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.io.File;
  13 import java.net.URI;
  14 import java.util.UUID;
  15
  16 import org.apache.log4j.Logger;
  17
  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.DwcaDataImportConfiguratorBase.DatasetUse;
  25 import eu.etaxonomy.cdm.io.dwca.in.DwcaImportConfigurator;
  26 import eu.etaxonomy.cdm.io.dwca.in.IImportMapping.MappingType;
  27 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  28 import eu.etaxonomy.cdm.model.reference.Reference;
  29 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  30
  31 /**
  32  * @author a.mueller
  33  * @created 03.04.2012
  34  * @version 1.0
  35  */
  36 public class DwcaScratchpadImportActivator {
  37         @SuppressWarnings("unused")
  38         private static final Logger logger = Logger.getLogger(DwcaScratchpadImportActivator.class);
  39
  40         //database validation status (create, update, validate ...)
  41         static DbSchemaValidation hbm2dll = DbSchemaValidation.UPDATE;//UPDATE;//CREATE;//UPDATE;
  42
  43         //      static final URI source =  dwca_emonocots_dioscoreaceae();
  44 //      static final URI source =  dwca_emonocots_zingiberaceae();
  45         //static final URI source =  dwca_emonocots_cypripedioideae();
  46         static final URI source =  null;//dwca_antkey();//dwca_emonocots_dioscoreaceae();
  47
  48
  49 //      static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  50         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  51 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
  52
  53         //default nom code is ICZN as it allows adding publication year
  54         static final NomenclaturalCode defaultNomCode = NomenclaturalCode.ICBN;
  55
  56         //classification Name
  57         static String classificationName = "Default classification";
  58
  59         //title
  60         static final String title = "Scratchpad test import";
  61
  62         //check - import
  63         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  64         static int partitionSize = 1000;
  65
  66         //config
  67         static DatasetUse datasetUse = DatasetUse.CLASSIFICATION;
  68
  69         //validate
  70         static boolean validateRankConsistency = false;
  71
  72
  73         //taxa
  74         static final boolean doTaxa = true;
  75         static final boolean doDistribution = true;
  76
  77
  78
  79         static final MappingType mappingType = MappingType.InMemoryMapping;
  80
  81         //classification
  82         static final UUID classificationUuid = UUID.fromString("d9d199b6-eaf4-47c8-a732-0639bc445c56");
  83
  84
  85         //config
  86         static boolean scientificNameIdAsOriginalSourceId = true;
  87         static boolean guessNomRef = false;
  88         private boolean handleAllRefsAsCitation = false;
  89         private static final boolean useSourceReferenceAsSec = true;
  90
  91
  92         //deduplicate
  93         static final boolean doDeduplicate = false;
  94
  95
  96
  97         protected void doImport(URI source, ICdmDataSource cdmDestination, UUID classificationUuid, String title, DbSchemaValidation hbm2dll){
  98
  99                 //make Source
 100                 DwcaImportConfigurator config= DwcaImportConfigurator.NewInstance(source, cdmDestination);
 101                 config.addObserver(new LoggingIoObserver());
 102                 config.setClassificationUuid(classificationUuid);
 103                 config.setCheck(check);
 104                 config.setDbSchemaValidation(hbm2dll);
 105                 config.setMappingType(mappingType);
 106
 107                 config.setScientificNameIdAsOriginalSourceId(scientificNameIdAsOriginalSourceId);
 108                 config.setValidateRankConsistency(validateRankConsistency);
 109                 config.setDefaultPartitionSize(partitionSize);
 110                 config.setNomenclaturalCode(defaultNomCode);
 111                 config.setDatasetUse(datasetUse);
 112                 config.setGuessNomenclaturalReferences(guessNomRef);
 113                 config.setHandleAllRefsAsCitation(handleAllRefsAsCitation);
 114                 config.setUseSourceReferenceAsSec(useSourceReferenceAsSec);
 115                 config.setSourceReferenceTitle(classificationName);//title);
 116                 config.setClassificationName(classificationName);
 117
 118                 config.setUseSourceReferenceAsSec(true);//Lorna: what shall we use as sec reference for Scratchpads data?
 119
 120                 CdmDefaultImport myImport = new CdmDefaultImport();
 121
 122
 123                 //...
 124                 if (true){
 125                         System.out.println("Start import from ("+ source.toString() + ") ...");
 126                         config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
 127                         myImport.invoke(config);
 128                         System.out.println("End import from ("+ source.toString() + ")...");
 129                 }
 130
 131
 132         }
 133
 134         private Reference<?> getSourceReference(String string) {
 135                 Reference<?> result = ReferenceFactory.newGeneric();
 136                 result.setTitleCache(string);
 137                 return result;
 138         }
 139
 140         //Dwca
 141         public static URI dwca_emonocots_local() {
 142                 URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/Scratchpads/dwca_dioscoreaceae_emonocots.zip");
 143                 return sourceUrl;
 144         }
 145
 146         //emonocots_dioscoreaceae
 147         public static URI dwca_emonocots_dioscoreaceae() {
 148                 //URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_dioscoreaceae.zip");//dwca_dioscoreaceae_e_monocot.zip
 149                 URI sourceUrl = URI.create("file:///C:/Users/l.morris/Downloads/dwca_scratchpads/dwca_dioscoreaceae_e_monocot_org.zip");
 150                 return sourceUrl;
 151         }
 152
 153         //dwca_antkey_org.zip
 154         public static URI dwca_antkey() {
 155                 //URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_dioscoreaceae.zip");//dwca_dioscoreaceae_e_monocot.zip
 156                 URI sourceUrl = URI.create("file:///C:/Users/l.morris/Downloads/amaryllidaceae.zip");//antkey.zip");//alismataceae.zip");//hypoxidaceae.zip");//dwca_antkey.zip");
 157                 return sourceUrl;
 158         }
 159
 160         //emonocots_zingiberaceae
 161         public static URI dwca_emonocots_zingiberaceae() {
 162                 URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_zingiberaceae.zip");
 163                 return sourceUrl;
 164         }
 165         //emonocots_cypripedioideae
 166         public static URI dwca_emonocots_cypripedioideae() {
 167                 //URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_cypripedioideae.zip");
 168                 URI sourceUrl = URI.create("file:///C:/Users/l.morris/Downloads/dwca_scratchpads/dwca_cypripedioideae_e-monocot_org.zip");
 169                 return sourceUrl;
 170         }
 171
 172
 173         /**
 174          * @param args
 175          */
 176         public static void main(String[] args) {
 177                 DwcaScratchpadImportActivator me = new DwcaScratchpadImportActivator();
 178
 179                 //lorna: TODO get the classification name from the dwca zip file name
 180                 classificationName = "Scratchpad classification";//"Amaryllidaceae";
 181
 182                 // Directory path here
 183                 String path = "C:/Users/l.morris/Downloads/dwca_scratchpads/nine";
 184                 URI sourceUrl;
 185                 //URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_zingiberaceae.zip");
 186
 187                 String zipFile;
 188                 File folder = new File(path);
 189                 File[] listOfFiles = folder.listFiles();
 190
 191                 for (int i = 0; i < listOfFiles.length; i++)
 192                 {
 193
 194                         if (listOfFiles[i].isFile())
 195                         {
 196                                 zipFile = listOfFiles[i].getName();
 197
 198                                 if (zipFile.endsWith(".zip"))
 199                                 {
 200                                         //classificationName = zipFile.split(".zip")[0];
 201                                         classificationName = zipFile.split("dwca_")[1];
 202                                         classificationName = classificationName.split("_")[0];
 203                                         System.out.println(classificationName);
 204                                         //start the Scratchpad name with uppercase.
 205                                         char[] stringArray = classificationName.toCharArray();
 206                                         stringArray[0] = Character.toUpperCase(stringArray[0]);
 207                                         classificationName = new String(stringArray) + " (Scratchpads)";
 208                                         System.out.println(classificationName);
 209                                         //System.exit(999);
 210
 211                                         sourceUrl = URI.create("file:///" + path + "/" + zipFile);
 212                                         System.out.println(sourceUrl);
 213                                         me.doImport(sourceUrl, cdmDestination, classificationUuid, title, hbm2dll);
 214                                         //System.exit(999);
 215                                 }
 216                         }
 217                 }
 218
 219                 //System.exit(999);
 220                 //list all files in the directory
 221                 //get the URI of each
 222                 //URI sourceUrl = URI.create("file:///C:/Users/l.morris/Downloads/amaryllidaceae.zip");
 223
 224                 //Lorna iterate through the dwca directly getting each dwca.zip and generate a URI for each source
 225                 //me.doImport(source, cdmDestination, classificationUuid, title, hbm2dll);
 226         }
 227
 228 }