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.io.IOException;
  13 import java.io.InputStream;
  14 import java.io.InputStreamReader;
  15 import java.io.Reader;
  16 import java.util.Arrays;
  17 import java.util.HashMap;
  18 import java.util.List;
  19 import java.util.Map;
  20 import java.util.Set;
  21 import java.util.UUID;
  22
  23 import org.apache.log4j.Logger;
  24 import org.springframework.security.core.GrantedAuthority;
  25 import org.springframework.transaction.TransactionStatus;
  26
  27 import eu.etaxonomy.cdm.api.application.FirstDataInserter;
  28 import eu.etaxonomy.cdm.api.application.ICdmRepository;
  29 import eu.etaxonomy.cdm.api.service.IGroupService;
  30 import eu.etaxonomy.cdm.api.service.description.TransmissionEngineDistribution;
  31 import eu.etaxonomy.cdm.api.service.description.TransmissionEngineDistribution.AggregationMode;
  32 import eu.etaxonomy.cdm.api.service.pager.Pager;
  33 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  34 import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor;
  35 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  36 import eu.etaxonomy.cdm.database.ICdmDataSource;
  37 import eu.etaxonomy.cdm.ext.geo.IEditGeoService;
  38 import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
  39 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  40 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  41 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  42 import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
  43 import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
  44 import eu.etaxonomy.cdm.io.common.Source;
  45 import eu.etaxonomy.cdm.model.agent.Person;
  46 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  47 import eu.etaxonomy.cdm.model.common.GrantedAuthorityImpl;
  48 import eu.etaxonomy.cdm.model.common.Group;
  49 import eu.etaxonomy.cdm.model.common.Language;
  50 import eu.etaxonomy.cdm.model.common.Representation;
  51 import eu.etaxonomy.cdm.model.common.User;
  52 import eu.etaxonomy.cdm.model.description.Feature;
  53 import eu.etaxonomy.cdm.model.description.FeatureNode;
  54 import eu.etaxonomy.cdm.model.description.FeatureTree;
  55 import eu.etaxonomy.cdm.model.location.NamedArea;
  56 import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
  57 import eu.etaxonomy.cdm.model.location.NamedAreaType;
  58 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  59 import eu.etaxonomy.cdm.model.name.Rank;
  60 import eu.etaxonomy.cdm.model.taxon.Taxon;
  61 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  62 import eu.etaxonomy.cdm.persistence.hibernate.permission.Role;
  63 import eu.etaxonomy.cdm.persistence.query.MatchMode;
  64 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  65
  66
  67 /**
  68  * TODO add the following to a wiki page:
  69  * 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
  70  * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
  71  *
  72  *
  73  * @author a.mueller
  74  *
  75  */
  76 public class EuroMedActivator {
  77         private static final Logger logger = Logger.getLogger(EuroMedActivator.class);
  78
  79         //database validation status (create, update, validate ...)
  80         static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
  81         static final Source berlinModelSource = BerlinModelSources.euroMed_BGBM42();
  82 //      static final Source berlinModelSource = BerlinModelSources.euroMed_PESI3();
  83
  84         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_euroMed();
  85 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_pesi_euromed();
  86
  87 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_euromed3();
  88 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
  89
  90 //      static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  91
  92         static final boolean includePesiExport = false;
  93
  94         static final int sourceSecId = 7000000; //500000
  95         static final UUID classificationUuid = UUID.fromString("314a68f9-8449-495a-91c2-92fde8bcf344");
  96         static final boolean useSingleClassification = true;
  97         static final String classificationName = "Euro+Med 2014";
  98         static final UUID featureTreeUuid = UUID.fromString("6a5e1c2b-ec0d-46c8-9c7d-a2059267ffb7");
  99         static final Object[] featureKeyList = new Integer[]{1, 31, 4, 98, 41};
 100
 101         // set to zero for unlimited nameFacts
 102         static final int maximumNumberOfNameFacts = 0;
 103
 104         static final int partitionSize = 2500;
 105
 106         //check - import
 107         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
 108
 109         //editor - import
 110         static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
 111
 112         //NomenclaturalCode
 113         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
 114
 115         //ignore null
 116         static final boolean ignoreNull = true;
 117
 118         static final boolean switchSpeciesGroup = true;
 119
 120         static boolean useClassification = true;
 121
 122         static boolean isSplitTdwgCodes = false;
 123         static boolean useEmAreaVocabulary = true;
 124
 125         private final boolean removeHttpMapsAnchor = true;
 126
 127
 128         static final String infrGenericRankAbbrev = "[unranked]";
 129         static final String infrSpecificRankAbbrev = "[unranked]";
 130
 131
 132         static String taxonTable = "v_cdm_exp_taxaAll";
 133         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;
 134         static String relPTaxonIdQuery = " SELECT r.RelPTaxonId " +
 135                                         " FROM RelPTaxon AS r INNER JOIN v_cdm_exp_taxaDirect AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk" +
 136                                         " WHERE r.RelPTaxonID NOT IN (1883791,1883800,1883823,1883852,1883853,1883864,1883896,1883921,1883943,1883944,1883955,1883972,1884008,1884030,1884031,1884035) " + //Unpublished Kew taxa which are not imported anymore
 137                                         " ";  // AND r.RelQualifierFk =1
 138         static String nameIdTable = " v_cdm_exp_namesAll ";
 139         static String referenceIdTable = " v_cdm_exp_refAll ";
 140         static String refDetailFilter =  " RefDetailID IN (SELECT RefDetailID FROM v_cdm_exp_RefDetail) ";
 141         static String factFilter = " factId IN ( SELECT factId FROM v_cdm_exp_factsAll WHERE FactCategoryFk NOT IN (12, 14, 249, 251))";
 142         static String occurrenceFilter = " occurrenceId IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
 143         static String occurrenceSourceFilter = " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
 144         static String commonNameFilter = " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )";
 145         static String webMarkerFilter = " TableNameFk <> 500 OR ( RIdentifierFk IN (SELECT RIdentifier FROM v_cdm_exp_taxaAll)) ";
 146         static String authorTeamFilter = null; // " authorTeamId IN (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) ";
 147         static String authorFilter = null;  // " authorId IN (SELECT authorId FROM v_cdm_exp_authorsAll) ";
 148
 149
 150
 151 // **************** ALL *********************
 152
 153         boolean invers = !(hbm2dll == DbSchemaValidation.CREATE);
 154
 155         static final boolean doUser = true;
 156 //      //authors
 157         static final boolean doAuthors = true;
 158         //references
 159         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
 160         //names
 161         static final boolean doTaxonNames = true;
 162         static final boolean doRelNames = true;
 163         static final boolean doNameStatus = true;
 164         static final boolean doTypes = false;  //serious types do not exist in E+M
 165         static final boolean doNameFacts = true;
 166
 167         //taxa
 168         static final boolean doTaxa = true;
 169         static final boolean doFacts = true;
 170         static final boolean doCommonNames = true;
 171         static final boolean doOccurences = true;
 172         static final boolean doRelTaxa = false;
 173         static final boolean doRunTransmissionEngine = (hbm2dll == DbSchemaValidation.VALIDATE);
 174
 175         //etc.
 176         static final boolean doMarker = true;
 177
 178
 179         public void importEm2CDM (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
 180                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
 181                 //make BerlinModel Source
 182
 183                 BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source,  destination);
 184
 185                 config.setClassificationName(classificationName);
 186
 187                 config.setClassificationUuid(classificationUuid);
 188                 config.setSourceSecId(sourceSecId);
 189                 config.setNomenclaturalCode(nomenclaturalCode);
 190                 config.setIgnoreNull(ignoreNull);
 191
 192                 config.setDoAuthors(doAuthors ^ invers);
 193                 config.setDoReferences(invers ? doReferences.invers() : doReferences);
 194                 config.setDoTaxonNames(doTaxonNames ^ invers);
 195                 config.setDoRelNames(doRelNames ^ invers);
 196                 config.setDoNameStatus(doNameStatus ^ invers);
 197                 config.setDoTypes(doTypes);  //always false
 198                 config.setDoNameFacts(doNameFacts ^ invers);
 199                 config.setDoTaxa(doTaxa ^ invers);
 200                 config.setDoRelTaxa(doRelTaxa ^ invers);
 201                 config.setDoFacts(doFacts ^ invers);
 202                 config.setDoOccurrence(doOccurences ^ invers);
 203                 config.setDoCommonNames(doCommonNames ^ invers);
 204
 205                 config.setDoMarker(doMarker ^ invers);
 206                 config.setDoUser(doUser ^ invers);
 207
 208                 config.setUseClassification(useClassification);
 209                 config.setSourceRefUuid(BerlinModelTransformer.uuidSourceRefEuroMed);
 210                 config.setEditor(editor);
 211                 config.setDbSchemaValidation(hbm2dll);
 212
 213                 // maximum number of name facts to import
 214                 config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
 215
 216                 config.setInfrGenericRankAbbrev(infrGenericRankAbbrev);
 217                 config.setInfrSpecificRankAbbrev(infrSpecificRankAbbrev);
 218                 config.setRemoveHttpMapsAnchor(removeHttpMapsAnchor);
 219
 220 //              filter
 221                 config.setTaxonTable(taxonTable);
 222                 config.setClassificationQuery(classificationQuery);
 223                 config.setRelTaxaIdQuery(relPTaxonIdQuery);
 224                 config.setNameIdTable(nameIdTable);
 225                 config.setReferenceIdTable(referenceIdTable);
 226                 config.setAuthorTeamFilter(authorTeamFilter);
 227                 config.setAuthorFilter(authorFilter);
 228                 config.setFactFilter(factFilter);
 229                 config.setRefDetailFilter(refDetailFilter);
 230                 config.setCommonNameFilter(commonNameFilter);
 231                 config.setOccurrenceFilter(occurrenceFilter);
 232                 config.setOccurrenceSourceFilter(occurrenceSourceFilter);
 233                 config.setWebMarkerFilter(webMarkerFilter);
 234                 config.setUseSingleClassification(useSingleClassification);
 235
 236                 //TDWG codes
 237                 config.setSplitTdwgCodes(isSplitTdwgCodes);
 238                 config.setUseEmAreaVocabulary(useEmAreaVocabulary);
 239
 240                 config.setCheck(check);
 241                 config.setEditor(editor);
 242                 config.setRecordsPerTransaction(partitionSize);
 243
 244                 config.setSwitchSpeciesGroup(switchSpeciesGroup);
 245
 246                 // invoke import
 247                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 248                 bmImport.invoke(config);
 249
 250                 renameRanks(config, bmImport);
 251
 252                 createFeatureTree(config, bmImport);
 253
 254                 changeCommonNameLabel(config, bmImport);
 255
 256                 createUsersAndRoles(config, bmImport);
 257
 258         runTransmissionEngine(config, bmImport);
 259
 260         importShapefile(config, bmImport);
 261
 262 //        markAreasAsHidden(config, bmImport);  //has been moved to BM occurrence import
 263
 264                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 265         }
 266
 267         //Rename Ranks (still needed?)
 268     private void renameRanks(BerlinModelImportConfigurator config,
 269             CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
 270
 271         if (config.isDoTaxonNames() && (config.getCheck().isImport() )  ){
 272                         ICdmRepository app = bmImport.getCdmAppController();
 273                         TransactionStatus tx = app.startTransaction();
 274                         try {
 275                                 Rank sectBot = (Rank)app.getTermService().find(Rank.SECTION_BOTANY().getUuid());
 276                                 Representation repr = sectBot.getRepresentation(Language.ENGLISH());
 277                                 repr.setAbbreviatedLabel(repr.getAbbreviatedLabel().replace("(bot.)", "").trim());
 278                                 repr.setLabel(repr.getLabel().replace("(Botany)", "").trim());
 279                                 sectBot.setTitleCache(null, false);  //to definetely update the titleCache also
 280                                 app.getTermService().saveOrUpdate(sectBot);
 281
 282                                 Rank subSectBot = (Rank)app.getTermService().find(Rank.SECTION_BOTANY().getUuid());
 283                                 repr = subSectBot.getRepresentation(Language.ENGLISH());
 284                                 repr.setAbbreviatedLabel(repr.getAbbreviatedLabel().replace("(bot.)", "").trim());
 285                                 repr.setLabel(repr.getLabel().replace("(Botany)", "").trim());
 286                                 subSectBot.setTitleCache(null, false);  //to definetely update the titleCache also
 287                                 app.getTermService().saveOrUpdate(subSectBot);
 288                                 app.commitTransaction(tx);
 289                         } catch (Exception e) {
 290                             e.printStackTrace();
 291                 logger.error("Exception in renameRanks: " + e.getMessage());
 292                         }
 293                 }
 294     }
 295
 296     //create feature tree
 297     private void createFeatureTree(BerlinModelImportConfigurator config,
 298             CdmDefaultImport<BerlinModelImportConfigurator> bmImport)
 299     {
 300             if (config.isDoFacts() && (config.getCheck().isImport()  )  ){
 301                         try {
 302                 ICdmRepository app = bmImport.getCdmAppController();
 303                 TransactionStatus tx = app.startTransaction();
 304
 305                 //make feature tree
 306                 FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
 307                 FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 308                 tree.getRoot().addChild(imageNode);
 309                 FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 310                 tree.getRoot().addChild(distributionNode, 1);
 311                 FeatureNode commonNameNode = FeatureNode.NewInstance(Feature.COMMON_NAME());
 312                 tree.getRoot().addChild(commonNameNode, 2);
 313                 app.getFeatureTreeService().saveOrUpdate(tree);
 314
 315                 app.commitTransaction(tx);
 316             } catch (Exception e) {
 317                 e.printStackTrace();
 318                 logger.error("Exception in createFeatureTree: " + e.getMessage());
 319             }
 320                 }
 321     }
 322
 323     //Change common name label
 324     private void changeCommonNameLabel(BerlinModelImportConfigurator config,
 325             CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
 326             if (config.isDoFacts() && (config.getCheck().isImport()  )  ){
 327                 try {
 328                 ICdmRepository app = bmImport.getCdmAppController();
 329                 TransactionStatus tx = app.startTransaction();
 330
 331                 DefinedTermBase<?> commonNameFeature = app.getTermService().find(Feature.COMMON_NAME().getUuid());
 332                 commonNameFeature.setLabel("Common Names", Language.ENGLISH());
 333                 commonNameFeature.setTitleCache(null, false);  //to definitely update the titleCache also
 334                 app.getTermService().saveOrUpdate(commonNameFeature);
 335
 336                 app.commitTransaction(tx);
 337             } catch (Exception e) {
 338                 e.printStackTrace();
 339                 logger.error("Exception in changeCommonNameLabel: " + e.getMessage());
 340             }
 341             }
 342     }
 343
 344     //1. run transmission engine #3979
 345     private void runTransmissionEngine(BerlinModelImportConfigurator config,
 346             CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
 347
 348         if (doRunTransmissionEngine && (config.getCheck().isImport()  )  ){
 349             try {
 350                 ICdmRepository app = bmImport.getCdmAppController();
 351
 352                 final List<String> term_init_strategy = Arrays.asList(new String []{
 353                         "representations"
 354                 });
 355
 356                 UUID uuidSuperAreaLevel = BerlinModelTransformer.uuidEuroMedAreaLevelFirst;
 357                 NamedAreaLevel euroMedLevel1 = (NamedAreaLevel)app.getTermService().find(uuidSuperAreaLevel);
 358
 359                 Pager<NamedArea> areaPager = app.getTermService().list(
 360                         euroMedLevel1,
 361                         (NamedAreaType) null,
 362                         null,
 363                         null,
 364                         (List<OrderHint>) null,
 365                         term_init_strategy);
 366                 TransmissionEngineDistribution transmissionEngineDistribution = (TransmissionEngineDistribution)app.getBean("transmissionEngineDistribution");
 367                 transmissionEngineDistribution.accumulate(
 368                         AggregationMode.byAreasAndRanks,
 369                         areaPager.getRecords(),
 370                         Rank.UNRANKED_INFRASPECIFIC(),   //or do we even want to start from lower (UNKNOWN?)
 371                         Rank.GENUS(),
 372                         null,
 373                         DefaultProgressMonitor.NewInstance());
 374             } catch (Exception e) {
 375                 e.printStackTrace();
 376                 logger.error("Exception in markAreasAsHidden: " + e.getMessage());
 377             }
 378         }
 379     }
 380
 381 //    //5.Mark areas to be hidden #3979 .5
 382 //    private void markAreasAsHidden(BerlinModelImportConfigurator config,
 383 //            CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
 384 //
 385 //        if (config.isDoOccurrence() && (config.getCheck().isImport())){
 386 //              try {
 387 //                ICdmRepository app = bmImport.getCdmAppController();
 388 //                TransactionStatus tx = app.startTransaction();
 389 //
 390 //                MarkerType hiddenAreaMarkerType = MarkerType.NewInstance("Used to hide distributions for the named areas in publications", "Hidden Area", null);
 391 //                hiddenAreaMarkerType.setUuid(BerlinModelTransformer.uuidHiddenArea);
 392 //                @SuppressWarnings("unchecked")
 393 //                TermVocabulary<MarkerType> vocUserDefinedMarkerTypes = app.getVocabularyService().find(CdmImportBase.uuidUserDefinedMarkerTypeVocabulary);
 394 //                if (vocUserDefinedMarkerTypes == null){
 395 //                    String message = "Marker type vocabulary could not be found. Hidden areas not added.";
 396 //                    logger.error(message);
 397 //                    System.out.println(message);
 398 //                }else{
 399 //                    vocUserDefinedMarkerTypes.addTerm(hiddenAreaMarkerType);
 400 //                    app.getVocabularyService().saveOrUpdate(vocUserDefinedMarkerTypes);
 401 //
 402 //                    //Add hidden area marker to Rs(C) and Rs(N)
 403 //                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs);
 404 //                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_B);
 405 //                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_C);
 406 //                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_E);
 407 //                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_N);
 408 //                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_K);
 409 //                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_W);
 410 //                 }
 411 //                app.commitTransaction(tx);
 412 //            } catch (Exception e) {
 413 //                e.printStackTrace();
 414 //                logger.error("Exception in markAreasAsHidden: " + e.getMessage());
 415 //            }
 416 //          }
 417 //    }
 418 //
 419 //    private void hideArea(ICdmRepository app, MarkerType hiddenAreaMarkerType, UUID areaUuid) {
 420 //        NamedArea area = (NamedArea)app.getTermService().find(areaUuid);
 421 //        area.addMarker(Marker.NewInstance(hiddenAreaMarkerType, true));
 422 //        app.getTermService().saveOrUpdate(area);
 423 //    }
 424
 425     //2. import shapefile attributes #3979 .2
 426     private void importShapefile(BerlinModelImportConfigurator config,
 427             CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
 428
 429         if (config.isDoOccurrence() && (config.getCheck().isImport())){
 430
 431                try {
 432             UUID areaVocabularyUuid = BerlinModelTransformer.uuidVocEuroMedAreas;
 433                List<String> idSearchFields = Arrays.asList(new String[]{"EMAREA","PARENT"});
 434                String wmsLayerName = "euromed_2013";
 435                Set<UUID> areaUuidSet = null;
 436
 437                ICdmRepository app = bmImport.getCdmAppController();
 438                IEditGeoService geoService = (IEditGeoService)app.getBean("editGeoService");
 439
 440                Map<NamedArea, String> resultMap;
 441                try {
 442 //             URL url =  ClassLoader.getSystemResource("myConfig.txt");
 443 //             FileReader fileReader = new FileReader(url.getFile());
 444                    InputStream in = EuroMedActivator.class.getResourceAsStream("/euromed/euromed_2013.csv");
 445                    Reader reader = new InputStreamReader(in, "UTF-8");
 446
 447                    resultMap = geoService.mapShapeFileToNamedAreas(
 448                                reader, idSearchFields , wmsLayerName , areaVocabularyUuid, areaUuidSet);
 449                    Map<String, String> flatResultMap = new HashMap<String, String>(resultMap.size());
 450                    for(NamedArea area : resultMap.keySet()){
 451                        flatResultMap.put(area.getTitleCache() + " [" + area.getUuid() + "]", resultMap.get(area));
 452                    }
 453                } catch (IOException e) {
 454                     String message = "IOException when reading from mapping file or creating result map.";
 455                     logger.error(message);
 456                     System.out.println(message);
 457                }
 458         } catch (Exception e) {
 459             e.printStackTrace();
 460             logger.error("Exception in importShapefile: " + e.getMessage());
 461         }
 462             }
 463     }
 464
 465     //4. Create users and assign roles  #3979
 466     private void createUsersAndRoles(BerlinModelImportConfigurator config,
 467             CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
 468
 469         try {
 470             if (config.isDoRelTaxa() && (config.getCheck().isImport())){
 471                 ICdmRepository app = bmImport.getCdmAppController();
 472                 TransactionStatus tx = app.startTransaction();
 473
 474                 //eraabstraube
 475                 String eraabstraube = "eraabstraube";
 476                 List<User> users = app.getUserService().listByUsername(eraabstraube, MatchMode.EXACT, null, null, null, null, null);
 477                 User userEraabStraube;
 478                 if (users.isEmpty()){
 479                     userEraabStraube = User.NewInstance(eraabstraube, eraabstraube);
 480                 }else{
 481                     userEraabStraube = users.get(0);
 482                 }
 483                 if (userEraabStraube.getPerson() == null){
 484                     Person eckhard = Person.NewInstance();
 485                     eckhard.setLastname("von Raab-Straube");
 486                     eckhard.setFirstname("Eckhard");
 487                     eckhard.setPrefix("Dr.");
 488                     userEraabStraube.setPerson(eckhard);
 489                 }
 490                 app.getUserService().saveOrUpdate(userEraabStraube);
 491
 492                 //groups
 493                 Group groupEditor = app.getGroupService().load(Group.groupEditorUuid);
 494                 groupEditor.addMember(userEraabStraube);
 495                 app.getGroupService().saveOrUpdate(groupEditor);
 496
 497                 Group groupProjectManager = app.getGroupService().load(Group.groupProjectManagerUuid);
 498                 groupProjectManager.addMember(userEraabStraube);
 499                 app.getGroupService().saveOrUpdate(groupProjectManager);
 500
 501                 String[] publishRoles = new String[]{Role.ROLE_PUBLISH.toString()};
 502                 Group groupPublisher = checkGroup(app.getGroupService(), Group.groupPublisherUuid, "Publisher", publishRoles);
 503                 groupPublisher.addMember(userEraabStraube);
 504                 app.getGroupService().saveOrUpdate(groupPublisher);
 505
 506                 UUID uuidEuroMedPlantBaseGroup = UUID.fromString("91be42ea-ad04-4458-9836-389277e773db");
 507                 String[] emPlantBaseRoles = new String[]{"TAXONNODE.[CREATE,READ,UPDATE,DELETE]"};
 508                 Group euroMedPlantbase = checkGroup(app.getGroupService(), uuidEuroMedPlantBaseGroup, "Euro+Med Plantbase", emPlantBaseRoles);
 509                 euroMedPlantbase.addMember(userEraabStraube);
 510                 app.getGroupService().saveOrUpdate(euroMedPlantbase);
 511
 512                 //cichorieae-editor
 513                 String cichorieaeEditor = "cichorieae-editor";
 514                 app.getUserService().listByUsername(cichorieaeEditor, MatchMode.EXACT, null, null, null, null, null);
 515                 User userCichEditor;
 516                 if (users.isEmpty()){
 517                     userCichEditor = User.NewInstance(cichorieaeEditor, cichorieaeEditor);
 518                 }else{
 519                     userCichEditor = users.get(0);
 520                 }
 521                 app.getUserService().saveOrUpdate(userCichEditor);
 522
 523                 //groups
 524                 groupEditor.addMember(userCichEditor);
 525                 app.getGroupService().saveOrUpdate(groupEditor);
 526
 527                 UUID uuidCichorieaeSubtree = null;
 528                 UUID uuidCichorieae = UUID.fromString("63c7dbeb-b9a2-48b8-a75f-e3fe5e161f7c");
 529                 Taxon cich = (Taxon)app.getTaxonService().find(uuidCichorieae);
 530                 if (cich != null){
 531                     if (!cich.getTaxonNodes().isEmpty()){
 532                         TaxonNode cichNode = cich.getTaxonNodes().iterator().next();
 533                         uuidCichorieaeSubtree = cichNode.getUuid();
 534                     }
 535                 }
 536
 537                 String[] cichorieaeRoles = new String[]{};
 538                 if (uuidCichorieaeSubtree != null){
 539                     cichorieaeRoles = new String[]{"TAXONNODE.[CREATE,READ,UPDATE,DELETE]{"+uuidCichorieaeSubtree.toString()+"}"};
 540                 }else{
 541                     String message = "Cichorieae node could not be found for cichorieae-editor role";
 542                     logger.warn(message);
 543                     System.out.println(message);
 544                 }
 545                 UUID uuidCichorieaeGroup = UUID.fromString("a630938d-dd4f-48c2-9406-91def487b11e");
 546                 String cichorieaeGroupName = "Cichorieae";
 547                 Group cichorieaeGroup = checkGroup(app.getGroupService(), uuidCichorieaeGroup, cichorieaeGroupName, cichorieaeRoles);
 548                 cichorieaeGroup.addMember(userCichEditor);
 549                 app.getGroupService().saveOrUpdate(cichorieaeGroup);
 550
 551                 app.commitTransaction(tx);
 552             }
 553         } catch (Exception e) {
 554             e.printStackTrace();
 555             logger.error("Exception in createUsersAndRoles: " + e.getMessage());
 556         }
 557     }
 558
 559         /**
 560           * copied from {@link FirstDataInserter#checkGroup}
 561      */
 562     private Group checkGroup(IGroupService groupService, UUID groupUuid, String groupName, String[] requiredAuthorities) {
 563         Group group = groupService.load(groupUuid);
 564         if(group == null){
 565             group = Group.NewInstance();
 566             group.setUuid(groupUuid);
 567             logger.info("New Group '" + groupName + "' created");
 568         }
 569         group.setName(groupName); // force name
 570
 571         Set<GrantedAuthority> grantedAuthorities = group.getGrantedAuthorities();
 572
 573         for(String a : requiredAuthorities){
 574             boolean isMissing = true;
 575             for(GrantedAuthority ga : grantedAuthorities){
 576                 if(a.equals(ga.getAuthority())){
 577                     isMissing = false;
 578                     break;
 579                 }
 580             }
 581             if(isMissing){
 582                 GrantedAuthorityImpl newGa = GrantedAuthorityImpl.NewInstance();
 583                 newGa.setAuthority(a);
 584                 group.addGrantedAuthority(newGa);
 585                 logger.info("New GrantedAuthority '" + a + "' added  to '" + groupName + "'");
 586             }
 587         }
 588         groupService.saveOrUpdate(group);
 589         logger.info("Check of group  '" + groupName + "' done");
 590         return group;
 591     }
 592
 593
 594         /**
 595          * @param args
 596          */
 597         public static void main(String[] args) {
 598                 EuroMedActivator importActivator = new EuroMedActivator();
 599                 Source source = berlinModelSource;
 600                 ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 601
 602                 importActivator.importEm2CDM(source, cdmRepository, hbm2dll);
 603                 if (includePesiExport){
 604                         //not available from here since E+M was moved to app-import
 605 //                      PesiExportActivatorEM exportActivator = new PesiExportActivatorEM();
 606 //                      exportActivator.doExport(cdmRepository);
 607                 }
 608
 609         }
 610
 611 }