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