app-import/src/main/java/eu/etaxonomy/cdm/app/viennaImport/ViennaActivator.java

   1 /**
   2 * Copyright (C) 2007 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
  10 package eu.etaxonomy.cdm.app.viennaImport;
  11
  12 import java.net.URI;
  13 import java.net.URISyntaxException;
  14 import java.sql.ResultSet;
  15 import java.sql.SQLException;
  16 import java.util.List;
  17
  18 import org.apache.log4j.Logger;
  19
  20 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  21 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  22 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  23 import eu.etaxonomy.cdm.common.AccountStore;
  24 import eu.etaxonomy.cdm.common.CdmUtils;
  25 import eu.etaxonomy.cdm.io.common.Source;
  26 import eu.etaxonomy.cdm.model.agent.Person;
  27 import eu.etaxonomy.cdm.model.common.Annotation;
  28 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  29 import eu.etaxonomy.cdm.model.media.ImageFile;
  30 import eu.etaxonomy.cdm.model.media.Media;
  31 import eu.etaxonomy.cdm.model.name.INonViralName;
  32 import eu.etaxonomy.cdm.model.name.TaxonName;
  33 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  34 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  35 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  36 import eu.etaxonomy.cdm.model.reference.Reference;
  37 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  38 import eu.etaxonomy.cdm.model.taxon.Taxon;
  39 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  40
  41 /**
  42  * @author AM
  43  * @since 08.05.2008
  44  * @version 1.0
  45  */
  46 public class ViennaActivator {
  47         private static final Logger logger = Logger.getLogger(ViennaActivator.class);
  48
  49         static final Source berlinModelSource = ViennaActivator.VIENNA();
  50
  51
  52         public static Source VIENNA(){
  53                 //      Vienna Asteraceae
  54                 String dbms = "ODBC";
  55                 String strServer = "AsteraceaeViennaAccess";
  56                 String strDB = "AsteraceaeViennaAccess";
  57                 String userName = "webUser";
  58                 return  makeSource(dbms, strServer, strDB, -1, userName, null);
  59         }
  60
  61         public boolean invoke(){
  62                 boolean result = true;
  63                 boolean withCdm = false;
  64                 berlinModelSource.setQuery("SELECT * FROM vienna"); // WHERE ID1 <> 1
  65                 CdmApplicationController app = null;
  66
  67
  68                 try {
  69                         if (withCdm){
  70                                 app = CdmApplicationController.NewInstance(CdmDestinations.localH2());
  71                         }else{
  72                                 //app = CdmApplicationController.NewInstance(DbSchemaValidation.VALIDATE);
  73                         }
  74                 } catch (Exception e1) {
  75                         e1.printStackTrace();
  76                         result = false;
  77                         return result;
  78                 }
  79
  80
  81                 ResultSet rs = berlinModelSource.getResultSet();
  82                 try {
  83                         while (rs.next()){
  84                                 String uriPath = "http://131.130.131.9/database/img/imgBrowser.php?ID=";
  85                                 int id = rs.getInt("ID");
  86                                 String strId = String.valueOf(id);
  87                                 String catalogNumber = rs.getString("catalogueNumber");
  88                                 String strTaxonName = rs.getString("TaxonName");
  89                                 String annotation = rs.getString("Annotation");
  90                                 String typeInformation = rs.getString("TypeInformation");
  91                                 String typifiedBy = rs.getString("TypifiedBy");
  92                                 String family = rs.getString("Family");
  93                                 String strActor = rs.getString("Actor");
  94                                 String timePeriod = rs.getString("TimePeriod");
  95                                 String collectingArea = rs.getString("CollectingArea");
  96                                 String locality = rs.getString("Locality");
  97                                 String assigned = rs.getString("assigned");
  98                                 String history = rs.getString("history");
  99
 100                                 if (! family.equals("Asteraceae")){
 101                                         logger.warn("Family not Asteracea: ID= " + strId);
 102                                 }
 103                                 Reference sec = ReferenceFactory.newDatabase();
 104                                 sec.setTitleCache("Vienna Asteraceae Images", true);
 105
 106                                 INonViralName taxonName = NonViralNameParserImpl.NewInstance().parseFullName(strTaxonName);
 107                                 if (withCdm){
 108                                         List<TaxonName> names = app.getNameService().findByName(null, strTaxonName, null, null, null, null, null, null).getRecords();
 109                                         if (names.size() == 0){
 110                                                 logger.warn("Name not found: " + strTaxonName);
 111                                         }else{
 112                                                 if (names.size() > 1){
 113                                                         logger.warn("More then 1 name found: " + strTaxonName);
 114                                                 }
 115                                                 taxonName = names.get(0);
 116                                         }
 117                                 }
 118                                 Taxon taxon = Taxon.NewInstance(taxonName, sec);
 119
 120                                 logger.info("Create new specimen ...");
 121                                 DerivedUnit specimenx = DerivedUnit.NewPreservedSpecimenInstance();
 122                                 DerivedUnitFacade specimen = DerivedUnitFacade.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
 123
 124                                 specimen.setCatalogNumber(catalogNumber);
 125                                 specimen.setStoredUnder(TaxonName.castAndDeproxy(taxonName));   //??
 126                                 //TODO
 127                                 //specimen.setCollection(collection);
 128                                 specimen.addAnnotation(Annotation.NewDefaultLanguageInstance(annotation));
 129                                 specimen.addDetermination(getDetermination(taxon, strActor));
 130                                 specimen.addDerivedUnitMedia(getMedia(uriPath, strId));
 131
 132                                 //Original ID
 133                                 specimen.addSource(IdentifiableSource.NewDataImportInstance(strId));
 134
 135
 136                         }
 137                 } catch (SQLException e) {
 138                         logger.warn("Error when reading record!!");
 139                         e.printStackTrace();
 140                         result = false;
 141                 }
 142                 return result;
 143         }
 144
 145         private Media getMedia(String uriPath, String id){
 146                 //"http://131.130.131.9/database/img/imgBrowser.php?ID=50599";
 147                 String uriString = uriPath + id;
 148                 if (CdmUtils.urlExists(uriString, false)){
 149                         String suffix = "jpg";
 150                         String mimeType = "image/jpg";
 151                         URI uri = null;
 152                         try {
 153                                 uri = new URI(uriString);
 154                         } catch (URISyntaxException e) {
 155                                 e.printStackTrace();
 156                         }
 157                         Media media = ImageFile.NewMediaInstance(null, null, uri, mimeType, suffix,  null, null, null);
 158                         return media;
 159                 }else{
 160                         logger.warn("URI does not exist: " + uriString);
 161                         return null;
 162                 }
 163         }
 164
 165         private DeterminationEvent getDetermination(Taxon taxon, String actor){
 166                 logger.info("Create determination event");
 167                 DeterminationEvent determinationEvent = DeterminationEvent.NewInstance();
 168                 determinationEvent.setTaxon(taxon);
 169                 Person person = Person.NewTitledInstance(actor);
 170                 determinationEvent.setActor(person);
 171                 return determinationEvent;
 172         }
 173
 174
 175
 176         /**
 177          * @param args
 178          */
 179         public static void main(String[] args) {
 180                 ViennaActivator viennaAct = new ViennaActivator();
 181                 viennaAct.invoke();
 182         }
 183
 184
 185         /**
 186          * Initialises source
 187          * @return true, if connection established
 188          */
 189         private static Source makeSource(String dbms, String strServer, String strDB, int port, String userName, String pwd ){
 190                 //establish connection
 191                 pwd = AccountStore.readOrStorePassword(dbms, strServer, userName, pwd);
 192                 Source source = new Source(dbms, strServer, strDB);
 193                 source.setPort(port);
 194                 source.setUserAndPwd(userName, pwd);
 195                 return source;
 196         }
 197 }