app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/SalvadorActivator.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.berlinModelImport;
  11
  12 import java.lang.reflect.Method;
  13 import java.util.UUID;
  14
  15 import org.apache.log4j.Logger;
  16
  17 import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources;
  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.berlinModel.in.BerlinModelImportConfigurator;
  22 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  23 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  24 import eu.etaxonomy.cdm.io.common.Source;
  25 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  26 import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
  27 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  28 import eu.etaxonomy.cdm.model.name.NonViralName;
  29
  30
  31 /**
  32  * TODO add the following to a wiki page:
  33  * 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
  34  * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
  35  *
  36  *
  37  * @author a.mueller
  38  *
  39  */
  40 public class SalvadorActivator {
  41         private static final Logger logger = Logger.getLogger(SalvadorActivator.class);
  42
  43         //database validation status (create, update, validate ...)
  44         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  45         static final Source berlinModelSource = BerlinModelSources.El_Salvador();
  46 //      static final ICdmDataSource cdmDestination = CdmDestinations.localH2Salvador();
  47         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
  48         static final UUID treeUuid = UUID.fromString("b010c84d-6049-45f4-9f13-c065101eaa26");
  49         static final UUID secUuid = UUID.fromString("d03ef02a-f226-4cb1-bdb4-f6c154f08a34");
  50         static final int sourceSecId = 7331;
  51
  52         static final UUID featureTreeUuid = UUID.fromString("ae9615b8-bc60-4ed0-ad96-897f9226d568");
  53         static final Object[] featureKeyList = new Integer[]{302, 303, 306, 307, 309, 310, 311, 312, 350, 1500, 1800, 1900, 1950, 1980, 2000, 10299};
  54         static boolean isIgnore0AuthorTeam = true;  //special case for Salvador.
  55         static boolean doExport = false;
  56         static boolean useClassification = true;
  57
  58         //check - import
  59         static final CHECK check = CHECK.CHECK_AND_IMPORT;
  60         static final IImportConfigurator.EDITOR editor = IImportConfigurator.EDITOR.EDITOR_AS_EDITOR;
  61
  62         //NomeclaturalCode
  63         static final NomenclaturalCode nomenclaturalCode  = NomenclaturalCode.ICNAFP;
  64
  65         //ignore null
  66         static final boolean ignoreNull = true;
  67
  68 // ****************** ALL *****************************************
  69
  70         //authors
  71         static final boolean doAuthors = true;
  72         //references
  73         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
  74         //names
  75         static final boolean doTaxonNames = true;
  76         static final boolean doRelNames = true;
  77         static final boolean doNameStatus = true;
  78         static final boolean doTypes = false;  //Types do not exist in El_Salvador DB
  79         static final boolean doNameFacts = false;  //Name Facts do not exist in El_Salvador DB
  80
  81         //taxa
  82         static final boolean doTaxa = true;
  83         static final boolean doRelTaxa = true;
  84         static final boolean doFacts = true;
  85         static final boolean doOccurences = false; //Occurrences do not exist in El_Salvador DB
  86         static final boolean doCommonNames = false; //CommonNames do not exist in Salvador DB
  87
  88         //etc.
  89         static final boolean doMarker = true;
  90         static final boolean doUser = true;
  91
  92
  93 // ************************ NONE **************************************** //
  94
  95 //      //authors
  96 //      static final boolean doAuthors = false;
  97 //      //references
  98 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.CONCEPT_REFERENCES;
  99 //      //names
 100 //      static final boolean doTaxonNames = false;
 101 //      static final boolean doRelNames = false;
 102 //      static final boolean doNameStatus = false;
 103 //      static final boolean doTypes = false;
 104 //      static final boolean doNameFacts = false;
 105 //
 106 //      //taxa
 107 //      static final boolean doTaxa = true;
 108 //      static final boolean doRelTaxa = true;
 109 //      static final boolean doFacts = false;
 110 //      static final boolean doOccurences = false;
 111 //
 112 //      //etc.
 113 //      static final boolean doMarker = false;
 114 //      static final boolean doUser = false;
 115
 116
 117         public boolean doImport(ICdmDataSource destination){
 118                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") ...");
 119
 120                 //make BerlinModel Source
 121                 Source source = berlinModelSource;
 122
 123                 BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source,  destination);
 124
 125                 config.setClassificationUuid(treeUuid);
 126                 config.setSecUuid(secUuid);
 127                 config.setSourceSecId(sourceSecId);
 128                 config.setNomenclaturalCode(nomenclaturalCode);
 129                 config.setIgnoreNull(ignoreNull);
 130
 131                 config.setDoAuthors(doAuthors);
 132                 config.setDoReferences(doReferences);
 133                 config.setDoTaxonNames(doTaxonNames);
 134                 config.setDoRelNames(doRelNames);
 135                 config.setDoNameStatus(doNameStatus);
 136                 config.setDoTypes(doTypes);
 137                 config.setDoNameFacts(doNameFacts);
 138
 139                 config.setDoTaxa(doTaxa);
 140                 config.setDoRelTaxa(doRelTaxa);
 141                 config.setDoFacts(doFacts);
 142                 config.setDoOccurrence(doOccurences);
 143                 config.setDoCommonNames(doCommonNames);
 144
 145                 config.setDoMarker(doMarker);
 146                 config.setDoUser(doUser);
 147
 148                 config.setDbSchemaValidation(hbm2dll);
 149
 150                 config.setCheck(check);
 151                 config.setEditor(editor);
 152                 config.setIgnore0AuthorTeam(isIgnore0AuthorTeam);
 153                 config.setUseClassification(useClassification);
 154
 155                 config.setNamerelationshipTypeMethod(getHandleNameRelationshipTypeMethod());
 156                 config.setUserTransformationMethod(getTransformUsernameMethod());
 157
 158                 // invoke import
 159                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 160                 boolean result = bmImport.invoke(config);
 161                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 162                 return result;
 163         }
 164
 165
 166         /**
 167          * @param args
 168          */
 169         public static void main(String[] args) {
 170                 SalvadorActivator activator = new SalvadorActivator();
 171                 ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 172
 173                 activator.doImport(destination);
 174                 if (doExport == true){
 175                         SalvadorExport export = new SalvadorExport();
 176                         export.doExport(destination);
 177                 }
 178         }
 179
 180
 181         private Method getHandleNameRelationshipTypeMethod(){
 182                 String methodName = "handleNameRelationshipType";
 183                 try {
 184                         Method method = this.getClass().getDeclaredMethod(methodName, Integer.class, NonViralName.class, NonViralName.class);
 185                         method.setAccessible(true);
 186                         return method;
 187                 } catch (Exception e) {
 188                         logger.error("Problem creating Method: " + methodName);
 189                         return null;
 190                 }
 191         }
 192
 193
 194         //used by BerlinModelImportConfigurator
 195         @SuppressWarnings("unused")
 196         private static boolean handleNameRelationshipType(Integer relQualifierFk, NonViralName nameTo, NonViralName nameFrom){
 197                 if (relQualifierFk == 72){
 198                         nameTo.getHomotypicalGroup().merge(nameFrom.getHomotypicalGroup());
 199                         return true;
 200                 }
 201                 return false;
 202         }
 203
 204         private Method getTransformUsernameMethod(){
 205                 String methodName = "transformUsername";
 206                 try {
 207                         Method method = this.getClass().getDeclaredMethod(methodName, String.class);
 208                         method.setAccessible(true);
 209                         return method;
 210                 } catch (Exception e) {
 211                         logger.error("Problem creating Method: " + methodName);
 212                         return null;
 213                 }
 214         }
 215
 216         //used by BerlinModelImportConfigurator
 217         @SuppressWarnings("unused")
 218         private static String transformUsername(String nameToBeTransformed){
 219                 if (nameToBeTransformed == null){
 220                         return null;
 221                 }else if ("W.G.Berendsohn".equals(nameToBeTransformed)){
 222                         return "wgb";
 223                 }else if(nameToBeTransformed.startsWith("fs") || nameToBeTransformed.equals("BGBM\\fs")){
 224                         return "Frank Specht";
 225                 }
 226                 return nameToBeTransformed;
 227         }
 228
 229 }