app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/MclActivator.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.lang.reflect.Method;
  13 import java.sql.ResultSet;
  14 import java.sql.SQLException;
  15 import java.util.UUID;
  16
  17 import org.apache.log4j.Logger;
  18
  19 import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources;
  20 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  21 import eu.etaxonomy.cdm.database.DatabaseTypeEnum;
  22 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  23 import eu.etaxonomy.cdm.database.ICdmDataSource;
  24 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  25 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  26 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  27 import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
  28 import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
  29 import eu.etaxonomy.cdm.io.common.Source;
  30 import eu.etaxonomy.cdm.model.common.ExtensionType;
  31 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  32 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  33
  34
  35 /**
  36  * TODO add the following to a wiki page:
  37  * HINT: If you are about to import into a mysql data base running under windows and if you wish to dump and restore the resulting data bas under another operation systen
  38  * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
  39  *
  40  *
  41  * @author a.mueller
  42  *
  43  */
  44 public class MclActivator {
  45         private static final Logger logger = Logger.getLogger(MclActivator.class);
  46
  47         //database validation status (create, update, validate ...)
  48         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  49         static final Source berlinModelSource = BerlinModelSources.mcl();
  50
  51         static final ICdmDataSource cdmDestination = VibrantActivator.cdm_test_local_vibrant();
  52 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  53
  54         static final boolean useSingleClassification = true;
  55         static final int sourceSecId = 1272;
  56         static final UUID classificationUuid = UUID.fromString("ba6efd26-5b45-4ce6-915d-4f9576e0bf0a");
  57
  58         static final UUID sourceRefUuid = UUID.fromString("ca8b25d6-e251-4d2b-8b45-142e1e6448f7");
  59
  60         // set to zero for unlimited nameFacts
  61         static final int maximumNumberOfNameFacts = 0;
  62
  63         static final int partitionSize = 5000;
  64
  65         //check - import
  66         static final CHECK check = CHECK.CHECK_AND_IMPORT;
  67
  68         //editor - import
  69         static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
  70
  71         //NomeclaturalCode
  72         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
  73
  74         //ignore null
  75         static final boolean ignoreNull = true;
  76
  77         static boolean useClassification = true;
  78
  79
  80 // **************** ALL *********************
  81
  82
  83         //authors
  84         static final boolean doAuthors = true;
  85         //references
  86         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
  87         //names
  88         static final boolean doTaxonNames = true;
  89         static final boolean doRelNames = true;
  90         static final boolean doNameStatus = true;
  91
  92         //taxa
  93         static final boolean doTaxa = true;
  94         static final boolean doRelTaxa = true;
  95         static final boolean doFacts = true;
  96
  97
  98
  99 // **************** SELECTED *********************
 100
 101 //      //authors
 102 //      static final boolean doAuthors = false;
 103 //      //references
 104 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
 105 //      //names
 106 //      static final boolean doTaxonNames = false;
 107 //      static final boolean doRelNames = false;
 108 //      static final boolean doNameStatus = false;
 109 //
 110 //      //taxa
 111 //      static final boolean doTaxa = false;
 112 //      static final boolean doRelTaxa = true;
 113 //      static final boolean doFacts = false;
 114
 115
 116
 117 // **********Always IGNORE:***********************************************
 118
 119         //etc.
 120         static final boolean doUser = false;
 121         static final boolean doTypes = false;   //not available in MCL
 122         static final boolean doNameFacts = false;  //not available in MCL
 123         static final boolean doOccurences = false;     //not available in MCL
 124         static final boolean doCommonNames = false;   //not available in MCL
 125         static final boolean doMarker = false;   //not available in MCL
 126
 127
 128         public void importMcl (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
 129                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
 130                 //make BerlinModel Source
 131
 132                 BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source,  destination);
 133
 134                 try {
 135                         Method makeUrlMethod = this.getClass().getDeclaredMethod("makeUrlForTaxon", TaxonBase.class, ResultSet.class);
 136                         config.setMakeUrlForTaxon(makeUrlMethod);
 137                 } catch (Exception e) {
 138                         e.printStackTrace();
 139                         return;
 140                 }
 141
 142
 143                 config.setClassificationUuid(classificationUuid);
 144                 config.setSourceSecId(sourceSecId);
 145
 146                 config.setNomenclaturalCode(nomenclaturalCode);
 147
 148                 config.setIgnoreNull(ignoreNull);
 149                 config.setDoAuthors(doAuthors);
 150                 config.setDoReferences(doReferences);
 151                 config.setDoTaxonNames(doTaxonNames);
 152                 config.setDoRelNames(doRelNames);
 153                 config.setDoNameStatus(doNameStatus);
 154                 config.setDoTypes(doTypes);
 155                 config.setDoNameFacts(doNameFacts);
 156                 config.setUseClassification(useClassification);
 157                 config.setSourceRefUuid(sourceRefUuid);
 158
 159                 config.setDoTaxa(doTaxa);
 160                 config.setDoRelTaxa(doRelTaxa);
 161                 config.setDoFacts(doFacts);
 162                 config.setDoOccurrence(doOccurences);
 163                 config.setDoCommonNames(doCommonNames);
 164
 165                 config.setDoMarker(doMarker);
 166                 config.setDoUser(doUser);
 167                 config.setEditor(editor);
 168                 config.setDbSchemaValidation(hbm2dll);
 169
 170                 // maximum number of name facts to import
 171                 config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
 172
 173                 config.setUseSingleClassification(useSingleClassification);
 174
 175
 176                 config.setCheck(check);
 177                 config.setEditor(editor);
 178                 config.setRecordsPerTransaction(partitionSize);
 179
 180
 181                 // invoke import
 182                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 183                 bmImport.invoke(config);
 184
 185                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 186
 187         }
 188
 189         /**
 190          * @param args
 191          */
 192         public static void main(String[] args) {
 193                 MclActivator importActivator = new MclActivator();
 194                 Source source = berlinModelSource;
 195                 ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 196
 197                 importActivator.importMcl(source, cdmRepository, hbm2dll);
 198
 199         }
 200
 201         public static ICdmDataSource cdm_test_local_mcl(){
 202                 DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
 203                 String cdmServer = "127.0.0.1";
 204                 String cdmDB = "mcl";
 205                 String cdmUserName = "root";
 206                 return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
 207         }
 208
 209         private static final String URLbase = "http://ww2.bgbm.org/mcl/PTaxonDetail.asp?";
 210         public static Method makeUrlForTaxon(TaxonBase<?> taxon, ResultSet rs){
 211                 Method result = null;
 212                 ExtensionType urlExtensionType = ExtensionType.URL();
 213                 int nameFk;
 214                 try {
 215                         nameFk = rs.getInt("PTNameFk");
 216                 int refFkInt = rs.getInt("PTRefFk");
 217                         if (nameFk != 0 && refFkInt != 0){
 218                                 String url = String.format(URLbase + "NameId=%s&PTRefFk=%s",nameFk, refFkInt);
 219                                 taxon.addExtension(url, urlExtensionType);
 220                         }else{
 221                                 logger.warn("NameFk or refFkInt is 0. Can't create url");
 222                         }
 223                 } catch (SQLException e) {
 224                         logger.warn("Exception when trying to access result set for url creation.");
 225                 }
 226
 227                 return result;
 228         }
 229
 230 }