app-import/src/main/java/eu/etaxonomy/cdm/app/cyprus/CyprusActivator.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.cyprus;
  11
  12 import java.net.URI;
  13 import java.net.URISyntaxException;
  14 import java.util.UUID;
  15
  16 import org.apache.log4j.Logger;
  17
  18 import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  19 import eu.etaxonomy.cdm.api.service.ITermService;
  20 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  21 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  22 import eu.etaxonomy.cdm.database.ICdmDataSource;
  23 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  24 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  25 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  26 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  27 import eu.etaxonomy.cdm.io.cyprus.CyprusImportConfigurator;
  28 import eu.etaxonomy.cdm.io.cyprus.CyprusTransformer;
  29 import eu.etaxonomy.cdm.model.agent.Person;
  30 import eu.etaxonomy.cdm.model.description.Feature;
  31 import eu.etaxonomy.cdm.model.description.FeatureNode;
  32 import eu.etaxonomy.cdm.model.description.FeatureTree;
  33 import eu.etaxonomy.cdm.model.reference.Reference;
  34 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  35
  36 /**
  37  * @author a.mueller
  38  * @created 16.12.2010
  39  */
  40 public class CyprusActivator {
  41         private static final Logger logger = Logger.getLogger(CyprusActivator.class);
  42
  43         //database validation status (create, update, validate ...)
  44         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  45 //      static final URI source = cyprus_distribution();
  46         static final URI source = cyprus_local();
  47
  48
  49         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  50 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest();
  51 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  52 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_dev();
  53 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_production();
  54
  55
  56         //feature tree uuid
  57         public static final UUID featureTreeUuid = UUID.fromString("14d1e912-5ec2-4d10-878b-828788b70a87");
  58
  59         //classification
  60         static final UUID classificationUuid = UUID.fromString("0c2b5d25-7b15-4401-8b51-dd4be0ee5cab");
  61
  62         //check - import
  63         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  64
  65         //taxa
  66         static final boolean doTaxa = true;
  67         static final boolean doDeduplicate = false;
  68         static final boolean doDistribution = false;
  69
  70
  71         private void doImport(ICdmDataSource cdmDestination){
  72
  73                 //make Source
  74                 CyprusImportConfigurator config= CyprusImportConfigurator.NewInstance(source, cdmDestination);
  75                 config.setClassificationUuid(classificationUuid);
  76                 config.setCheck(check);
  77                 config.setDoDistribution(doDistribution);
  78                 config.setDoTaxa(doTaxa);
  79                 config.setDbSchemaValidation(hbm2dll);
  80
  81                 CdmDefaultImport myImport = new CdmDefaultImport();
  82
  83
  84                 //...
  85                 if (true){
  86                         System.out.println("Start import from ("+ source.toString() + ") ...");
  87                         config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
  88                         myImport.invoke(config);
  89                         if (doTaxa){
  90                                 FeatureTree tree = makeFeatureNodes(myImport.getCdmAppController().getTermService());
  91                                 myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
  92                         }
  93
  94                         System.out.println("End import from ("+ source.toString() + ")...");
  95                 }
  96
  97
  98
  99                 //deduplicate
 100                 if (doDeduplicate){
 101                         ICdmApplicationConfiguration app = myImport.getCdmAppController();
 102                         int count = app.getAgentService().deduplicate(Person.class, null, null);
 103                         logger.warn("Deduplicated " + count + " persons.");
 104 //                      count = app.getAgentService().deduplicate(Team.class, null, null);
 105 //                      logger.warn("Deduplicated " + count + " teams.");
 106                         count = app.getReferenceService().deduplicate(Reference.class, null, null);
 107                         logger.warn("Deduplicated " + count + " references.");
 108                 }
 109
 110         }
 111
 112         private Reference getSourceReference(String string) {
 113                 Reference result = ReferenceFactory.newGeneric();
 114                 result.setTitleCache(string, true);
 115                 return result;
 116         }
 117
 118         private FeatureTree makeFeatureNodes(ITermService service){
 119                 CyprusTransformer transformer = new CyprusTransformer();
 120
 121                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 122                 result.setTitleCache("Cyprus Feature Tree", true);
 123                 FeatureNode root = result.getRoot();
 124                 FeatureNode newNode;
 125
 126                 newNode = FeatureNode.NewInstance(Feature.STATUS());
 127                 root.addChild(newNode);
 128
 129                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 130                 root.addChild(newNode);
 131
 132                 newNode = FeatureNode.NewInstance(Feature.SYSTEMATICS());
 133                 root.addChild(newNode);
 134
 135                 //user defined features
 136                 String [] featureList = new String[]{"Red Book", "Endemism"};
 137                 addFeataureNodesByStringList(featureList, root, transformer, service);
 138
 139                 return result;
 140         }
 141
 142
 143         //Cyprus
 144         public static URI cyprus_local() {
 145                 URI sourceUrl;
 146                 try {
 147                         sourceUrl = new URI("file:/C:/localCopy/Data/zypern/Zypern.xls");
 148                         return sourceUrl;
 149                 } catch (URISyntaxException e) {
 150                         e.printStackTrace();
 151                         return null;
 152                 }
 153         }
 154         //Cyprus distriution
 155         public static URI cyprus_distribution() {
 156                 URI sourceUrl;
 157                 try {
 158                         sourceUrl = new URI("file:/C:/localCopy/Data/zypern/Zypern_distribution_RH_corr.xls");
 159                         return sourceUrl;
 160                 } catch (URISyntaxException e) {
 161                         e.printStackTrace();
 162                         return null;
 163                 }
 164         }
 165
 166         public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 167                 try {
 168                         for (String featureString : featureStringList){
 169                         UUID featureUuid;
 170                         featureUuid = transformer.getFeatureUuid(featureString);
 171                         Feature feature = (Feature)termService.find(featureUuid);
 172                         if (feature != null){
 173                                 FeatureNode child = FeatureNode.NewInstance(feature);
 174                                 root.addChild(child);
 175                         }
 176                 }
 177                 } catch (UndefinedTransformerMethodException e) {
 178                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 179                 }
 180         }
 181
 182
 183         /**
 184          * @param args
 185          */
 186         public static void main(String[] args) {
 187                 CyprusActivator me = new CyprusActivator();
 188                 me.doImport(cdmDestination);
 189         }
 190
 191 }