource loadedDataSource = null;

       //ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("192.168.2.10", "cdm_test_niels2", 3306, "edit", password, code);

       String dataSourceName = CdmUtils.readInputLine("Database name: ");

       String username = CdmUtils.readInputLine("Username: ");

       String password = CdmUtils.readInputLine("Password: ");

       dataSourceName = (dataSourceName.equals("")) ? "cdm_test4" : dataSourceName;

       username = (username.equals("")) ? "ljm" : username;

       ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("127.0.0.1", dataSourceName, 3306, username, password, NomenclaturalCode.ICBN);

       //ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("127.0.0.1", "cdm_edit_cichorieae", 3306, "ljm", password, NomenclaturalCode.ICBN);

       //ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("160.45.63.201", "cdm_edit_cichorieae", 3306, "edit", password, NomenclaturalCode.ICBN);

       boolean connectionAvailable;

       try {

           connectionAvailable = dataSource.testConnection();

           logger.debug("LORNA connection avaiable " + connectionAvailable);

           Assert.assertTrue("Testdatabase is not available", connectionAvailable);

       } catch (ClassNotFoundException e1) {

           // TODO Auto-generated catch block

           e1.printStackTrace();

       } catch (SQLException e1) {

           // TODO Auto-generated catch block

           e1.printStackTrace();

       }

       CdmPersistentDataSource.save(dataSourceName, dataSource);

       try {

           loadedDataSource = CdmPersistentDataSource.NewInstance(dataSourceName);

//			CdmApplicationController.NewInstance(loadedDataSource, DbSchemaValidation.CREATE);

           NomenclaturalCode loadedCode = loadedDataSource.getNomenclaturalCode();

           Assert.assertEquals(NomenclaturalCode.ICBN, loadedCode);

       } catch (DataSourceNotFoundException e) {

           // TODO Auto-generated catch block

           e.printStackTrace();

       }

       //return loadedDataSource;

       return dataSource;

   }

		//String sddSource = SDDSources.SDDImport_local(args[0]+args[1]);

		//System.out.println("Start import from SDD("+ sddSource.toString() + ") ...");

			//source = new URI(sddSource);

	        //URL url = SDDImportActivator.class.getResource("/eu/etaxonomy/cdm/io/sdd/SDDImportTest-input3.xml");

	        //URL url = SDDImportActivator.class.getResource("/eu/etaxonomy/cdm/app/sdd/SDDImportTest-input3.xml"); //eu.etaxonomy.cdm.app.sdd;

	        //URL url = SDDImportActivator.class.getResource("/sdd/SDD-Test-Simple.xml");

	        URL url = SDDImportActivator.class.getResource("/sdd/ant.sdd.xml");

	        //sdd/SDD-Test-Simple.xml

	        System.out.println("url"+ url);

	        source = url.toURI();

			//source = new URI("/eu/etaxonomy/cdm/app/sdd/SDDImportTest-input3.xml");

			System.out.println("Start import from SDD("+ source.toString() + ") ...");

			//lorna//ICdmDataSource destination = CdmDestinations.localH2(args[3],"sa",args[2]);

			ICdmDataSource destination = customDataSource();

			///sddImportConfigurator.setSourceSecId(sourceSecId);

			///sddImportConfigurator.setCheck(check);

			///sddImportConfigurator.setDbSchemaValidation(hbm2dll);