app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/diptera/DipteraActivator.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.wp6.diptera;
  11
  12 import java.util.UUID;
  13
  14 import org.apache.log4j.Logger;
  15
  16 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  17 import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources;
  18 import eu.etaxonomy.cdm.app.berlinModelImport.TreeCreator;
  19 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  20 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  21 import eu.etaxonomy.cdm.database.ICdmDataSource;
  22 import eu.etaxonomy.cdm.io.berlinModel.BerlinModelImportConfigurator;
  23 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  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.description.Feature;
  28 import eu.etaxonomy.cdm.model.description.FeatureNode;
  29 import eu.etaxonomy.cdm.model.description.FeatureTree;
  30 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  31 import eu.etaxonomy.cdm.model.name.Rank;
  32
  33
  34 /**
  35  * TODO add the following to a wiki page:
  36  * 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
  37  * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
  38  *
  39  *
  40  * @author a.mueller
  41  *
  42  */
  43 public class DipteraActivator {
  44         @SuppressWarnings("unused")
  45         private static final Logger logger = Logger.getLogger(DipteraActivator.class);
  46
  47         //database validation status (create, update, validate ...)
  48         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  49         static final Source berlinModelSource = BerlinModelSources.EDIT_Diptera();
  50         static final ICdmDataSource cdmDestination = CdmDestinations.localH2Diptera();
  51         static final UUID secUuid = UUID.fromString("06fd671f-1226-4e3b-beca-1959b3b32e20");
  52         static final int sourceSecId = 1000000;
  53         static final UUID featureTreeUuid = UUID.fromString("ae9615b8-bc60-4ed0-ad96-897f9226d568");
  54         static final Object[] featureKeyList = new Integer[]{1,4,5,10,11,12,13,99};
  55
  56         //check - import
  57         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  58
  59         static final boolean doDistributionParser = true;  //also run DipteraDistributionParser
  60
  61         //NomeclaturalCode
  62         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICZN;
  63
  64 //      //ignore null
  65         static final boolean ignoreNull = true;
  66
  67         //authors
  68         static final boolean doAuthors = true;
  69         //references
  70         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
  71         //names
  72         static final boolean doTaxonNames = true;
  73         static final boolean doRelNames = true;
  74         static final boolean doNameStatus = true;
  75         static final boolean doTypes = true;
  76         static final boolean doNameFacts = true;
  77
  78         //taxa
  79         static final boolean doTaxa = true;
  80         static final boolean doRelTaxa = true;
  81         static final boolean doFacts = true;
  82         static final boolean doOccurences = false;
  83
  84 //      //authors
  85 //      static final boolean doAuthors = true;
  86 //      //references
  87 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
  88 //      //names
  89 //      static final boolean doTaxonNames = false;
  90 //      static final boolean doRelNames = false;
  91 //      static final boolean doNameStatus = false;
  92 //      static final boolean doTypes = false;
  93 //      static final boolean doNameFacts = false;
  94 //
  95 //      //taxa
  96 //      static final boolean doTaxa = true;
  97 //      static final boolean doRelTaxa = false;
  98 //      static final boolean doFacts = true;
  99 //      static final boolean doOccurences = false;
 100
 101
 102
 103         /**
 104          * @param args
 105          */
 106         public static void main(String[] args) {
 107                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") ...");
 108
 109                 //make BerlinModel Source
 110                 Source source = berlinModelSource;
 111                 ICdmDataSource destination = cdmDestination;
 112
 113                 BerlinModelImportConfigurator bmImportConfigurator = BerlinModelImportConfigurator.NewInstance(source,  destination);
 114
 115                 bmImportConfigurator.setSecUuid(secUuid);
 116                 bmImportConfigurator.setSourceSecId(sourceSecId);
 117                 bmImportConfigurator.setNomenclaturalCode(nomenclaturalCode);
 118
 119                 bmImportConfigurator.setIgnoreNull(ignoreNull);
 120                 bmImportConfigurator.setDoAuthors(doAuthors);
 121                 bmImportConfigurator.setDoReferences(doReferences);
 122                 bmImportConfigurator.setDoTaxonNames(doTaxonNames);
 123                 bmImportConfigurator.setDoRelNames(doRelNames);
 124                 bmImportConfigurator.setDoNameStatus(doNameStatus);
 125                 bmImportConfigurator.setDoTypes(doTypes);
 126                 bmImportConfigurator.setDoNameFacts(doNameFacts);
 127
 128                 bmImportConfigurator.setDoTaxa(doTaxa);
 129                 bmImportConfigurator.setDoRelTaxa(doRelTaxa);
 130                 bmImportConfigurator.setDoFacts(doFacts);
 131                 bmImportConfigurator.setDoOccurrence(doOccurences);
 132                 bmImportConfigurator.setDbSchemaValidation(hbm2dll);
 133
 134                 bmImportConfigurator.setCheck(check);
 135
 136                 // invoke import
 137                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 138                 bmImport.invoke(bmImportConfigurator);
 139
 140                 if (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK)    ){
 141                         CdmApplicationController app = bmImport.getCdmApp();
 142
 143                         //parse distributions
 144                         if (doDistributionParser){
 145                                 DipteraDistributionParser dipDist = new DipteraDistributionParser();
 146                                 dipDist.doDistribution(app);
 147                         }
 148                         //make feature tree
 149                         app = bmImport.getCdmApp();
 150                         FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList);
 151                         FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 152                         tree.getRoot().addChild(distributionNode);
 153                         app.getDescriptionService().saveFeatureTree(tree);
 154                 }
 155                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 156         }
 157
 158 }