app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/DwcaScratchpadImportActivator.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.vibrant;
  11
  12 import java.net.URI;
  13 import java.util.UUID;
  14
  15 import org.apache.log4j.Logger;
  16
  17 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  18 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  19 import eu.etaxonomy.cdm.database.ICdmDataSource;
  20 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  21 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  22 import eu.etaxonomy.cdm.io.common.events.LoggingIoObserver;
  23 import eu.etaxonomy.cdm.io.dwca.in.DwcaDataImportConfiguratorBase.DatasetUse;
  24 import eu.etaxonomy.cdm.io.dwca.in.DwcaImportConfigurator;
  25 import eu.etaxonomy.cdm.io.dwca.in.IImportMapping.MappingType;
  26 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  27 import eu.etaxonomy.cdm.model.reference.Reference;
  28 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  29
  30 /**
  31  * @author a.mueller
  32  * @created 03.04.2012
  33  * @version 1.0
  34  */
  35 public class DwcaScratchpadImportActivator {
  36         @SuppressWarnings("unused")
  37         private static final Logger logger = Logger.getLogger(DwcaScratchpadImportActivator.class);
  38
  39         //database validation status (create, update, validate ...)
  40         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  41
  42         //      static final URI source =  dwca_emonocots_dioscoreaceae();
  43 //      static final URI source =  dwca_emonocots_zingiberaceae();
  44         //static final URI source =  dwca_emonocots_cypripedioideae();
  45         static final URI source =  dwca_emonocots_dioscoreaceae();
  46
  47
  48 //      static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  49         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  50 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
  51
  52         //default nom code is ICZN as it allows adding publication year
  53         static final NomenclaturalCode defaultNomCode = NomenclaturalCode.ICBN;
  54
  55         //title
  56         static final String title = "Scratchpad test import";
  57
  58         //check - import
  59         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  60         static int partitionSize = 1000;
  61
  62         //config
  63         static DatasetUse datasetUse = DatasetUse.CLASSIFICATION;
  64
  65         //validate
  66         static boolean validateRankConsistency = false;
  67
  68
  69         //taxa
  70         static final boolean doTaxa = true;
  71         static final boolean doDistribution = true;
  72
  73
  74
  75         static final MappingType mappingType = MappingType.InMemoryMapping;
  76
  77         //classification
  78         static final UUID classificationUuid = UUID.fromString("d9d199b6-eaf4-47c8-a732-0639bc445c56");
  79
  80
  81         //config
  82         static boolean scientificNameIdAsOriginalSourceId = true;
  83         static boolean guessNomRef = false;
  84         private boolean handleAllRefsAsCitation = false;
  85         private static final boolean useSourceReferenceAsSec = true;
  86
  87
  88         //deduplicate
  89         static final boolean doDeduplicate = false;
  90
  91
  92
  93         protected void doImport(URI source, ICdmDataSource cdmDestination, UUID classificationUuid, String title, DbSchemaValidation hbm2dll){
  94
  95                 //make Source
  96                 DwcaImportConfigurator config= DwcaImportConfigurator.NewInstance(source, cdmDestination);
  97                 config.addObserver(new LoggingIoObserver());
  98                 config.setClassificationUuid(classificationUuid);
  99                 config.setCheck(check);
 100                 config.setDbSchemaValidation(hbm2dll);
 101                 config.setMappingType(mappingType);
 102
 103                 config.setScientificNameIdAsOriginalSourceId(scientificNameIdAsOriginalSourceId);
 104                 config.setValidateRankConsistency(validateRankConsistency);
 105                 config.setDefaultPartitionSize(partitionSize);
 106                 config.setNomenclaturalCode(defaultNomCode);
 107                 config.setDatasetUse(datasetUse);
 108                 config.setGuessNomenclaturalReferences(guessNomRef);
 109                 config.setHandleAllRefsAsCitation(handleAllRefsAsCitation);
 110                 config.setUseSourceReferenceAsSec(useSourceReferenceAsSec);
 111                 config.setSourceReferenceTitle(title);
 112
 113                 CdmDefaultImport myImport = new CdmDefaultImport();
 114
 115
 116                 //...
 117                 if (true){
 118                         System.out.println("Start import from ("+ source.toString() + ") ...");
 119                         config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
 120                         myImport.invoke(config);
 121                         System.out.println("End import from ("+ source.toString() + ")...");
 122                 }
 123
 124
 125         }
 126
 127         private Reference<?> getSourceReference(String string) {
 128                 Reference<?> result = ReferenceFactory.newGeneric();
 129                 result.setTitleCache(string);
 130                 return result;
 131         }
 132
 133         //Dwca
 134         public static URI dwca_emonocots_local() {
 135                 URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/Scratchpads/dwca_dioscoreaceae_emonocots.zip");
 136                 return sourceUrl;
 137         }
 138
 139         //emonocots_dioscoreaceae
 140         public static URI dwca_emonocots_dioscoreaceae() {
 141                 //URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_dioscoreaceae.zip");//dwca_dioscoreaceae_e_monocot.zip
 142                 URI sourceUrl = URI.create("file:///C:/Users/l.morris/Downloads/dwca_scratchpads/dwca_dioscoreaceae_e_monocot_org.zip");
 143                 return sourceUrl;
 144         }
 145
 146         //emonocots_zingiberaceae
 147         public static URI dwca_emonocots_zingiberaceae() {
 148                 URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_zingiberaceae.zip");
 149                 return sourceUrl;
 150         }
 151         //emonocots_cypripedioideae
 152         public static URI dwca_emonocots_cypripedioideae() {
 153                 //URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_cypripedioideae.zip");
 154                 URI sourceUrl = URI.create("file:///C:/Users/l.morris/Downloads/dwca_scratchpads/dwca_cypripedioideae_e-monocot_org.zip");
 155                 return sourceUrl;
 156         }
 157
 158
 159         /**
 160          * @param args
 161          */
 162         public static void main(String[] args) {
 163                 DwcaScratchpadImportActivator me = new DwcaScratchpadImportActivator();
 164                 me.doImport(source, cdmDestination, classificationUuid, title, hbm2dll);
 165         }
 166
 167 }