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.io.pesi.out.PesiTransformer;
  29 import eu.etaxonomy.cdm.model.description.Feature;
  30 import eu.etaxonomy.cdm.model.description.FeatureNode;
  31 import eu.etaxonomy.cdm.model.description.FeatureTree;
  32 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  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 EuroMedActivator {
  45         @SuppressWarnings("unused")
  46         private static final Logger logger = Logger.getLogger(EuroMedActivator.class);
  47
  48         //database validation status (create, update, validate ...)
  49         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  50 //      static final Source berlinModelSource = BerlinModelSources.euroMed();
  51         static final Source berlinModelSource = BerlinModelSources.PESI3_euroMed();
  52
  53 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_pesi_euroMed();
  54 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  55         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  56
  57         static final boolean includePesiExport = false;
  58
  59         static final int sourceSecId = 7000000; //500000
  60         static final UUID classificationUuid = UUID.fromString("314a68f9-8449-495a-91c2-92fde8bcf344");
  61         static final boolean useSingleClassification = true;
  62
  63         static final UUID featureTreeUuid = UUID.fromString("6a5e1c2b-ec0d-46c8-9c7d-a2059267ffb7");
  64         static final Object[] featureKeyList = new Integer[]{1, 31, 4, 98, 41};
  65
  66         // set to zero for unlimited nameFacts
  67         static final int maximumNumberOfNameFacts = 0;
  68
  69         static final int partitionSize = 5000;
  70
  71         //check - import
  72         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  73
  74         //editor - import
  75         static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
  76
  77         //NomeclaturalCode
  78         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICBN;
  79
  80         //ignore null
  81         static final boolean ignoreNull = true;
  82
  83         static final boolean switchSpeciesGroup = true;
  84
  85         static boolean useClassification = true;
  86
  87         static boolean  isSplitTdwgCodes = false;
  88
  89         static String taxonTable = "v_cdm_exp_taxaAll";
  90         static String classificationQuery = " SELECT DISTINCT t.PTRefFk, r.RefCache FROM _EM_CDM_exp_taxaDirect t INNER JOIN Reference r ON t.PTRefFk = r.RefId ";
  91         static String relPTaxonIdQuery = " SELECT r.RelPTaxonId " +
  92                                         " FROM RelPTaxon AS r INNER JOIN v_cdm_exp_taxaDirect AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk ";
  93         static String nameIdTable = " v_cdm_exp_namesAll ";
  94         static String referenceIdTable = " v_cdm_exp_refAll ";
  95         static String factFilter = " factId IN ( SELECT factId FROM v_cdm_exp_factsAll )";
  96         static String occurrenceFilter = " occurrenceId IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
  97         static String occurrenceSourceFilter = " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
  98         static String commonNameFilter = " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )";
  99         static String webMarkerFilter = " TableNameFk <> 500 OR ( RIdentifierFk IN (SELECT RIdentifier FROM v_cdm_exp_taxaAll)) ";
 100         static String authorTeamFilter = null; // " authorTeamId IN (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) ";
 101         static String authorFilter = null;  // " authorId IN (SELECT authorId FROM v_cdm_exp_authorsAll) ";
 102
 103
 104
 105 // **************** ALL *********************
 106
 107         static final boolean doUser = true;
 108         //authors
 109         static final boolean doAuthors = true;
 110         //references
 111         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
 112         //names
 113         static final boolean doTaxonNames = true;
 114         static final boolean doRelNames = true;
 115         static final boolean doNameStatus = true;
 116         static final boolean doTypes = false;  //serious types do not exist in E+M
 117         static final boolean doNameFacts = true;
 118
 119         //taxa
 120         static final boolean doTaxa = true;
 121         static final boolean doRelTaxa = true;
 122         static final boolean doFacts = true;
 123         static final boolean doOccurences = true;
 124         static final boolean doCommonNames = true;
 125
 126         //etc.
 127         static final boolean doMarker = true;
 128
 129
 130 // **************** SELECTED *********************
 131
 132 //      static final boolean doUser = true;
 133 //      //authors
 134 //      static final boolean doAuthors = false;
 135 //      //references
 136 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
 137 //      //names
 138 //      static final boolean doTaxonNames = false;
 139 //      static final boolean doRelNames = false;
 140 //      static final boolean doNameStatus = false;
 141 //      static final boolean doTypes = false;
 142 //      static final boolean doNameFacts = false;
 143 //
 144 //      //taxa
 145 //      static final boolean doTaxa = false;
 146 //      static final boolean doRelTaxa = false;
 147 //      static final boolean doFacts = false;
 148 //      static final boolean doOccurences = false;
 149 //      static final boolean doCommonNames = false;
 150 //
 151 //      //etc.
 152 //      static final boolean doMarker = false;
 153
 154
 155         public void importEm2CDM (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
 156                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
 157                 //make BerlinModel Source
 158
 159                 BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source,  destination);
 160
 161                 config.setClassificationUuid(classificationUuid);
 162                 config.setSourceSecId(sourceSecId);
 163
 164                 config.setNomenclaturalCode(nomenclaturalCode);
 165
 166                 config.setIgnoreNull(ignoreNull);
 167                 config.setDoAuthors(doAuthors);
 168                 config.setDoReferences(doReferences);
 169                 config.setDoTaxonNames(doTaxonNames);
 170                 config.setDoRelNames(doRelNames);
 171                 config.setDoNameStatus(doNameStatus);
 172                 config.setDoTypes(doTypes);
 173                 config.setDoNameFacts(doNameFacts);
 174                 config.setUseClassification(useClassification);
 175                 config.setSourceRefUuid(PesiTransformer.uuidSourceRefEuroMed);
 176
 177                 config.setDoTaxa(doTaxa);
 178                 config.setDoRelTaxa(doRelTaxa);
 179                 config.setDoFacts(doFacts);
 180                 config.setDoOccurrence(doOccurences);
 181                 config.setDoCommonNames(doCommonNames);
 182
 183                 config.setDoMarker(doMarker);
 184                 config.setDoUser(doUser);
 185                 config.setEditor(editor);
 186                 config.setDbSchemaValidation(hbm2dll);
 187
 188                 // maximum number of name facts to import
 189                 config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
 190
 191 //              filter
 192                 config.setTaxonTable(taxonTable);
 193                 config.setClassificationQuery(classificationQuery);
 194                 config.setRelTaxaIdQuery(relPTaxonIdQuery);
 195                 config.setNameIdTable(nameIdTable);
 196                 config.setReferenceIdTable(referenceIdTable);
 197                 config.setAuthorTeamFilter(authorTeamFilter);
 198                 config.setAuthorFilter(authorFilter);
 199                 config.setFactFilter(factFilter);
 200                 config.setCommonNameFilter(commonNameFilter);
 201                 config.setOccurrenceFilter(occurrenceFilter);
 202                 config.setOccurrenceSourceFilter(occurrenceSourceFilter);
 203                 config.setWebMarkerFilter(webMarkerFilter);
 204                 config.setUseSingleClassification(useSingleClassification);
 205
 206                 //TDWG codes
 207                 config.setSplitTdwgCodes(isSplitTdwgCodes);
 208
 209
 210                 config.setCheck(check);
 211                 config.setEditor(editor);
 212                 config.setRecordsPerTransaction(partitionSize);
 213
 214                 config.setSwitchSpeciesGroup(switchSpeciesGroup);
 215
 216                 // invoke import
 217                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 218                 bmImport.invoke(config);
 219
 220                 if (doFacts && config.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK)    ){
 221                         ICdmApplicationConfiguration app = bmImport.getCdmAppController();
 222
 223                         //make feature tree
 224                         FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
 225                         FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 226                         tree.getRoot().addChild(imageNode);
 227                         FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 228                         tree.getRoot().addChild(distributionNode, 2);
 229                         app.getFeatureTreeService().saveOrUpdate(tree);
 230                 }
 231
 232                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 233
 234         }
 235
 236         /**
 237          * @param args
 238          */
 239         public static void main(String[] args) {
 240                 EuroMedActivator importActivator = new EuroMedActivator();
 241                 Source source = berlinModelSource;
 242                 ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 243
 244                 importActivator.importEm2CDM(source, cdmRepository, hbm2dll);
 245                 if (includePesiExport){
 246                         PesiExportActivatorEM exportActivator = new PesiExportActivatorEM();
 247                         exportActivator.doExport(cdmRepository);
 248                 }
 249
 250         }
 251
 252 }