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
  70  * dump and restore the resulting data bas under another operation systen
  71  * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
  72  *
  73  * @author a.mueller
  74  */
  75 public class EuroMedActivator {
  76         private static final Logger logger = Logger.getLogger(EuroMedActivator.class);
  77
  78         //database validation status (create, update, validate ...)
  79         static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
  80 //  static final Source berlinModelSource = BerlinModelSources.euroMed_Pub2();
  81         static final Source berlinModelSource = BerlinModelSources.euroMed_BGBM42();
  82 //      static final Source berlinModelSource = BerlinModelSources.euroMed_PESI3();
  83 //
  84     static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  85 //  static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_euromed();
  86 //    static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_euromed2();
  87 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_euroMed();
  88 //    static final ICdmDataSource cdmDestination = CdmDestinations.cdm_euroMed_production();
  89
  90     //check - import
  91     static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  92
  93     static final boolean doUser = true;
  94 //  //authors
  95     static final boolean doAuthors = true;
  96     //references
  97     static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
  98     //names
  99     static final boolean doTaxonNames = true;
 100     static final boolean doRelNames = true;
 101     static final boolean doNameStatus = true;
 102     static final boolean doNameFacts = true;
 103
 104     //taxa
 105     static final boolean doTaxa = true;
 106     static final boolean doFacts = true;
 107     static final boolean doRelTaxa = true;
 108     static final boolean doOccurrences = false;
 109     static final boolean doOccurrenceSources = false;
 110     static final boolean doCommonNames = false;  //currently takes very long
 111
 112   //serious types do not exist in E+M except for name types which are handled in name relations
 113     static final boolean doTypes = false;  //serious types do not exist in E+M except for name types which are handled in name relations
 114
 115
 116     static final boolean doRunTransmissionEngine = false; // (hbm2dll == DbSchemaValidation.VALIDATE);
 117
 118     //etc.
 119     static final boolean doMarker = false;  //no relevant markers exist
 120
 121     boolean invers = !(hbm2dll == DbSchemaValidation.CREATE);
 122
 123     boolean doPreliminaryRefDetailsWithNames = true;
 124
 125     boolean logNotMatchingOldNames = false;
 126     boolean logMatchingNotExportedOldNames = false;  //true
 127     boolean checkOldNameIsSynonym = true;
 128
 129         static final boolean includePesiExport = false;
 130
 131         static final int sourceSecId = 7000000; //500000
 132         static final UUID classificationUuid = UUID.fromString("314a68f9-8449-495a-91c2-92fde8bcf344");
 133         static final boolean useSingleClassification = true;
 134         static final String classificationName = "Euro+Med 2018";
 135         static final UUID featureTreeUuid = UUID.fromString("6a5e1c2b-ec0d-46c8-9c7d-a2059267ffb7");
 136         static final Object[] featureKeyList = new Integer[]{1, 31, 4, 98, 41};
 137
 138         // set to zero for unlimited nameFacts
 139         static final int maximumNumberOfNameFacts = 0;
 140
 141         static final int partitionSize = 2500;
 142
 143
 144         //editor - import
 145         static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
 146
 147         //NomenclaturalCode
 148         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
 149
 150         //ignore null
 151         static final boolean ignoreNull = false;
 152
 153         static final boolean switchSpeciesGroup = true;
 154
 155         static boolean useClassification = true;
 156
 157         static boolean isSplitTdwgCodes = false;
 158         static boolean useEmAreaVocabulary = true;
 159
 160         private final boolean removeHttpMapsAnchor = true;
 161
 162
 163         static final String infrGenericRankAbbrev = "[unranked]";
 164         static final String infrSpecificRankAbbrev = "[unranked]";
 165
 166         static boolean useLastScrutinyAsSec = true;
 167         static boolean warnForDifferingSynonymReference = false;
 168
 169
 170         static String taxonTable = "v_cdm_exp_taxaAll";
 171         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;
 172         static String relPTaxonIdQuery = " SELECT r.RelPTaxonId "
 173                                         + " FROM RelPTaxon AS r "
 174                                         + "   INNER JOIN v_cdm_exp_taxaDirect AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk "
 175                                         + "   INNER JOIN PTaxon As pt1 ON pt1.PTNameFk = r.PTNameFk1 AND pt1.PTRefFk = r.PTRefFk1 "
 176                                         + " WHERE r.RelPTaxonID NOT IN (1874890,1874959,1874932,1874793,1874956,1874971,1874902,1874696) " //Relations to unpublished Kew genus taxa of Bethulaceae which are not imported anymore, but Bethalaceae is still imported
 177                                         + "     AND NOT (pt1.PTRefFk = 8000000 AND pt1.publishFlag = 0) ";
 178         static String nameIdTable = " v_cdm_exp_namesAll ";
 179         static String referenceIdTable = " v_cdm_exp_refAll ";
 180         static String refDetailFilter =  " RefDetailID IN (SELECT RefDetailID FROM v_cdm_exp_RefDetail) ";
 181         static String factFilter = " factId IN ( SELECT factId FROM v_cdm_exp_factsAll WHERE FactCategoryFk NOT IN (12, 14, 249, 251))";
 182         static String occurrenceFilter = " occurrenceId IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
 183         static String occurrenceSourceFilter = " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
 184         static String commonNameFilter = " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )";
 185         static String webMarkerFilter = " TableNameFk <> 500 OR ( RIdentifierFk IN (SELECT RIdentifier FROM v_cdm_exp_taxaAll)) ";
 186         static String authorTeamFilter =  " authorTeamId IN (SELECT drvTab.authorTeamId FROM (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) as drvTab) ";
 187         static String authorFilter = " authorId IN (SELECT drvTab.authorId FROM (SELECT authorId FROM v_cdm_exp_authorsAll) as drvTab) ";
 188
 189
 190
 191 // **************** ALL *********************
 192
 193
 194
 195
 196         public void importEm2CDM (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
 197                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
 198                 //make BerlinModel Source
 199
 200                 BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source,  destination);
 201
 202                 config.setClassificationName(classificationName);
 203
 204                 config.setClassificationUuid(classificationUuid);
 205                 config.setSourceSecId(sourceSecId);
 206                 config.setNomenclaturalCode(nomenclaturalCode);
 207                 config.setIgnoreNull(ignoreNull);
 208
 209                 config.setDoAuthors(doAuthors ^ invers);
 210                 config.setDoReferences(invers ? doReferences.invers() : doReferences);
 211                 config.setDoTaxonNames(doTaxonNames ^ invers);
 212                 config.setDoRelNames(doRelNames ^ invers);
 213                 config.setDoNameStatus(doNameStatus ^ invers);
 214                 config.setDoTypes(doTypes);  //always false
 215                 config.setDoNameFacts(doNameFacts ^ invers);
 216                 config.setDoTaxa(doTaxa ^ invers);
 217                 config.setDoRelTaxa(doRelTaxa ^ invers);
 218                 config.setDoFacts(doFacts ^ invers);
 219                 config.setDoOccurrence(doOccurrences ^ invers);
 220                 config.setDoOccurrenceSources(doOccurrenceSources ^ invers);
 221         config.setDoCommonNames(doCommonNames ^ invers);
 222
 223                 config.setDoMarker(doMarker);
 224                 config.setDoUser(doUser ^ invers);
 225
 226                 config.setEuroMed(true);
 227
 228                 config.setLogNotMatchingOldNames(logNotMatchingOldNames);
 229                 config.setLogMatchingNotExportedOldNames(logMatchingNotExportedOldNames);
 230                 config.setCheckOldNameIsSynonym(checkOldNameIsSynonym);
 231
 232                 config.setUseClassification(useClassification);
 233                 config.setSourceRefUuid(BerlinModelTransformer.uuidSourceRefEuroMed);
 234                 config.setEditor(editor);
 235                 config.setDbSchemaValidation(hbm2dll);
 236                 config.setUseLastScrutinyAsSec(useLastScrutinyAsSec);
 237                 config.setWarnForDifferingSynonymReference(warnForDifferingSynonymReference);
 238
 239                 // maximum number of name facts to import
 240                 config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
 241
 242                 config.setInfrGenericRankAbbrev(infrGenericRankAbbrev);
 243                 config.setInfrSpecificRankAbbrev(infrSpecificRankAbbrev);
 244                 config.setRemoveHttpMapsAnchor(removeHttpMapsAnchor);
 245
 246                 config.setDoPreliminaryRefDetailsWithNames(doPreliminaryRefDetailsWithNames);
 247
 248 //              filter
 249                 config.setTaxonTable(taxonTable);
 250                 config.setClassificationQuery(classificationQuery);
 251                 config.setRelTaxaIdQuery(relPTaxonIdQuery);
 252                 config.setNameIdTable(nameIdTable);
 253                 config.setReferenceIdTable(referenceIdTable);
 254                 config.setAuthorTeamFilter(authorTeamFilter);
 255                 config.setAuthorFilter(authorFilter);
 256                 config.setFactFilter(factFilter);
 257                 config.setRefDetailFilter(refDetailFilter);
 258                 config.setCommonNameFilter(commonNameFilter);
 259                 config.setOccurrenceFilter(occurrenceFilter);
 260                 config.setOccurrenceSourceFilter(occurrenceSourceFilter);
 261                 config.setWebMarkerFilter(webMarkerFilter);
 262                 config.setUseSingleClassification(useSingleClassification);
 263
 264                 //TDWG codes
 265                 config.setSplitTdwgCodes(isSplitTdwgCodes);
 266                 config.setUseEmAreaVocabulary(useEmAreaVocabulary);
 267
 268                 config.setCheck(check);
 269                 config.setEditor(editor);
 270                 config.setRecordsPerTransaction(partitionSize);
 271
 272                 config.setSwitchSpeciesGroup(switchSpeciesGroup);
 273
 274                 // invoke import
 275                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<>();
 276                 bmImport.invoke(config);
 277
 278                 renameRanks(config, bmImport);
 279
 280                 createFeatureTree(config, bmImport);
 281
 282                 changeCommonNameLabel(config, bmImport);
 283
 284                 createUsersAndRoles(config, bmImport);
 285
 286         runTransmissionEngine(config, bmImport);
 287
 288         importShapefile(config, bmImport);
 289
 290 //        markAreasAsHidden(config, bmImport);  //has been moved to BM occurrence import
 291
 292                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 293         }
 294
 295         //Rename Ranks (still needed?)
 296     private void renameRanks(BerlinModelImportConfigurator config,
 297             CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
 298
 299         if (config.isDoTaxonNames() && (config.getCheck().isImport() )  ){
 300                         ICdmRepository app = bmImport.getCdmAppController();
 301                         TransactionStatus tx = app.startTransaction();
 302                         try {
 303                                 Rank sectBot = (Rank)app.getTermService().find(Rank.SECTION_BOTANY().getUuid());
 304                                 Representation repr = sectBot.getRepresentation(Language.ENGLISH());
 305                                 repr.setAbbreviatedLabel(repr.getAbbreviatedLabel().replace("(bot.)", "").trim());
 306                                 repr.setLabel(repr.getLabel().replace("(Botany)", "").trim());
 307                                 sectBot.setTitleCache(null, false);  //to definitely update the titleCache also
 308                                 app.getTermService().saveOrUpdate(sectBot);
 309
 310                                 Rank subSectBot = (Rank)app.getTermService().find(Rank.SECTION_BOTANY().getUuid());
 311                                 repr = subSectBot.getRepresentation(Language.ENGLISH());
 312                                 repr.setAbbreviatedLabel(repr.getAbbreviatedLabel().replace("(bot.)", "").trim());
 313                                 repr.setLabel(repr.getLabel().replace("(Botany)", "").trim());
 314                                 subSectBot.setTitleCache(null, false);  //to definitely update the titleCache also
 315                                 app.getTermService().saveOrUpdate(subSectBot);
 316                                 app.commitTransaction(tx);
 317                         } catch (Exception e) {
 318                             e.printStackTrace();
 319                 logger.error("Exception in renameRanks: " + e.getMessage());
 320                         }
 321                 }
 322     }
 323
 324     //create feature tree
 325     private void createFeatureTree(BerlinModelImportConfigurator config,
 326             CdmDefaultImport<BerlinModelImportConfigurator> bmImport){
 327             if (config.isDoFacts() && (config.getCheck().isImport()  )  ){
 328                         try {
 329                 ICdmRepository app = bmImport.getCdmAppController();
 330                 TransactionStatus tx = app.startTransaction();
 331
 332                 //make feature tree
 333                 FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
 334                 tree.setTitleCache("Euro+Med Feature Tree", true);
 335                 FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 336                 tree.getRoot().addChild(imageNode);
 337                 FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 338                 tree.getRoot().addChild(distributionNode, 1);
 339                 FeatureNode commonNameNode = FeatureNode.NewInstance(Feature.COMMON_NAME());
 340                 tree.getRoot().addChild(commonNameNode, 2);
 341                 app.getFeatureTreeService().saveOrUpdate(tree);
 342
 343                 app.commitTransaction(tx);
 344             } catch (Exception e) {
 345                 e.printStackTrace();
 346                 logger.error("Exception in createFeatureTree: " + e.getMessage());
 347             }
 348                 }
 349     }
 350
 351     //Change common name label
 352     private void changeCommonNameLabel(BerlinModelImportConfigurator config,
 353             CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
 354             if (config.isDoFacts() && (config.getCheck().isImport()  )  ){
 355                 try {
 356                 ICdmRepository app = bmImport.getCdmAppController();
 357                 TransactionStatus tx = app.startTransaction();
 358
 359                 DefinedTermBase<?> commonNameFeature = app.getTermService().find(Feature.COMMON_NAME().getUuid());
 360                 commonNameFeature.setLabel("Common Names", Language.ENGLISH());
 361                 commonNameFeature.setTitleCache(null, false);  //to definitely update the titleCache also
 362                 app.getTermService().saveOrUpdate(commonNameFeature);
 363
 364                 app.commitTransaction(tx);
 365             } catch (Exception e) {
 366                 e.printStackTrace();
 367                 logger.error("Exception in changeCommonNameLabel: " + e.getMessage());
 368             }
 369             }
 370     }
 371
 372     //1. run transmission engine #3979
 373     private void runTransmissionEngine(BerlinModelImportConfigurator config,
 374             CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
 375
 376         if (doRunTransmissionEngine && (config.getCheck().isImport()  )  ){
 377             try {
 378                 ICdmRepository app = bmImport.getCdmAppController();
 379
 380                 final List<String> term_init_strategy = Arrays.asList(new String []{
 381                         "representations"
 382                 });
 383
 384                 UUID uuidSuperAreaLevel = BerlinModelTransformer.uuidEuroMedAreaLevelFirst;
 385                 NamedAreaLevel euroMedLevel1 = (NamedAreaLevel)app.getTermService().find(uuidSuperAreaLevel);
 386
 387                 Pager<NamedArea> areaPager = app.getTermService().list(
 388                         euroMedLevel1,
 389                         (NamedAreaType) null,
 390                         null,
 391                         null,
 392                         (List<OrderHint>) null,
 393                         term_init_strategy);
 394                 TransmissionEngineDistribution transmissionEngineDistribution = (TransmissionEngineDistribution)app.getBean("transmissionEngineDistribution");
 395                 transmissionEngineDistribution.accumulate(
 396                         AggregationMode.byAreasAndRanks,
 397                         areaPager.getRecords(),
 398                         Rank.UNRANKED_INFRASPECIFIC(),   //or do we even want to start from lower (UNKNOWN?)
 399                         Rank.GENUS(),
 400                         null,
 401                         DefaultProgressMonitor.NewInstance());
 402             } catch (Exception e) {
 403                 e.printStackTrace();
 404                 logger.error("Exception in markAreasAsHidden: " + e.getMessage());
 405             }
 406         }
 407     }
 408
 409 //    //5.Mark areas to be hidden #3979 .5
 410 //    private void markAreasAsHidden(BerlinModelImportConfigurator config,
 411 //            CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
 412 //
 413 //        if (config.isDoOccurrence() && (config.getCheck().isImport())){
 414 //              try {
 415 //                ICdmRepository app = bmImport.getCdmAppController();
 416 //                TransactionStatus tx = app.startTransaction();
 417 //
 418 //                MarkerType hiddenAreaMarkerType = MarkerType.NewInstance("Used to hide distributions for the named areas in publications", "Hidden Area", null);
 419 //                hiddenAreaMarkerType.setUuid(BerlinModelTransformer.uuidHiddenArea);
 420 //                @SuppressWarnings("unchecked")
 421 //                TermVocabulary<MarkerType> vocUserDefinedMarkerTypes = app.getVocabularyService().find(CdmImportBase.uuidUserDefinedMarkerTypeVocabulary);
 422 //                if (vocUserDefinedMarkerTypes == null){
 423 //                    String message = "Marker type vocabulary could not be found. Hidden areas not added.";
 424 //                    logger.error(message);
 425 //                    System.out.println(message);
 426 //                }else{
 427 //                    vocUserDefinedMarkerTypes.addTerm(hiddenAreaMarkerType);
 428 //                    app.getVocabularyService().saveOrUpdate(vocUserDefinedMarkerTypes);
 429 //
 430 //                    //Add hidden area marker to Rs(C) and Rs(N)
 431 //                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs);
 432 //                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_B);
 433 //                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_C);
 434 //                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_E);
 435 //                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_N);
 436 //                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_K);
 437 //                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_W);
 438 //                 }
 439 //                app.commitTransaction(tx);
 440 //            } catch (Exception e) {
 441 //                e.printStackTrace();
 442 //                logger.error("Exception in markAreasAsHidden: " + e.getMessage());
 443 //            }
 444 //          }
 445 //    }
 446 //
 447 //    private void hideArea(ICdmRepository app, MarkerType hiddenAreaMarkerType, UUID areaUuid) {
 448 //        NamedArea area = (NamedArea)app.getTermService().find(areaUuid);
 449 //        area.addMarker(Marker.NewInstance(hiddenAreaMarkerType, true));
 450 //        app.getTermService().saveOrUpdate(area);
 451 //    }
 452
 453     //2. import shapefile attributes #3979 .2
 454     private void importShapefile(BerlinModelImportConfigurator config,
 455             CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
 456
 457         if (config.isDoOccurrence() && (config.getCheck().isImport())){
 458
 459                try {
 460                    UUID areaVocabularyUuid = BerlinModelTransformer.uuidVocEuroMedAreas;
 461                List<String> idSearchFields = Arrays.asList(new String[]{"EMAREA","PARENT"});
 462                String wmsLayerName = "euromed_2013";
 463                Set<UUID> areaUuidSet = null;
 464
 465                ICdmRepository app = bmImport.getCdmAppController();
 466                IEditGeoService geoService = (IEditGeoService)app.getBean("editGeoService");
 467
 468                Map<NamedArea, String> resultMap;
 469                try {
 470                    InputStream in = EuroMedActivator.class.getResourceAsStream("/euromed/euromed_2013.csv");
 471                    Reader reader = new InputStreamReader(in, "UTF-8");
 472
 473                    resultMap = geoService.mapShapeFileToNamedAreas(
 474                                reader, idSearchFields , wmsLayerName , areaVocabularyUuid, areaUuidSet);
 475                    Map<String, String> flatResultMap = new HashMap<>(resultMap.size());
 476                    for(NamedArea area : resultMap.keySet()){
 477                        flatResultMap.put(area.getTitleCache() + " [" + area.getUuid() + "]", resultMap.get(area));
 478                    }
 479                } catch (IOException e) {
 480                     String message = "IOException when reading from mapping file or creating result map.";
 481                     logger.error(message);
 482                     System.out.println(message);
 483                }
 484             } catch (Exception e) {
 485                 e.printStackTrace();
 486                 logger.error("Exception in importShapefile: " + e.getMessage());
 487             }
 488             }
 489     }
 490
 491     //4. Create users and assign roles  #3979
 492     private void createUsersAndRoles(BerlinModelImportConfigurator config,
 493             CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
 494
 495         try {
 496             if (config.isDoRelTaxa() && (config.getCheck().isImport())){
 497                 ICdmRepository app = bmImport.getCdmAppController();
 498                 TransactionStatus tx = app.startTransaction();
 499
 500                 //eraabstraube
 501                 String eraabstraube = "eraabstraube";
 502                 List<User> users = app.getUserService().listByUsername(eraabstraube, MatchMode.EXACT, null, null, null, null, null);
 503                 User userEraabStraube;
 504                 if (users.isEmpty()){
 505                     userEraabStraube = User.NewInstance(eraabstraube, eraabstraube);
 506                 }else{
 507                     userEraabStraube = users.get(0);
 508                 }
 509                 if (userEraabStraube.getPerson() == null){
 510                     Person eckhard = Person.NewInstance();
 511                     eckhard.setFamilyName("von Raab-Straube");
 512                     eckhard.setGivenName("Eckhard");
 513                     eckhard.setPrefix("Dr.");
 514                     userEraabStraube.setPerson(eckhard);
 515                 }
 516                 app.getUserService().saveOrUpdate(userEraabStraube);
 517
 518                 //groups
 519                 Group groupEditor = app.getGroupService().load(Group.GROUP_EDITOR_UUID);
 520                 groupEditor.addMember(userEraabStraube);
 521                 app.getGroupService().saveOrUpdate(groupEditor);
 522
 523                 Group groupProjectManager = app.getGroupService().load(Group.GROUP_PROJECT_MANAGER_UUID);
 524                 groupProjectManager.addMember(userEraabStraube);
 525                 app.getGroupService().saveOrUpdate(groupProjectManager);
 526
 527                 String[] publishRoles = new String[]{Role.ROLE_PUBLISH.toString()};
 528                 Group groupPublisher = checkGroup(app.getGroupService(), Group.GROUP_PUBLISHER_UUID, "Publisher", publishRoles);
 529                 groupPublisher.addMember(userEraabStraube);
 530                 app.getGroupService().saveOrUpdate(groupPublisher);
 531
 532                 UUID uuidEuroMedPlantBaseGroup = UUID.fromString("91be42ea-ad04-4458-9836-389277e773db");
 533                 String[] emPlantBaseRoles = new String[]{"TAXONNODE.[CREATE,READ,UPDATE,DELETE]"};
 534                 Group euroMedPlantbase = checkGroup(app.getGroupService(), uuidEuroMedPlantBaseGroup, "Euro+Med Plantbase", emPlantBaseRoles);
 535                 euroMedPlantbase.addMember(userEraabStraube);
 536                 app.getGroupService().saveOrUpdate(euroMedPlantbase);
 537
 538                 //cichorieae-editor
 539                 String cichorieaeEditor = "cichorieae-editor";
 540                 app.getUserService().listByUsername(cichorieaeEditor, MatchMode.EXACT, null, null, null, null, null);
 541                 User userCichEditor;
 542                 if (users.isEmpty()){
 543                     userCichEditor = User.NewInstance(cichorieaeEditor, cichorieaeEditor);
 544                 }else{
 545                     userCichEditor = users.get(0);
 546                 }
 547                 app.getUserService().saveOrUpdate(userCichEditor);
 548
 549                 //groups
 550                 groupEditor.addMember(userCichEditor);
 551                 app.getGroupService().saveOrUpdate(groupEditor);
 552
 553                 UUID uuidCichorieaeSubtree = null;
 554                 UUID uuidCichorieae = UUID.fromString("63c7dbeb-b9a2-48b8-a75f-e3fe5e161f7c");
 555                 Taxon cich = (Taxon)app.getTaxonService().find(uuidCichorieae);
 556                 if (cich != null){
 557                     if (!cich.getTaxonNodes().isEmpty()){
 558                         TaxonNode cichNode = cich.getTaxonNodes().iterator().next();
 559                         uuidCichorieaeSubtree = cichNode.getUuid();
 560                     }
 561                 }
 562
 563                 String[] cichorieaeRoles = new String[]{};
 564                 if (uuidCichorieaeSubtree != null){
 565                     cichorieaeRoles = new String[]{"TAXONNODE.[CREATE,READ,UPDATE,DELETE]{"+uuidCichorieaeSubtree.toString()+"}"};
 566                 }else{
 567                     String message = "Cichorieae node could not be found for cichorieae-editor role";
 568                     logger.warn(message);
 569                     System.out.println(message);
 570                 }
 571                 UUID uuidCichorieaeGroup = UUID.fromString("a630938d-dd4f-48c2-9406-91def487b11e");
 572                 String cichorieaeGroupName = "Cichorieae";
 573                 Group cichorieaeGroup = checkGroup(app.getGroupService(), uuidCichorieaeGroup, cichorieaeGroupName, cichorieaeRoles);
 574                 cichorieaeGroup.addMember(userCichEditor);
 575                 app.getGroupService().saveOrUpdate(cichorieaeGroup);
 576
 577                 app.commitTransaction(tx);
 578             }
 579         } catch (Exception e) {
 580             e.printStackTrace();
 581             logger.error("Exception in createUsersAndRoles: " + e.getMessage());
 582         }
 583     }
 584
 585         /**
 586           * copied from {@link FirstDataInserter#checkGroup}
 587      */
 588     private Group checkGroup(IGroupService groupService, UUID groupUuid, String groupName, String[] requiredAuthorities) {
 589         Group group = groupService.load(groupUuid);
 590         if(group == null){
 591             group = Group.NewInstance();
 592             group.setUuid(groupUuid);
 593             logger.info("New Group '" + groupName + "' created");
 594         }
 595         group.setName(groupName); // force name
 596
 597         Set<GrantedAuthority> grantedAuthorities = group.getGrantedAuthorities();
 598
 599         for(String a : requiredAuthorities){
 600             boolean isMissing = true;
 601             for(GrantedAuthority ga : grantedAuthorities){
 602                 if(a.equals(ga.getAuthority())){
 603                     isMissing = false;
 604                     break;
 605                 }
 606             }
 607             if(isMissing){
 608                 GrantedAuthorityImpl newGa = GrantedAuthorityImpl.NewInstance(a);
 609                 group.addGrantedAuthority(newGa);
 610                 logger.info("New GrantedAuthority '" + a + "' added  to '" + groupName + "'");
 611             }
 612         }
 613         groupService.saveOrUpdate(group);
 614         logger.info("Check of group  '" + groupName + "' done");
 615         return group;
 616     }
 617
 618
 619         /**
 620          * @param args
 621          */
 622         public static void main(String[] args) {
 623                 EuroMedActivator importActivator = new EuroMedActivator();
 624                 Source source = berlinModelSource;
 625                 ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 626
 627                 importActivator.importEm2CDM(source, cdmRepository, hbm2dll);
 628                 if (includePesiExport){
 629                         //not available from here since E+M was moved to app-import
 630 //                      PesiExportActivatorEM exportActivator = new PesiExportActivatorEM();
 631 //                      exportActivator.doExport(cdmRepository);
 632                 }
 633                 System.exit(0);
 634
 635         }
 636
 637 }