app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/MTMooseActivator.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 package eu.etaxonomy.cdm.app.berlinModelImport;
  10
  11 import java.util.UUID;
  12
  13 import org.apache.logging.log4j.LogManager;
  14 import org.apache.logging.log4j.Logger;
  15
  16 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  17 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  18 import eu.etaxonomy.cdm.database.ICdmDataSource;
  19 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  20 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  21 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  22 import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
  23 import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
  24 import eu.etaxonomy.cdm.io.common.Source;
  25 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  26
  27
  28 /**
  29  * TODO add the following to a wiki page:
  30  * 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
  31  * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
  32  *
  33  * @author a.mueller
  34  */
  35 public class MTMooseActivator {
  36
  37         private static final Logger logger = LogManager.getLogger();
  38
  39         //database validation status (create, update, validate ...)
  40         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  41         static final Source berlinModelSource = BerlinModelSources.MT_MOOSE();
  42
  43 //      static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  44 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_redlist_moose_production();
  45         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
  46
  47         static final UUID classificationUuid = UUID.fromString("601d8a00-cffe-4509-af93-b15b543ccf8d");
  48         static final UUID sourceRefUuid = UUID.fromString("601d8a00-cffe-4509-af93-b15b543ccf8d");
  49
  50 //      static final UUID featureTreeUuid = UUID.fromString("4c5b5bbe-6fef-4607-96b2-1b0104eac19e");
  51 //      static final Object[] featureKeyList = new Integer[]{7,201,202,203,204,205,206,207};
  52
  53         static final boolean includeFlatClassifications = true;
  54
  55         static final String relPTaxonIdQuery = "SELECT * FROM RelPTaxon r " +
  56                         " WHERE NOT (r.PTRefFk1 <> r.PTRefFk2 AND r.RelQualifierFk = 1)";
  57         static final String taxonTable = "PTaxon WHERE notIntoCdm = 0";
  58         static final String authorTable = "v_cdmExport_authors";
  59         static final String authorTeamTable = "v_cdmExport_authorTeamsAll";
  60         static final String referenceTable = "v_cdmExport_references";
  61
  62         //check - import
  63         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  64
  65         //NomenclaturalCode
  66         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
  67
  68         static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
  69
  70 // ****************** ALL *****************************************
  71
  72         //authors
  73         static final boolean doAuthors = true;
  74         //references
  75         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
  76         //names
  77         static final boolean doTaxonNames = true;
  78         static final boolean doRelNames = true;
  79         static final boolean doNameStatus = true;
  80         static final boolean doTypes = true;
  81         static final boolean doNameFacts = false;   //no name facts exist
  82
  83         //taxa
  84         static final boolean doTaxa = true;
  85         static final boolean doRelTaxa = true;
  86         static final boolean doFacts = false;    //no facts exist
  87   static final boolean doNamedAreas = false;     //no areas exist
  88         static final boolean doOccurences = false;   //no occurrences exist
  89   static final boolean doOccurenceSources = false;  //no occurrences exist
  90         static final boolean doCommonNames = false;  //no common names exist
  91
  92 // ************************ NONE **************************************** //
  93
  94 //      //authors
  95 //      static final boolean doAuthors = false;
  96 //      //references
  97 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
  98 //      //names
  99 //      static final boolean doTaxonNames = false;
 100 //      static final boolean doRelNames = false;
 101 //      static final boolean doNameStatus = false;
 102 //      static final boolean doTypes = false;
 103 //      static final boolean doNameFacts = false;
 104 //
 105 //      //taxa
 106 //      static final boolean doTaxa = false;
 107 //      static final boolean doRelTaxa = false;
 108 //      static final boolean doFacts = false;
 109 //    static final boolean doNamedAreas = false;
 110 //      static final boolean doOccurences = false;
 111 //    static final boolean doOccurenceSources = false;
 112 //    static final boolean doCommonNames = false;
 113
 114
 115         public void invoke(String[] args){
 116                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") ...");
 117                 logger.debug("Start");
 118                 //make BerlinModel Source
 119                 Source source = berlinModelSource;
 120                 ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 121
 122                 BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source,  destination);
 123
 124                 config.setClassificationUuid(classificationUuid);
 125 //              bmImportConfigurator.setSourceSecId(sourceSecId);
 126                 config.setNomenclaturalCode(nomenclaturalCode);
 127                 config.setEditor(editor);
 128                 config.setIncludeFlatClassifications(includeFlatClassifications);
 129
 130                 config.setDoAuthors(doAuthors);
 131                 config.setDoReferences(doReferences);
 132                 config.setDoTaxonNames(doTaxonNames);
 133                 config.setDoRelNames(doRelNames);
 134                 config.setDoNameStatus(doNameStatus);
 135                 config.setDoTypes(doTypes);
 136                 config.setDoNameFacts(doNameFacts);
 137
 138                 config.setDoTaxa(doTaxa);
 139                 config.setDoRelTaxa(doRelTaxa);
 140                 config.setDoFacts(doFacts);
 141                 config.setDoNamedAreas(doNamedAreas);
 142                 config.setDoOccurrence(doOccurences);
 143                 config.setDoOccurrenceSources(doOccurenceSources);
 144                 config.setDoCommonNames(doCommonNames);
 145                 config.setSourceRefUuid(sourceRefUuid);
 146
 147                 //filter
 148                 config.setRelTaxaIdQuery(relPTaxonIdQuery);
 149                 config.setTaxonTable(taxonTable);
 150                 config.setAuthorFilter(authorTable);
 151                 config.setAuthorTeamFilter(authorTeamTable);
 152                 config.setReferenceIdTable(referenceTable);
 153
 154                 config.setDbSchemaValidation(hbm2dll);
 155
 156                 config.setCheck(check);
 157
 158                 // invoke import
 159                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 160                 bmImport.invoke(config);
 161
 162 //              if (doFacts && (config.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) )   ){
 163 //                      ICdmRepository app = bmImport.getCdmAppController();
 164 //
 165 //                      //make feature tree
 166 //                      FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
 167 //                      FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 168 //                      tree.getRoot().addChild(distributionNode, 0);
 169 //                      app.getTermTreeService().saveOrUpdate(tree);
 170 //              }
 171
 172                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 173         }
 174
 175         public static void main(String[] args) {
 176             logger.warn("test");
 177                 MTMooseActivator activator = new MTMooseActivator();
 178                 try {
 179             activator.invoke(args);
 180         } catch (Exception e) {
 181             e.printStackTrace();
 182         }
 183                 System.exit(0);
 184         }
 185 }