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

   1 /**
   2 * Copyright (C) 2009 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9 package eu.etaxonomy.cdm.app.sdd;
  10
  11 import java.io.File;
  12 import java.net.MalformedURLException;
  13 import java.sql.SQLException;
  14
  15 import org.apache.log4j.Logger;
  16 import org.springframework.util.Assert;
  17
  18 import eu.etaxonomy.cdm.common.CdmUtils;
  19 import eu.etaxonomy.cdm.database.CdmDataSource;
  20 import eu.etaxonomy.cdm.database.CdmPersistentDataSource;
  21 import eu.etaxonomy.cdm.database.DataSourceNotFoundException;
  22 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  23 import eu.etaxonomy.cdm.database.ICdmDataSource;
  24 import eu.etaxonomy.cdm.io.common.CdmDefaultExport;
  25 import eu.etaxonomy.cdm.io.common.IExportConfigurator.DO_REFERENCES;
  26 import eu.etaxonomy.cdm.io.sdd.out.SDDExportConfigurator;
  27 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  28
  29 /**
  30  * @author l.morris
  31  * @date 29 Nov 2012
  32  *
  33  */
  34 public class SDDExportActivator {
  35
  36         /* SerializeFrom DB **/
  37         private static final String sourceDbName = "cdm";
  38         //private static final String destinationFileName = "ViolaFromCDM.xml";
  39         //private static final String destinationFolder = "/Developer/exports SDD";
  40         //private static final String destinationFolder = "C:/tmp/viola/exports_SDD";
  41
  42         /** NUMBER_ROWS_TO_RETRIEVE = 0 is the default case to retrieve all rows.
  43          * For testing purposes: If NUMBER_ROWS_TO_RETRIEVE >0 then retrieve
  44          *  as many rows as specified for agents, references, etc.
  45          *  Only root taxa and no synonyms and relationships are retrieved. */
  46         private static final int NUMBER_ROWS_TO_RETRIEVE = 0;
  47
  48         private static final String server = "134.157.190.207";
  49         private static final String username = "sa";
  50
  51         public static ICdmDataSource CDM_DB(String dbname) {
  52
  53                 logger.info("Setting DB " + dbname);
  54                 ICdmDataSource datasource = CdmDataSource.NewH2EmbeddedInstance(dbname, username, "");
  55                 return datasource;
  56         }
  57
  58     private static ICdmDataSource customDataSource() {
  59
  60         CdmPersistentDataSource loadedDataSource = null;
  61        //ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("192.168.2.10", "cdm_test_niels2", 3306, "edit", password, code);
  62
  63        String dataSourceName = CdmUtils.readInputLine("Database name: ");
  64        String username = CdmUtils.readInputLine("Username: ");
  65        String password = CdmUtils.readInputLine("Password: ");
  66
  67        dataSourceName = (dataSourceName.equals("")) ? "cdm_test3" : dataSourceName;
  68        username = (username.equals("")) ? "ljm" : username;
  69
  70        //ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("127.0.0.1", "cdm_test3", 3306, "ljm", password, NomenclaturalCode.ICBN);
  71        ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("127.0.0.1", dataSourceName, 3306, username, password, NomenclaturalCode.ICNAFP);
  72        //ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("127.0.0.1", "cdm_edit_cichorieae", 3306, "ljm", password, NomenclaturalCode.ICBN);
  73        //ICdmDataSource dataSource =
  74        CdmDataSource.NewMySqlInstance("160.45.63.201", "cdm_edit_cichorieae", 3306, "edit", password, NomenclaturalCode.ICNAFP);
  75        boolean connectionAvailable;
  76        try {
  77            connectionAvailable = dataSource.testConnection();
  78            System.out.println("LORNA connection available " + connectionAvailable);
  79            Assert.isTrue(connectionAvailable, "Testdatabase is not available");
  80
  81        } catch (ClassNotFoundException e1) {
  82            // TODO Auto-generated catch block
  83            e1.printStackTrace();
  84        } catch (SQLException e1) {
  85            // TODO Auto-generated catch block
  86            e1.printStackTrace();
  87        }
  88
  89        CdmPersistentDataSource.save(dataSourceName, dataSource);
  90        try {
  91            loadedDataSource = CdmPersistentDataSource.NewInstance(dataSourceName);
  92 //                      CdmApplicationController.NewInstance(loadedDataSource, DbSchemaValidation.CREATE);
  93            NomenclaturalCode loadedCode = loadedDataSource.getNomenclaturalCode();
  94
  95            Assert.isTrue(NomenclaturalCode.ICNAFP.equals(loadedCode));
  96        } catch (DataSourceNotFoundException e) {
  97            // TODO Auto-generated catch block
  98            e.printStackTrace();
  99        }
 100        //return loadedDataSource;
 101        return dataSource;
 102    }
 103
 104
 105
 106         private static final Logger logger = Logger.getLogger(ViolaExportActivator.class);
 107
 108         //private static final ICdmDataSource sourceDb = ViolaExportActivator.CDM_DB(sourceDbName);
 109         private static final ICdmDataSource sourceDb = customDataSource();
 110         //private static final File destinationFile = new File(destinationFolder + File.separator + destinationFileName);
 111
 112         private static boolean doAgents = true;
 113         private static boolean doAgentData = true;
 114         private static boolean doLanguageData = true;
 115         private static boolean doFeatureData = true;
 116         private static boolean doDescriptions = true;
 117         private static boolean doMedia = true;
 118         private static boolean doOccurrences = true;
 119         //private static boolean doReferences = true;
 120         private static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
 121     private static boolean doReferencedEntities = true;
 122         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
 123         private static boolean doSynonyms = true;
 124         private static boolean doTaxonNames = true;
 125         private static boolean doTaxa = true;
 126         private static boolean doTerms = true;
 127         private static boolean doTermVocabularies = true;
 128         private static boolean doHomotypicalGroups = true;//try export again
 129
 130         private void invokeExport() {
 131
 132         // export data
 133         //String exporturlStr = "/sdd/SDDImportExportTest.sdd.xml";
 134         String exporturlStr = "SDDImportExportTest.sdd.xml";
 135         File f = new File(exporturlStr);
 136         try {
 137                         exporturlStr = f.toURI().toURL().toString();
 138                 } catch (MalformedURLException e) {
 139                         // TODO Auto-generated catch block
 140                         e.printStackTrace();
 141                 }
 142
 143                 //lorna//SDDExportConfigurator sddExportConfigurator =
 144                         //SDDExportConfigurator.NewInstance(sourceDb, destinationFileName, destinationFolder);
 145
 146                 SDDExportConfigurator sddExportConfigurator =
 147                                 SDDExportConfigurator.NewInstance(sourceDb, exporturlStr);
 148
 149
 150                 CdmDefaultExport<SDDExportConfigurator> sddExport =
 151                         new CdmDefaultExport<SDDExportConfigurator>();
 152
 153                 sddExportConfigurator.setSource(sourceDb);
 154                 //lorna//sddExportConfigurator.setDestination(destinationFile);
 155                 sddExportConfigurator.setDbSchemaValidation(DbSchemaValidation.VALIDATE);
 156
 157                 sddExportConfigurator.setMaxRows(NUMBER_ROWS_TO_RETRIEVE);
 158
 159                 sddExportConfigurator.setDoAuthors(doAgents);
 160                 sddExportConfigurator.setDoAgentData(doAgentData);
 161                 sddExportConfigurator.setDoLanguageData(doLanguageData);
 162                 sddExportConfigurator.setDoFeatureData(doFeatureData);
 163                 sddExportConfigurator.setDoDescriptions(doDescriptions);
 164                 sddExportConfigurator.setDoMedia(doMedia);
 165                 sddExportConfigurator.setDoOccurrence(doOccurrences);
 166                 sddExportConfigurator.setDoReferences(doReferences);
 167                 sddExportConfigurator.setDoReferencedEntities(doReferencedEntities);
 168                 sddExportConfigurator.setDoRelTaxa(doRelationships);
 169                 sddExportConfigurator.setDoSynonyms(doSynonyms);
 170                 sddExportConfigurator.setDoTaxonNames(doTaxonNames);
 171                 sddExportConfigurator.setDoTaxa(doTaxa);
 172                 sddExportConfigurator.setDoTerms(doTerms);
 173                 sddExportConfigurator.setDoTermVocabularies(doTermVocabularies);
 174                 sddExportConfigurator.setDoHomotypicalGroups(doHomotypicalGroups);
 175
 176                 // invoke export
 177                 logger.debug("Invoking SDD export");
 178                 sddExport.invoke(sddExportConfigurator);
 179
 180         }
 181
 182         /**
 183          * @param args
 184          */
 185         public static void main(String[] args) {
 186
 187                 SDDExportActivator sddex = new SDDExportActivator();
 188
 189                 sddex.invokeExport();
 190
 191         }
 192
 193 }