app-import/src/main/java/eu/etaxonomy/cdm/app/dwca/DwcaImportActivator.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.dwca;
  11
  12 import java.net.URI;
  13 import java.util.UUID;
  14
  15 import org.apache.log4j.Logger;
  16
  17 import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  18 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  19 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  20 import eu.etaxonomy.cdm.database.ICdmDataSource;
  21 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  22 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  23 import eu.etaxonomy.cdm.io.common.events.LoggingIoObserver;
  24 import eu.etaxonomy.cdm.io.dwca.in.DwcaImportConfigurator;
  25 import eu.etaxonomy.cdm.io.dwca.in.DwcaImportConfigurator.DatasetUse;
  26 import eu.etaxonomy.cdm.io.dwca.in.IImportMapping.MappingType;
  27 import eu.etaxonomy.cdm.model.agent.Person;
  28 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  29 import eu.etaxonomy.cdm.model.reference.Reference;
  30 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  31
  32 /**
  33  * @author a.mueller
  34  * @created 10.11.2011
  35  */
  36 public class DwcaImportActivator {
  37         private static final Logger logger = Logger.getLogger(DwcaImportActivator.class);
  38
  39         //database validation status (create, update, validate ...)
  40         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  41 //      static final URI source = dwca_test_in();
  42 //      static final URI source = dwca_test_cich_len();
  43 //      static final URI source = dwca_test_col_sapindaceae();
  44 //      static final URI source = dwca_test_col_cichorium();
  45 //      static final URI source = dwca_test_scratch_test();
  46 //      static final URI source = dwca_test_col_All();
  47 //      static final URI source = dwca_test_col_All_Pesi2();
  48         static final URI source =  dwca_import_emonocots();
  49
  50
  51         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  52 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_dwca();
  53 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
  54 //      static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  55 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_pesi_test();
  56 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_pesi();
  57 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  58
  59
  60
  61         //classification
  62         static final UUID classificationUuid = UUID.fromString("29d4011f-a6dd-4081-beb8-559ba6b84a6b");
  63
  64         //default nom code is ICZN as it allows adding publication year
  65         static final NomenclaturalCode defaultNomCode = NomenclaturalCode.ICZN;
  66
  67
  68         //check - import
  69         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  70         static int partitionSize = 1000;
  71
  72         //config
  73         static DatasetUse datasetUse = DatasetUse.SECUNDUM;
  74         static boolean scientificNameIdAsOriginalSourceId = true;
  75         static boolean guessNomRef = true;
  76         private boolean handleAllRefsAsCitation = true;
  77
  78         //validate
  79         static boolean validateRankConsistency = false;
  80
  81
  82         //taxa
  83         static final boolean doTaxa = true;
  84         static final boolean doDistribution = false;
  85         //deduplicate
  86         static final boolean doDeduplicate = false;
  87
  88
  89
  90         static final MappingType mappingType = MappingType.InMemoryMapping;
  91
  92         private void doImport(ICdmDataSource cdmDestination){
  93
  94                 //make Source
  95                 DwcaImportConfigurator config= DwcaImportConfigurator.NewInstance(source, cdmDestination);
  96                 config.addObserver(new LoggingIoObserver());
  97                 config.setClassificationUuid(classificationUuid);
  98                 config.setCheck(check);
  99                 config.setDbSchemaValidation(hbm2dll);
 100                 config.setMappingType(mappingType);
 101
 102                 config.setScientificNameIdAsOriginalSourceId(scientificNameIdAsOriginalSourceId);
 103                 config.setValidateRankConsistency(validateRankConsistency);
 104                 config.setDefaultPartitionSize(partitionSize);
 105                 config.setNomenclaturalCode(defaultNomCode);
 106                 config.setDatasetUse(datasetUse);
 107                 config.setGuessNomenclaturalReferences(guessNomRef);
 108                 config.setHandleAllRefsAsCitation(handleAllRefsAsCitation);
 109
 110                 CdmDefaultImport myImport = new CdmDefaultImport();
 111
 112
 113                 //...
 114                 if (true){
 115                         System.out.println("Start import from ("+ source.toString() + ") ...");
 116                         config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
 117                         myImport.invoke(config);
 118                         System.out.println("End import from ("+ source.toString() + ")...");
 119                 }
 120
 121
 122
 123                 //deduplicate
 124                 if (doDeduplicate){
 125                         ICdmApplicationConfiguration app = myImport.getCdmAppController();
 126                         int count = app.getAgentService().deduplicate(Person.class, null, null);
 127                         logger.warn("Deduplicated " + count + " persons.");
 128 //                      count = app.getAgentService().deduplicate(Team.class, null, null);
 129 //                      logger.warn("Deduplicated " + count + " teams.");
 130                         count = app.getReferenceService().deduplicate(Reference.class, null, null);
 131                         logger.warn("Deduplicated " + count + " references.");
 132                 }
 133
 134         }
 135
 136         private Reference<?> getSourceReference(String string) {
 137                 Reference<?> result = ReferenceFactory.newGeneric();
 138                 result.setTitleCache(string);
 139                 return result;
 140         }
 141
 142         //Dwca
 143         public static URI dwca_test_in() {
 144 //              URI sourceUrl = URI.create("http://dev.e-taxonomy.eu/trac/export/14463/trunk/cdmlib/cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/dwca/in/DwcaZipToStreamConverterTest-input.zip");
 145                 URI sourceUrl = URI.create("file:///C:/Users/pesiimport/Documents/pesi_cdmlib/cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/dwca/in/DwcaZipToStreamConverterTest-input.zip");
 146                 return sourceUrl;
 147         }
 148
 149
 150         //Dwca
 151         public static URI dwca_test_cich() {
 152                 URI sourceUrl = URI.create("file:///E:/opt/data/dwca/20110621_1400_cichorieae_dwca.zip");
 153                 return sourceUrl;
 154         }
 155
 156         //Dwca
 157         public static URI dwca_test_cich_len() {
 158                 URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/export/20110621_1400_cichorieae_dwca.zip");
 159                 return sourceUrl;
 160         }
 161
 162         //Dwca
 163         public static URI dwca_test_col_cichorium() {
 164                 URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/CoL/Cichorium/archive-genus-Cichorium-bl3.zip");
 165                 return sourceUrl;
 166         }
 167
 168         //Dwca
 169         public static URI dwca_test_col_sapindaceae() {
 170                 URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/CoL/Sapindaceae/archive-family-Sapindaceae-bl3.zip");
 171                 return sourceUrl;
 172         }
 173
 174         //Dwca
 175         public static URI dwca_import_emonocots() {
 176                 URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/Scratchpads/dwca_dioscoreaceae_emonocots.zip");
 177                 return sourceUrl;
 178         }
 179
 180         //CoL
 181         public static URI dwca_test_col_All() {
 182                 URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/CoL/All/archive-complete.zip");
 183                 return sourceUrl;
 184         }
 185
 186         //CoL
 187         public static URI dwca_test_col_All_Pesi2() {
 188                 URI sourceUrl = URI.create("file:///C:/opt/data/CoL/All/archive-complete.zip");
 189                 return sourceUrl;
 190         }
 191
 192         //Scratchpads test
 193         public static URI dwca_test_scratch_test() {
 194                 URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_export_scratchpads_test.zip");
 195                 return sourceUrl;
 196         }
 197
 198
 199         /**
 200          * @param args
 201          */
 202         public static void main(String[] args) {
 203                 DwcaImportActivator me = new DwcaImportActivator();
 204                 me.doImport(cdmDestination);
 205         }
 206
 207 }