cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/EuroMedActivator.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.pesi;
  11
  12 import java.util.UUID;
  13
  14 import org.apache.log4j.Logger;
  15
  16 import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  17 import eu.etaxonomy.cdm.app.common.BerlinModelSources;
  18 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  19 import eu.etaxonomy.cdm.app.common.TreeCreator;
  20 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  21 import eu.etaxonomy.cdm.database.ICdmDataSource;
  22 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  23 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  24 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  25 import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
  26 import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
  27 import eu.etaxonomy.cdm.io.common.Source;
  28 import eu.etaxonomy.cdm.model.description.Feature;
  29 import eu.etaxonomy.cdm.model.description.FeatureNode;
  30 import eu.etaxonomy.cdm.model.description.FeatureTree;
  31 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  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 EuroMedActivator {
  44         @SuppressWarnings("unused")
  45         private static final Logger logger = Logger.getLogger(EuroMedActivator.class);
  46
  47         //database validation status (create, update, validate ...)
  48         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  49         static final Source berlinModelSource = BerlinModelSources.euroMed();
  50 //      static final Source berlinModelSource = BerlinModelSources.EDIT_Diptera();
  51
  52 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_pesi_euroMed();
  53         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  54
  55         static final int sourceSecId = 7000000; //500000
  56         static final UUID classificationUuid = UUID.fromString("314a68f9-8449-495a-91c2-92fde8bcf344");
  57         static final boolean useSingleClassification = true;
  58
  59         static final UUID featureTreeUuid = UUID.fromString("6a5e1c2b-ec0d-46c8-9c7d-a2059267ffb7");
  60         static final Object[] featureKeyList = new Integer[]{1, 31, 4, 98, 41};
  61
  62         // set to zero for unlimited nameFacts
  63         static final int maximumNumberOfNameFacts = 0;
  64
  65         static final int partitionSize = 2000;
  66
  67         //check - import
  68         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  69
  70         //editor - import
  71         static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
  72
  73         //NomeclaturalCode
  74         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICBN;
  75
  76         //ignore null
  77         static final boolean ignoreNull = true;
  78
  79         static boolean useClassification = true;
  80
  81         static String taxonTable = "v_cdm_exp_taxaAll";
  82         static String classificationQuery = " SELECT DISTINCT t.PTRefFk, r.RefCache FROM _EM_CDM_exp_taxaDirect t INNER JOIN Reference r ON t.PTRefFk = r.RefId ";
  83         static String relPTaxonIdQuery = " SELECT r.RelPTaxonId " +
  84                                         " FROM RelPTaxon AS r INNER JOIN v_cdm_exp_taxaDirect AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk ";
  85         static String nameIdTable = " v_cdm_exp_namesAll ";
  86         static String referenceIdTable = " v_cdm_exp_refAll ";
  87         static String factFilter = " factId IN ( SELECT factId FROM v_cdm_exp_factsAll )";
  88         static String occurrenceFilter = " occurrenceId IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
  89         static String occurrenceSourceFilter = " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
  90         static String commonNameFilter = " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )";
  91         static String webMarkerFilter = " TableNameFk <> 500 OR ( RIdentifierFk IN (SELECT RIdentifier FROM v_cdm_exp_taxaAll)) ";
  92
  93
  94
  95
  96
  97 // **************** ALL *********************
  98
  99         static final boolean doUser = true;
 100         //authors
 101         static final boolean doAuthors = true;
 102         //references
 103         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
 104         //names
 105         static final boolean doTaxonNames = true;
 106         static final boolean doRelNames = true;
 107         static final boolean doNameStatus = true;
 108         static final boolean doTypes = true;
 109         static final boolean doNameFacts = true;
 110
 111         //taxa
 112         static final boolean doTaxa = true;
 113         static final boolean doRelTaxa = true;
 114         static final boolean doFacts = true;
 115         static final boolean doOccurences = true;
 116         static final boolean doCommonNames = true;
 117
 118         //etc.
 119         static final boolean doMarker = true;
 120
 121
 122 // **************** SELECTED *********************
 123
 124 //      static final boolean doUser = true;
 125 //      //authors
 126 //      static final boolean doAuthors = false;
 127 //      //references
 128 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
 129 //      //names
 130 //      static final boolean doTaxonNames = false;
 131 //      static final boolean doRelNames = false;
 132 //      static final boolean doNameStatus = false;
 133 //      static final boolean doTypes = false;
 134 //      static final boolean doNameFacts = false;
 135 //
 136 //      //taxa
 137 //      static final boolean doTaxa = false;
 138 //      static final boolean doRelTaxa = false;
 139 //      static final boolean doFacts = false;
 140 //      static final boolean doOccurences = false;
 141 //      static final boolean doCommonNames = false;
 142 //
 143 //      //etc.
 144 //      static final boolean doMarker = false;
 145
 146
 147         /**
 148          * @param args
 149          */
 150         public static void main(String[] args) {
 151                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
 152
 153                 //make BerlinModel Source
 154                 Source source = berlinModelSource;
 155                 ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 156
 157                 BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source,  destination);
 158
 159                 config.setClassificationUuid(classificationUuid);
 160                 config.setSourceSecId(sourceSecId);
 161
 162                 config.setNomenclaturalCode(nomenclaturalCode);
 163
 164                 config.setIgnoreNull(ignoreNull);
 165                 config.setDoAuthors(doAuthors);
 166                 config.setDoReferences(doReferences);
 167                 config.setDoTaxonNames(doTaxonNames);
 168                 config.setDoRelNames(doRelNames);
 169                 config.setDoNameStatus(doNameStatus);
 170                 config.setDoTypes(doTypes);
 171                 config.setDoNameFacts(doNameFacts);
 172                 config.setUseClassification(useClassification);
 173
 174                 config.setDoTaxa(doTaxa);
 175                 config.setDoRelTaxa(doRelTaxa);
 176                 config.setDoFacts(doFacts);
 177                 config.setDoOccurrence(doOccurences);
 178                 config.setDoCommonNames(doCommonNames);
 179
 180                 config.setDoMarker(doMarker);
 181                 config.setDoUser(doUser);
 182                 config.setEditor(editor);
 183                 config.setDbSchemaValidation(hbm2dll);
 184
 185                 // maximum number of name facts to import
 186                 config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
 187
 188 //              filter
 189                 config.setTaxonTable(taxonTable);
 190                 config.setClassificationQuery(classificationQuery);
 191                 config.setRelTaxaIdQuery(relPTaxonIdQuery);
 192                 config.setNameIdTable(nameIdTable);
 193                 config.setReferenceIdTable(referenceIdTable);
 194                 config.setFactFilter(factFilter);
 195                 config.setCommonNameFilter(commonNameFilter);
 196                 config.setOccurrenceFilter(occurrenceFilter);
 197                 config.setOccurrenceSourceFilter(occurrenceSourceFilter);
 198                 config.setWebMarkerFilter(webMarkerFilter);
 199                 config.setUseSingleClassification(useSingleClassification);
 200
 201
 202                 config.setCheck(check);
 203                 config.setEditor(editor);
 204                 config.setRecordsPerTransaction(partitionSize);
 205
 206                 // invoke import
 207                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 208                 bmImport.invoke(config);
 209
 210                 if (doFacts && config.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK)    ){
 211                         ICdmApplicationConfiguration app = bmImport.getCdmAppController();
 212
 213                         //make feature tree
 214                         FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
 215                         FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 216                         tree.getRoot().addChild(imageNode);
 217                         FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 218                         tree.getRoot().addChild(distributionNode, 2);
 219                         app.getFeatureTreeService().saveOrUpdate(tree);
 220                 }
 221
 222                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 223
 224         }
 225
 226 }