app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/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.berlinModelImport;
  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.CdmDestinations;
  18 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  19 import eu.etaxonomy.cdm.database.ICdmDataSource;
  20 import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
  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.CHECK;
  24 import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
  25 import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
  26 import eu.etaxonomy.cdm.io.common.Source;
  27 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  28 import eu.etaxonomy.cdm.model.common.Language;
  29 import eu.etaxonomy.cdm.model.common.Representation;
  30 import eu.etaxonomy.cdm.model.description.Feature;
  31 import eu.etaxonomy.cdm.model.description.FeatureNode;
  32 import eu.etaxonomy.cdm.model.description.FeatureTree;
  33 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  34 import eu.etaxonomy.cdm.model.name.Rank;
  35
  36
  37 /**
  38  * TODO add the following to a wiki page:
  39  * 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
  40  * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
  41  *
  42  *
  43  * @author a.mueller
  44  *
  45  */
  46 public class EuroMedActivator {
  47         @SuppressWarnings("unused")
  48         private static final Logger logger = Logger.getLogger(EuroMedActivator.class);
  49
  50         //database validation status (create, update, validate ...)
  51         static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
  52 //      static final Source berlinModelSource = BerlinModelSources.euroMed();
  53         static final Source berlinModelSource = BerlinModelSources.euroMed_PESI3();
  54
  55 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_pesi_euroMed();
  56         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_euromed();
  57 //      static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  58
  59         static final boolean includePesiExport = false;
  60
  61         static final int sourceSecId = 7000000; //500000
  62         static final UUID classificationUuid = UUID.fromString("314a68f9-8449-495a-91c2-92fde8bcf344");
  63         static final boolean useSingleClassification = true;
  64
  65         static final UUID featureTreeUuid = UUID.fromString("6a5e1c2b-ec0d-46c8-9c7d-a2059267ffb7");
  66         static final Object[] featureKeyList = new Integer[]{1, 31, 4, 98, 41};
  67
  68         // set to zero for unlimited nameFacts
  69         static final int maximumNumberOfNameFacts = 0;
  70
  71         static final int partitionSize = 2500;
  72
  73         //check - import
  74         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  75
  76         //editor - import
  77         static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
  78
  79         //NomeclaturalCode
  80         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
  81
  82         //ignore null
  83         static final boolean ignoreNull = true;
  84
  85         static final boolean switchSpeciesGroup = true;
  86
  87         static boolean useClassification = true;
  88
  89         static boolean isSplitTdwgCodes = false;
  90         static boolean useEmAreaVocabulary = true;
  91
  92         private boolean removeHttpMapsAnchor = true;
  93
  94
  95         static final String infrGenericRankAbbrev = "[unranked]";
  96         static final String infrSpecificRankAbbrev = "[unranked]";
  97
  98
  99         static String taxonTable = "v_cdm_exp_taxaAll";
 100         static String classificationQuery = " SELECT DISTINCT t.PTRefFk, r.RefCache FROM PTaxon t INNER JOIN Reference r ON t.PTRefFk = r.RefId WHERE t.PTRefFk = " + sourceSecId;
 101         static String relPTaxonIdQuery = " SELECT TOP (100) PERCENT r.RelPTaxonId " +
 102                                         " FROM RelPTaxon AS r INNER JOIN v_cdm_exp_taxaDirect AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk" +
 103                                         " ORDER BY r.RelPTaxonId ";  // AND r.RelQualifierFk =1
 104         static String nameIdTable = " v_cdm_exp_namesAll ";
 105         static String referenceIdTable = " v_cdm_exp_refAll ";
 106         static String factFilter = " factId IN ( SELECT factId FROM v_cdm_exp_factsAll WHERE FactCategoryFk NOT IN (12, 14, 249, 251))";
 107         static String occurrenceFilter = " occurrenceId IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
 108         static String occurrenceSourceFilter = " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
 109         static String commonNameFilter = " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )";
 110         static String webMarkerFilter = " TableNameFk <> 500 OR ( RIdentifierFk IN (SELECT RIdentifier FROM v_cdm_exp_taxaAll)) ";
 111         static String authorTeamFilter = null; // " authorTeamId IN (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) ";
 112         static String authorFilter = null;  // " authorId IN (SELECT authorId FROM v_cdm_exp_authorsAll) ";
 113
 114
 115
 116 // **************** ALL *********************
 117
 118 //      static final boolean doUser = true;
 119 //      //authors
 120 //      static final boolean doAuthors = true;
 121 //      //references
 122 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
 123 //      //names
 124 //      static final boolean doTaxonNames = true;
 125 //      static final boolean doRelNames = true;
 126 //      static final boolean doNameStatus = true;
 127 //      static final boolean doTypes = false;  //serious types do not exist in E+M
 128 //      static final boolean doNameFacts = true;
 129 //
 130 //      //taxa
 131 //      static final boolean doTaxa = true;
 132 //      static final boolean doRelTaxa = false;
 133 //      static final boolean doFacts = true;
 134 //      static final boolean doOccurences = true;
 135 //      static final boolean doCommonNames = true;
 136 //
 137 //      //etc.
 138 //      static final boolean doMarker = true;
 139
 140
 141 // **************** SELECTED *********************
 142
 143         static final boolean doUser = false;
 144         //authors
 145         static final boolean doAuthors = false;
 146         //references
 147         static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
 148         //names
 149         static final boolean doTaxonNames = false;
 150         static final boolean doRelNames = false;
 151         static final boolean doNameStatus = false;
 152         static final boolean doTypes = false;
 153         static final boolean doNameFacts = false;
 154
 155         //taxa
 156         static final boolean doTaxa = false;
 157         static final boolean doRelTaxa = true;
 158         static final boolean doFacts = false;
 159         static final boolean doOccurences = false;
 160         static final boolean doCommonNames = false;
 161
 162         //etc.
 163         static final boolean doMarker = false;
 164
 165
 166         public void importEm2CDM (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
 167                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
 168                 //make BerlinModel Source
 169
 170                 BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source,  destination);
 171
 172                 config.setClassificationUuid(classificationUuid);
 173                 config.setSourceSecId(sourceSecId);
 174
 175                 config.setNomenclaturalCode(nomenclaturalCode);
 176
 177                 config.setIgnoreNull(ignoreNull);
 178                 config.setDoAuthors(doAuthors);
 179                 config.setDoReferences(doReferences);
 180                 config.setDoTaxonNames(doTaxonNames);
 181                 config.setDoRelNames(doRelNames);
 182                 config.setDoNameStatus(doNameStatus);
 183                 config.setDoTypes(doTypes);
 184                 config.setDoNameFacts(doNameFacts);
 185                 config.setUseClassification(useClassification);
 186                 config.setSourceRefUuid(BerlinModelTransformer.uuidSourceRefEuroMed);
 187
 188                 config.setDoTaxa(doTaxa);
 189                 config.setDoRelTaxa(doRelTaxa);
 190                 config.setDoFacts(doFacts);
 191                 config.setDoOccurrence(doOccurences);
 192                 config.setDoCommonNames(doCommonNames);
 193
 194                 config.setDoMarker(doMarker);
 195                 config.setDoUser(doUser);
 196                 config.setEditor(editor);
 197                 config.setDbSchemaValidation(hbm2dll);
 198
 199                 // maximum number of name facts to import
 200                 config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
 201
 202                 config.setInfrGenericRankAbbrev(infrGenericRankAbbrev);
 203                 config.setInfrSpecificRankAbbrev(infrSpecificRankAbbrev);
 204                 config.setRemoveHttpMapsAnchor(removeHttpMapsAnchor);
 205
 206 //              filter
 207                 config.setTaxonTable(taxonTable);
 208                 config.setClassificationQuery(classificationQuery);
 209                 config.setRelTaxaIdQuery(relPTaxonIdQuery);
 210                 config.setNameIdTable(nameIdTable);
 211                 config.setReferenceIdTable(referenceIdTable);
 212                 config.setAuthorTeamFilter(authorTeamFilter);
 213                 config.setAuthorFilter(authorFilter);
 214                 config.setFactFilter(factFilter);
 215                 config.setCommonNameFilter(commonNameFilter);
 216                 config.setOccurrenceFilter(occurrenceFilter);
 217                 config.setOccurrenceSourceFilter(occurrenceSourceFilter);
 218                 config.setWebMarkerFilter(webMarkerFilter);
 219                 config.setUseSingleClassification(useSingleClassification);
 220
 221                 //TDWG codes
 222                 config.setSplitTdwgCodes(isSplitTdwgCodes);
 223                 config.setUseEmAreaVocabulary(useEmAreaVocabulary);
 224
 225                 config.setCheck(check);
 226                 config.setEditor(editor);
 227                 config.setRecordsPerTransaction(partitionSize);
 228
 229                 config.setSwitchSpeciesGroup(switchSpeciesGroup);
 230
 231                 // invoke import
 232                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 233                 bmImport.invoke(config);
 234
 235                 if (doTaxonNames && (config.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK)  )  ){
 236                         ICdmApplicationConfiguration app = bmImport.getCdmAppController();
 237                         Rank sectBot = (Rank)app.getTermService().find(Rank.SECTION_BOTANY().getUuid());
 238                         Representation repr = sectBot.getRepresentation(Language.ENGLISH());
 239                         repr.setAbbreviatedLabel(repr.getAbbreviatedLabel().replace("(bot.)", "").trim());
 240                         repr.setLabel(repr.getLabel().replace("(Botany)", "").trim());
 241                         sectBot.setTitleCache(null, false);  //to definetely update the titleCache also
 242                         app.getTermService().saveOrUpdate(sectBot);
 243
 244                         Rank subSectBot = (Rank)app.getTermService().find(Rank.SECTION_BOTANY().getUuid());
 245                         repr = subSectBot.getRepresentation(Language.ENGLISH());
 246                         repr.setAbbreviatedLabel(repr.getAbbreviatedLabel().replace("(bot.)", "").trim());
 247                         repr.setLabel(repr.getLabel().replace("(Botany)", "").trim());
 248                         subSectBot.setTitleCache(null, false);  //to definetely update the titleCache also
 249                         app.getTermService().saveOrUpdate(subSectBot);
 250
 251                 }
 252
 253                 if (doFacts && (config.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK)  )  ){
 254                         ICdmApplicationConfiguration app = bmImport.getCdmAppController();
 255
 256                         //make feature tree
 257                         FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
 258                         FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 259                         tree.getRoot().addChild(imageNode);
 260                         FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 261                         tree.getRoot().addChild(distributionNode, 2);
 262                         FeatureNode commonNameNode = FeatureNode.NewInstance(Feature.COMMON_NAME());
 263                         tree.getRoot().addChild(commonNameNode, 3);
 264                         app.getFeatureTreeService().saveOrUpdate(tree);
 265
 266                         //Change common name label
 267                         DefinedTermBase<?> commonNameFeature = app.getTermService().find(Feature.COMMON_NAME().getUuid());
 268                         commonNameFeature.setLabel("Common Names", Language.ENGLISH());
 269                         commonNameFeature.setTitleCache(null, false);  //to definetely update the titleCache also
 270                         app.getTermService().saveOrUpdate(commonNameFeature);
 271                 }
 272
 273                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 274
 275         }
 276
 277         /**
 278          * @param args
 279          */
 280         public static void main(String[] args) {
 281                 EuroMedActivator importActivator = new EuroMedActivator();
 282                 Source source = berlinModelSource;
 283                 ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 284
 285                 importActivator.importEm2CDM(source, cdmRepository, hbm2dll);
 286                 if (includePesiExport){
 287                         //not available from here since E+M was moved to app-import
 288 //                      PesiExportActivatorEM exportActivator = new PesiExportActivatorEM();
 289 //                      exportActivator.doExport(cdmRepository);
 290                 }
 291
 292         }
 293
 294 }