eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/preference/PreferencesUtil.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.taxeditor.preference;
  11
  12 import java.io.File;
  13 import java.io.FileInputStream;
  14 import java.io.FileOutputStream;
  15 import java.io.IOException;
  16 import java.net.URI;
  17 import java.net.URISyntaxException;
  18 import java.util.ArrayList;
  19 import java.util.Arrays;
  20 import java.util.Collections;
  21 import java.util.HashMap;
  22 import java.util.List;
  23 import java.util.Map;
  24 import java.util.Properties;
  25 import java.util.Set;
  26 import java.util.StringTokenizer;
  27 import java.util.UUID;
  28
  29 import org.apache.commons.lang.StringUtils;
  30 import org.apache.log4j.Logger;
  31 import org.eclipse.equinox.internal.p2.ui.model.MetadataRepositoryElement;
  32 import org.eclipse.jface.preference.IPreferenceStore;
  33 import org.eclipse.jface.window.Window;
  34 import org.eclipse.swt.widgets.Composite;
  35 import org.eclipse.swt.widgets.Control;
  36 import org.eclipse.swt.widgets.Shell;
  37 import org.eclipse.ui.PlatformUI;
  38
  39 import eu.etaxonomy.cdm.api.application.ICdmRepository;
  40 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeConfigurator;
  41 import eu.etaxonomy.cdm.api.service.IFeatureTreeService;
  42 import eu.etaxonomy.cdm.api.service.ITermService;
  43 import eu.etaxonomy.cdm.api.service.config.FindTaxaAndNamesConfiguratorImpl;
  44 import eu.etaxonomy.cdm.api.service.config.IFindTaxaAndNamesConfigurator;
  45 import eu.etaxonomy.cdm.common.CdmUtils;
  46 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  47 import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
  48 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  49 import eu.etaxonomy.cdm.model.common.ICdmBase;
  50 import eu.etaxonomy.cdm.model.common.IDefinedTerm;
  51 import eu.etaxonomy.cdm.model.common.ISimpleTerm;
  52 import eu.etaxonomy.cdm.model.common.Language;
  53 import eu.etaxonomy.cdm.model.common.MarkerType;
  54 import eu.etaxonomy.cdm.model.common.TermBase;
  55 import eu.etaxonomy.cdm.model.common.TermType;
  56 import eu.etaxonomy.cdm.model.description.FeatureTree;
  57 import eu.etaxonomy.cdm.model.metadata.CdmPreference;
  58 import eu.etaxonomy.cdm.model.metadata.CdmPreference.PrefKey;
  59 import eu.etaxonomy.cdm.model.metadata.PreferencePredicate;
  60 import eu.etaxonomy.cdm.model.metadata.PreferenceSubject;
  61 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  62 import eu.etaxonomy.cdm.strategy.match.DefaultMatchStrategy;
  63 import eu.etaxonomy.cdm.strategy.match.IMatchStrategy;
  64 import eu.etaxonomy.cdm.strategy.match.MatchException;
  65 import eu.etaxonomy.cdm.strategy.match.MatchMode;
  66 import eu.etaxonomy.taxeditor.model.AbstractUtility;
  67 import eu.etaxonomy.taxeditor.model.MessagingUtils;
  68 import eu.etaxonomy.taxeditor.model.NomenclaturalCodeHelper;
  69 import eu.etaxonomy.taxeditor.store.CdmStore;
  70 import eu.etaxonomy.taxeditor.store.TermStore;
  71 import eu.etaxonomy.taxeditor.store.internal.TaxeditorStorePlugin;
  72 import eu.etaxonomy.taxeditor.ui.dialog.DefaultLanguageDialog;
  73
  74 /**
  75  * <p>
  76  * PreferencesUtil class.
  77  * </p>
  78  *
  79  * @author p.ciardelli
  80  * @author n.hoffmann
  81  * @created 05.12.2008
  82  * @version 1.0
  83  */
  84 public class PreferencesUtil implements IPreferenceKeys {
  85
  86         /**
  87          *
  88          */
  89         public static final String PREFERRED_TERMS_CHANGE = "preferred_terms";
  90
  91         public static final String P2_REPOSITORIES_DELIM = ",";
  92         public static final String P2_REPOSITORY_FIELDS_DELIM = ";";
  93
  94         private final static Logger logger = Logger.getLogger(PreferencesUtil.class);
  95
  96
  97
  98         /**
  99          * <p>
 100          * getPreferenceStore
 101          * </p>
 102          *
 103          * @return a {@link org.eclipse.jface.preference.IPreferenceStore} object.
 104          */
 105         public static IPreferenceStore getPreferenceStore() {
 106                 return TaxeditorStorePlugin.getDefault().getPreferenceStore();
 107         }
 108
 109         /**
 110          * <p>
 111          * setPreferredNomenclaturalCode
 112          * </p>
 113          *
 114          * @param preferredCode
 115          *            a {@link eu.etaxonomy.cdm.model.name.NomenclaturalCode}
 116          *            object.
 117          */
 118         public static CdmPreference setPreferredNomenclaturalCode(
 119                         String preferenceKey, boolean local) {
 120             if (local){
 121                 getPreferenceStore().setValue(PREFERRED_NOMENCLATURAL_CODE_KEY,
 122                         preferenceKey);
 123             }
 124             else{
 125                 ICdmRepository controller;
 126                 controller = CdmStore.getCurrentApplicationConfiguration();
 127                 if (controller == null){
 128                 return null;
 129             }
 130                 PrefKey key = null;
 131                 try{
 132                     key = CdmPreference.NewKey(PreferenceSubject.NewDatabaseInstance(), PreferencePredicate.NomenclaturalCode);
 133                 }catch (Exception e){
 134                     System.out.println(e.getStackTrace());
 135                 }
 136                 CdmPreference preference = null;
 137
 138                 if (preferenceKey == null){
 139                         preference = controller.getPreferenceService().find(key);
 140                         if (preference == null){
 141                                 return null;
 142                         } else{
 143                                 getPreferenceStore().setValue(PREFERRED_NOMENCLATURAL_CODE_KEY,
 144                                         preferenceKey);
 145                                 getPreferenceStore().setValue(ALLOW_OVERRIDE_NOMENCLATURAL_CODE_KEY,preference.isAllowOverride());
 146                                 return preference;
 147                         }
 148                 } else{
 149                         preference = CdmPreference.NewInstance(PreferenceSubject.NewDatabaseInstance(), PreferencePredicate.NomenclaturalCode, preferenceKey);
 150                         controller.getPreferenceService().set(preference);
 151
 152                 }
 153             }
 154         return null;
 155
 156
 157
 158         }
 159
 160         public static NomenclaturalCode getPreferredNomenclaturalCode(){
 161             if (getPreferenceStore().getBoolean(OVERRIDE_NOMENCLATURAL_CODE_KEY)) {
 162             return getPreferredNomenclaturalCode(true);
 163         } else{
 164             return getPreferredNomenclaturalCode(false);
 165         }
 166         }
 167
 168         /**
 169          * <p>
 170          * getPreferredNomenclaturalCode
 171          * </p>
 172          *
 173          * @return a {@link eu.etaxonomy.cdm.model.name.NomenclaturalCode} object.
 174          */
 175         public static NomenclaturalCode getPreferredNomenclaturalCode(boolean useLocal) {
 176
 177                 CdmPreference pref = null;
 178                 if (!useLocal){
 179                     pref = getPreferenceFromDB(PreferencePredicate.NomenclaturalCode);
 180                 }
 181
 182             String preferredCode;
 183             if(pref == null){
 184                 preferredCode = getPreferenceStore().getString(
 185                                         PREFERRED_NOMENCLATURAL_CODE_KEY);
 186
 187             }else{
 188                 preferredCode = pref.getValue();
 189             }
 190
 191             return getPreferredNomenclaturalCode(preferredCode);
 192
 193         }
 194
 195         /**
 196      * <p>
 197      * getPreferredNomenclaturalCode
 198      * </p>
 199      *
 200      * @return a {@link eu.etaxonomy.cdm.model.name.NomenclaturalCode} object.
 201      */
 202     public static NomenclaturalCode getPreferredNomenclaturalCode(String preferenceKeyNomenclaturalCode) {
 203
 204         for (NomenclaturalCode code : NomenclaturalCodeHelper.getAllCodes()) {
 205             if (getPreferenceKey(code).equals(preferenceKeyNomenclaturalCode)) {
 206                 return code;
 207             }
 208         }
 209         return null;
 210     }
 211
 212         public static boolean isShowTaxonAssociations(){
 213         if (getPreferenceStore().getBoolean(SHOW_TAXON_ASSOCIATIONS_OVERRIDE) && getPreferenceStore().getBoolean(SHOW_TAXON_ASSOCIATIONS_ALLOW_OVERRIDE)) {
 214             return getPreferenceStore().getBoolean(SHOW_TAXON_ASSOCIATIONS);
 215         } else{
 216             CdmPreference pref = getPreferenceFromDB(PreferencePredicate.ShowTaxonAssociations);
 217
 218             return pref!=null?Boolean.valueOf(pref.getValue()):false;
 219         }
 220     }
 221
 222         public static boolean isShowLifeForm(){
 223         if (getPreferenceStore().getBoolean(SHOW_LIFE_FORM_OVERRIDE) && getPreferenceStore().getBoolean(SHOW_LIFE_FORM_ALLOW_OVERRIDE)) {
 224             return getPreferenceStore().getBoolean(SHOW_LIFE_FORM);
 225         } else{
 226             CdmPreference pref = getPreferenceFromDB(PreferencePredicate.ShowLifeForm);
 227
 228             return pref!=null?Boolean.valueOf(pref.getValue()):false;
 229         }
 230     }
 231
 232         public static boolean isDeterminationOnlyForFieldUnits(){
 233         if (getPreferenceStore().getBoolean(DETERMINATION_ONLY_FOR_FIELD_UNITS_OVERRIDE) && getPreferenceStore().getBoolean(DETERMINATIONS_ONLY_FOR_FIELDUNITS_ALLOW_OVERRIDE)) {
 234             return getPreferenceStore().getBoolean(DETERMINATION_ONLY_FOR_FIELD_UNITS);
 235         } else{
 236             CdmPreference pref = getPreferenceFromDB(PreferencePredicate.DeterminationOnlyForFieldUnits);
 237
 238             return pref!=null?Boolean.valueOf(pref.getValue()):false;
 239         }
 240     }
 241
 242         public static boolean isCollectingAreaInGeneralSection(){
 243         if (getPreferenceStore().getBoolean(SHOW_COLLECTING_AREAS_IN_GENERAL_SECTION_OVERRIDE) && getPreferenceStore().getBoolean(SHOW_COLLECTING_AREAS_IN_GENERAL_SECTION_ALLOW_OVERRIDE)) {
 244             return getPreferenceStore().getBoolean(SHOW_COLLECTING_AREAS_IN_GENERAL_SECTION);
 245         } else{
 246             CdmPreference pref = getPreferenceFromDB(PreferencePredicate.ShowCollectingAreasInGeneralSection);
 247
 248             return pref!=null?Boolean.valueOf(pref.getValue()):false;
 249         }
 250     }
 251
 252         public static boolean isShowSimpleDetailsView(){
 253         if (getPreferenceStore().getBoolean(OVERRIDE_NAME_DETAILS) && getPreferenceStore().getBoolean(ALLOW_OVERRIDE_NAME_DETAILS)) {
 254             return getPreferenceStore().getBoolean(SHOW_SIMPLE_NAME_DETAILS_SECTION);
 255         } else{
 256             CdmPreference pref = getPreferenceFromDB(PreferencePredicate.NameDetailsView);
 257
 258             return pref!=null?Boolean.valueOf(pref.getValue()):false;
 259         }
 260     }
 261
 262
 263
 264     public static CdmPreference getPreferenceFromDB(PreferencePredicate predicate){
 265         ICdmRepository controller;
 266         CdmPreference pref = null;
 267
 268         try{
 269             if(CdmStore.isActive()){
 270                 controller = CdmStore.getCurrentApplicationConfiguration();
 271                 PrefKey key = CdmPreference.NewKey(PreferenceSubject.NewTaxEditorInstance(), predicate);
 272                 pref = controller.getPreferenceService().find(key);
 273             }
 274         }catch(Exception e){
 275             e.printStackTrace();
 276         }
 277
 278         return pref;
 279
 280     }
 281
 282     public static void setPreferenceToDB(CdmPreference preference){
 283         ICdmRepository controller;
 284         try{
 285             if(CdmStore.isActive()){
 286                 controller = CdmStore.getCurrentApplicationConfiguration();
 287                 controller.getPreferenceService().set(preference);
 288             }
 289         }catch(Exception e){
 290             e.printStackTrace();
 291         }
 292
 293     }
 294
 295
 296
 297         public static String getPreferredDefaultLangugae(){
 298             String preferredLanguage = getPreferenceStore().getString(DEFAULT_LANGUAGE_EDITOR);
 299             if(StringUtils.isNotEmpty(preferredLanguage) && StringUtils.isNotBlank(preferredLanguage)){
 300                 return preferredLanguage;
 301             }
 302             return null;
 303         }
 304
 305         public static boolean isShowMediaPreview(){
 306         boolean isShowMediaPreview = getPreferenceStore().getBoolean(SHOW_MEDIA_PREVIEW);
 307         return isShowMediaPreview;
 308     }
 309
 310         /**
 311          * Get the match strategy for the given class that was stored in preferences
 312          * or the default strategy if it was not stored in preferences
 313          *
 314          * @param clazz
 315          *            a {@link java.lang.Class} object.
 316          * @return a {@link eu.etaxonomy.cdm.strategy.match.IMatchStrategy} object.
 317          */
 318         public static IMatchStrategy getMatchStrategy(Class clazz) {
 319                 String className = clazz.getName();
 320                 if (getPreferenceStore().getBoolean(MATCH_STRATEGY_PREFIX + className)) {
 321                         IMatchStrategy matchStrategy = getDefaultMatchStrategy(clazz);
 322
 323                         for (String fieldName : matchStrategy.getMatchFieldPropertyNames()) {
 324                                 String matchModeName = getPreferenceStore().getString(
 325                                                 getMatchStrategyFieldName(className, fieldName));
 326                                 MatchMode matchMode = MatchMode.valueOf(matchModeName);
 327                                 try {
 328                                         matchStrategy.setMatchMode(fieldName, matchMode);
 329                                 } catch (MatchException e) {
 330                                         MessagingUtils.error(PreferencesUtil.class, e);
 331                                         throw new RuntimeException(e);
 332                                 }
 333                         }
 334
 335                         return matchStrategy;
 336                 }
 337                 return getDefaultMatchStrategy(clazz);
 338         }
 339
 340         /**
 341          * Stores a matchStrategy into the preference store.
 342          *
 343          * @param matchStrategy
 344          *            a {@link eu.etaxonomy.cdm.strategy.match.IMatchStrategy}
 345          *            object.
 346          */
 347         public static void setMatchStrategy(IMatchStrategy matchStrategy) {
 348                 String className = matchStrategy.getMatchClass().getName();
 349                 getPreferenceStore().setValue(MATCH_STRATEGY_PREFIX + className, true);
 350
 351                 Set<String> matchFields = matchStrategy.getMatchFieldPropertyNames();
 352
 353                 for (String fieldName : matchFields) {
 354                         getPreferenceStore().setValue(
 355                                         getMatchStrategyFieldName(className, fieldName),
 356                                         matchStrategy.getMatchMode(fieldName).name());
 357                 }
 358         }
 359
 360         /**
 361          * Helper method to create the preference property for a match field.
 362          *
 363          * @param className
 364          * @param fieldName
 365          * @return
 366          */
 367         private static String getMatchStrategyFieldName(String className,
 368                         String fieldName) {
 369                 return MATCH_STRATEGY_PREFIX + className + "." + fieldName;
 370         }
 371
 372         /**
 373          * Returns the default match strategy for a given class.
 374          *
 375          * @param clazz
 376          *            a {@link java.lang.Class} object.
 377          * @return a {@link eu.etaxonomy.cdm.strategy.match.IMatchStrategy} object.
 378          */
 379         public static IMatchStrategy getDefaultMatchStrategy(Class clazz) {
 380                 return DefaultMatchStrategy.NewInstance(clazz);
 381         }
 382
 383         /**
 384          * <p>
 385          * getDateFormatPattern
 386          * </p>
 387          *
 388          * @return a {@link java.lang.String} object.
 389          */
 390         public static String getDateFormatPattern() {
 391                 // TODO make this configurable in properties
 392                 String pattern = "Y-M-d H:m";
 393                 return pattern;
 394         }
 395
 396         /**
 397          * <p>
 398          * addTermToPreferredTerms
 399          * </p>
 400          *
 401          * @param term
 402          *            a T object.
 403          * @param <T>
 404          *            a T object.
 405          */
 406         public static <T extends TermBase> void addTermToPreferredTerms(T term) {
 407
 408                 // VocabularyEnum vocabulary =
 409                 // VocabularyEnum.getVocabularyEnum(term.getClass());
 410                 //
 411                 // getPreferenceStore().setValue(getPreferenceKey(term),
 412                 // VocabularyStore.getTermVocabulary(vocabulary).getTerms().contains(term));
 413                 //
 414                 // firePreferencesChanged(term.getClass());
 415         }
 416
 417         /**
 418          * Construct a unique key using the CdmBase object's uuid
 419          *
 420          * @param cdmBase
 421          * @return
 422          */
 423         private static String getPreferenceKey(ICdmBase cdmBase) {
 424                 cdmBase = HibernateProxyHelper.deproxy(cdmBase);
 425
 426                 String key = cdmBase.getClass().getName().concat(".")
 427                                 .concat(cdmBase.getUuid().toString());
 428                 if (key.contains("javassist")) {
 429                         MessagingUtils.info("proxy");
 430                 }
 431                 return key;
 432         }
 433
 434         /**
 435          * Construct a unique key using the CdmBase object's uuid
 436          *
 437          * @param cdmBase
 438          * @return
 439          */
 440         public static String getPreferenceKey(ISimpleTerm simpleTerm) {
 441                 simpleTerm = HibernateProxyHelper.deproxy(simpleTerm);
 442                 String key = simpleTerm.getClass().getName().concat(".")
 443                                 .concat(simpleTerm.getUuid().toString());
 444                 if (key.contains("javassist")) {
 445                         MessagingUtils.warn(PreferencesUtil.class,
 446                                         "Trying to persist a preference based on a proxy class.");
 447                 }
 448                 return key;
 449         }
 450
 451
 452
 453         /**
 454          * Construct a unique key using the CdmBase object's uuid
 455          *
 456          * @param cdmBase
 457          * @return
 458          */
 459         public static String getPreferenceKey(IDefinedTerm definedTerm) {
 460                 definedTerm = HibernateProxyHelper.deproxy(definedTerm);
 461                 String key = definedTerm.getClass().getName().concat(".")
 462                                 .concat(definedTerm.getUuid().toString());
 463                 if (key.contains("javassist")) {
 464                         MessagingUtils.warn(PreferencesUtil.class,
 465                                         "Trying to persist a preference based on a proxy class.");
 466                 }
 467                 return key;
 468         }
 469
 470         /**
 471          * Retrieves search preferences from the preference store
 472          *
 473          * @return an {@link ITaxonServiceConfigurator} to pass to search methods
 474          */
 475         public static IFindTaxaAndNamesConfigurator getSearchConfigurator() {
 476                 IFindTaxaAndNamesConfigurator configurator = initializeSearchConfigurator();
 477
 478                 configurator.setDoTaxa(getPreferenceStore().getBoolean(
 479                                 TAXON_SERVICE_CONFIGURATOR_TAXA));
 480                 configurator.setDoSynonyms(getPreferenceStore().getBoolean(
 481                                 TAXON_SERVICE_CONFIGURATOR_SYNONYMS));
 482                 configurator.setDoNamesWithoutTaxa(getPreferenceStore().getBoolean(
 483                                 TAXON_SERVICE_CONFIGURATOR_NAMES));
 484                 configurator.setDoTaxaByCommonNames(getPreferenceStore().getBoolean(
 485                                 TAXON_SERVICE_CONFIGURATOR_COMMON_NAMES));
 486                 //configurator.setMatchMode(eu.etaxonomy.cdm.persistence.query.MatchMode.valueOf(getPreferenceStore().getString(TAXON_SERVICE_CONFIGURATOR_MATCH_MODE)));
 487
 488                 return configurator;
 489         }
 490
 491         /**
 492          * create new preferences, setting all search options to true
 493          *
 494          * @return a
 495          *         {@link eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator}
 496          *         object.
 497          */
 498         public static IFindTaxaAndNamesConfigurator initializeSearchConfigurator() {
 499                 IFindTaxaAndNamesConfigurator configurator = FindTaxaAndNamesConfiguratorImpl.NewInstance();
 500
 501                 configurator.setDoTaxa(true);
 502                 configurator.setDoSynonyms(true);
 503                 configurator.setDoNamesWithoutTaxa(true);
 504                 configurator.setDoTaxaByCommonNames(true);
 505
 506                 configurator.setTaxonPropertyPath(Arrays.asList("$", "titleCache",
 507                                 "name", "name.$", "relationsFromThisTaxon.$"));
 508
 509                 configurator.setSynonymPropertyPath(Arrays.asList("$", "titleCache",
 510                                 "name", "name.$", "synonyms.relatedTo.*"));
 511
 512                 // DEFAULT VALUES
 513                 // match mode is a simple like, actually all other match modes are kind
 514                 // of bogus
 515                 configurator
 516                                 .setMatchMode(eu.etaxonomy.cdm.persistence.query.MatchMode.ANYWHERE);
 517                 // we set page number and size here as this should always be unlimited
 518                 configurator.setPageNumber(0);
 519                 // TODO currently limit results to 10000
 520                 configurator.setPageSize(10000);
 521
 522                 return configurator;
 523         }
 524
 525         /**
 526          * Store search preferences
 527          *
 528          * @param configurator
 529          *            a
 530          *            {@link eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator}
 531          *            object.
 532          */
 533         public static void setSearchConfigurator(
 534                         IFindTaxaAndNamesConfigurator configurator) {
 535                 getPreferenceStore().setValue(TAXON_SERVICE_CONFIGURATOR_TAXA,
 536                                 configurator.isDoTaxa());
 537                 getPreferenceStore().setValue(TAXON_SERVICE_CONFIGURATOR_SYNONYMS,
 538                                 configurator.isDoSynonyms());
 539                 getPreferenceStore().setValue(TAXON_SERVICE_CONFIGURATOR_NAMES,
 540                                 configurator.isDoNamesWithoutTaxa());
 541                 getPreferenceStore().setValue(TAXON_SERVICE_CONFIGURATOR_COMMON_NAMES,
 542                                 configurator.isDoTaxaByCommonNames());
 543         }
 544
 545         /**
 546          * <p>
 547          * firePreferencesChanged
 548          * </p>
 549          *
 550          * @param clazz
 551          *            a {@link java.lang.Class} object.
 552          */
 553         public static void firePreferencesChanged(Class clazz) {
 554                 getPreferenceStore().firePropertyChangeEvent(PREFERRED_TERMS_CHANGE,
 555                                 null, clazz);
 556         }
 557
 558         /**
 559          * Set default values for preferences
 560          */
 561         public static void setDefaults() {
 562                 getPreferenceStore().setDefault(TAXON_SERVICE_CONFIGURATOR_TAXA, true);
 563                 getPreferenceStore().setDefault(TAXON_SERVICE_CONFIGURATOR_SYNONYMS,
 564                                 true);
 565                 getPreferenceStore().setDefault(EDIT_MAP_SERVICE_ACCES_POINT,
 566                                 "http://edit.africamuseum.be/edit_wp5/v1.2/rest_gen.php");
 567                 //FIXME : changed default for SHOULD_CONNECT_AT_STARTUP to false (ticket 3828) until resolution
 568                 getPreferenceStore().setDefault(SHOULD_CONNECT_AT_STARTUP, false);
 569                 getPreferenceStore().setDefault(OPENURL_ACCESS_POINT,
 570                                 "http://www.biodiversitylibrary.org/openurl");
 571                 getPreferenceStore().setDefault(OPENURL_IMAGE_MAX_WIDTH, "1000");
 572                 getPreferenceStore().setDefault(OPENURL_IMAGE_MAX_HEIGHT, "1000");
 573                 //Distribution Editor:
 574                 getPreferenceStore().setDefault(DISTRIBUTION_AREA_PREFRENCES_ACTIVE, false);
 575                 getPreferenceStore().setDefault(CHECKLIST_AREA_DISPLAY, CHECKLIST_AREA_DISPLAY_TITLE);
 576                 getPreferenceStore().setDefault(CHECKLIST_SYMBOL, false);
 577
 578
 579                 //Name Details
 580                 getPreferenceStore().setDefault(SHOW_NAME_DETAILS_SECTION_ATOMISED_EPITHETS, true);
 581                 getPreferenceStore().setDefault(SHOW_NAME_DETAILS_SECTION_AUTHORSHIP_CACHE, true);
 582                 getPreferenceStore().setDefault(SHOW_NAME_DETAILS_SECTION_AUTHORSHIP, true);
 583                 getPreferenceStore().setDefault(SHOW_NAME_DETAILS_SECTION_HYBRID, true);
 584                 getPreferenceStore().setDefault(SHOW_NAME_DETAILS_SECTION_LSID, true);
 585                 getPreferenceStore().setDefault(SHOW_NAME_DETAILS_SECTION_NAME_RELATIONSHIP, true);
 586                 getPreferenceStore().setDefault(SHOW_NAME_DETAILS_SECTION_NAMECACHE, true);
 587                 getPreferenceStore().setDefault(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_CODE, true);
 588                 getPreferenceStore().setDefault(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_REFERENCE, true);
 589                 getPreferenceStore().setDefault(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_STATUS, true);
 590                 getPreferenceStore().setDefault(SHOW_NAME_DETAILS_SECTION_PROTOLOGUE, true);
 591                 getPreferenceStore().setDefault(SHOW_NAME_DETAILS_SECTION_RANK, true);
 592                 getPreferenceStore().setDefault(SHOW_NAME_DETAILS_SECTION_TYPE_DESIGNATION, true);
 593                 //Navigator preferences
 594                 getPreferenceStore().setDefault(SORT_NODES_NATURALLY, false);
 595                 getPreferenceStore().setDefault(SORT_NODES_ALPHABETICALLY, false);
 596                 getPreferenceStore().setDefault(SORT_TAXA_BY_RANK_AND_NAME, true);
 597                 //override db preferences
 598                 getPreferenceStore().setDefault(ABCD_IMPORT_OVERRIDE, false);
 599                 getPreferenceStore().setDefault(SHOW_SPECIMEN_OVERRIDE, false);
 600                 getPreferenceStore().setDefault(OVERRIDE_NAME_DETAILS, false);
 601                 getPreferenceStore().setDefault(DISTRIBUTION_AREA_PREFRENCES_ACTIVE_OVERRIDE, false);
 602
 603                 getPreferenceStore().setDefault(FILTER_COMMON_NAME_REFERENCES, false);
 604                 getPreferenceStore().setDefault(SHOW_SPECIMEN, true);
 605                 getPreferenceStore().setDefault(SHOW_TAXONNODE_WIZARD, true);
 606                 getPreferenceStore().setDefault(SHOW_NAME_IN_SOURCE, true);
 607                 getPreferenceStore().setDefault(SHOW_ID_IN_SOURCE, true);
 608                 getPreferenceStore().setDefault(DISABLE_MULTI_CLASSIFICATION, false);
 609
 610         }
 611
 612         /**
 613          * <p>
 614          * checkNomenclaturalCode
 615          * </p>
 616          */
 617         public static void checkNomenclaturalCode() {
 618                 // First time Editor is opened, no nomenclatural code has been set
 619                 if (PreferencesUtil.getPreferredNomenclaturalCode(true) == null) {
 620                         PreferencesUtil.setPreferredNomenclaturalCode(getPreferenceKey(NomenclaturalCode.ICNAFP), true);
 621                 }
 622
 623
 624
 625         }
 626         public static void setNomenclaturalCodePreferences(){
 627             ICdmRepository controller;
 628         controller = CdmStore.getCurrentApplicationConfiguration();
 629         PrefKey key = CdmPreference.NewKey(PreferenceSubject.NewDatabaseInstance(), PreferencePredicate.NomenclaturalCode);
 630         CdmPreference preference = null;
 631         if (controller == null){
 632             return ;
 633         }
 634         preference = controller.getPreferenceService().find(key);
 635         if (preference == null){
 636             return;
 637         }
 638         getPreferenceStore().setValue(ALLOW_OVERRIDE_NOMENCLATURAL_CODE_KEY, preference.isAllowOverride());
 639
 640         int index = StringUtils.lastIndexOf(preference.getValue(), ".");
 641         UUID uuid = UUID.fromString(preference.getValue().substring(index +1, preference.getValue().length()));
 642         NomenclaturalCode preferredCode = NomenclaturalCode.getByUuid(uuid);
 643
 644         getPreferenceStore().setValue(PREFERRED_NOMENCLATURAL_CODE_KEY,
 645                 getPreferenceKey(preferredCode));
 646
 647         }
 648
 649         public static void checkDefaultLanguage(){
 650             if(PreferencesUtil.getPreferredDefaultLangugae() == null){
 651                Shell shell = AbstractUtility.getShell();
 652                int open = new DefaultLanguageDialog(shell).open();
 653                if(open == Window.OK){
 654                    PlatformUI.getWorkbench().restart();
 655                }
 656             }else{
 657                 //TODO:In case of a reinstall, the config.ini will be overwritten
 658                 //     here you create config.ini with the stored key from preferences
 659             }
 660         }
 661
 662         /**
 663          * <p>
 664          * getMapServiceAccessPoint
 665          * </p>
 666          *
 667          * @return a {@link java.lang.String} object.
 668          */
 669         public static String getMapServiceAccessPoint() {
 670                 return getPreferenceStore().getString(EDIT_MAP_SERVICE_ACCES_POINT);
 671         }
 672
 673         /**
 674          * <p>
 675          * shouldConnectAtStartUp
 676          * </p>
 677          *
 678          * @return a boolean.
 679          */
 680         public static boolean shouldConnectAtStartUp() {
 681                 //FIXME :  force SHOULD_CONNECT_AT_STARTUP to false (ticket 3828) until resolution
 682                 //return getPreferenceStore().getBoolean(SHOULD_CONNECT_AT_STARTUP);
 683                 return false;
 684         }
 685
 686         /**
 687          * <p>
 688          * getDefaultFeatureTreeForTextualDescription
 689          * </p>
 690          *
 691          * @return a {@link eu.etaxonomy.cdm.model.description.FeatureTree} object.
 692          */
 693         public static FeatureTree getDefaultFeatureTreeForTextualDescription() {
 694                 String uuidString = getPreferenceStore().getString(
 695                                 FEATURE_TREE_DEFAULT_TEXT);
 696                 return CdmUtils.isEmpty(uuidString) ? null : CdmStore.getService(
 697                                 IFeatureTreeService.class).load(UUID.fromString(uuidString));
 698         }
 699
 700         /**
 701          * <p>
 702          * getDefaultFeatureTreeForStructuredDescription
 703          * </p>
 704          *
 705          * @return a {@link eu.etaxonomy.cdm.model.description.FeatureTree} object.
 706          */
 707         public static FeatureTree getDefaultFeatureTreeForStructuredDescription() {
 708                 String uuidString = getPreferenceStore().getString(
 709                                 FEATURE_TREE_DEFAULT_STRUCTURE);
 710                 return CdmUtils.isEmpty(uuidString) ? null : CdmStore.getService(
 711                                 IFeatureTreeService.class).load(UUID.fromString(uuidString));
 712         }
 713
 714         /**
 715          * <p>
 716          * setSortRanksHierarchichally
 717          * </p>
 718          *
 719          * @param selection
 720          *            a boolean.
 721          */
 722         public static void setSortRanksHierarchichally(boolean selection) {
 723                 getPreferenceStore().setValue(SORT_RANKS_HIERARCHICHALLY, selection);
 724         }
 725
 726         /**
 727          * <p>
 728          * getSortRanksHierarchichally
 729          * </p>
 730          *
 731          * @return a boolean.
 732          */
 733         public static boolean getSortRanksHierarchichally() {
 734                 return getPreferenceStore().getBoolean(SORT_RANKS_HIERARCHICHALLY);
 735         }
 736
 737         public static boolean isMultilanguageTextEditingCapability() {
 738                 return getPreferenceStore().getBoolean(
 739                                 MULTILANGUAGE_TEXT_EDITING_CAPABILITY);
 740         }
 741
 742         public static Language getGlobalLanguage() {
 743
 744
 745                 String languageUuidString = getPreferenceStore().getString(
 746                                 GLOBAL_LANGUAGE_UUID);
 747
 748                 if(!CdmStore.isActive()) {
 749             MessagingUtils.noDataSourceWarningDialog(languageUuidString);
 750             return null;
 751         }
 752
 753                 if (CdmUtils.isBlank(languageUuidString)) {
 754                         return Language.getDefaultLanguage();
 755                 }
 756
 757                 UUID languageUuid = UUID.fromString(languageUuidString);
 758                 return (Language) CdmStore.getService(ITermService.class).load(
 759                                 languageUuid);
 760         }
 761
 762         public static void setGlobalLanguage(Language language) {
 763             if(language != null) {
 764                 getPreferenceStore().setValue(GLOBAL_LANGUAGE_UUID,language.getUuid().toString());
 765                 CdmStore.setDefaultLanguage(language);
 766             }
 767
 768         }
 769
 770         /**
 771          * @return
 772          */
 773         public static Map<MarkerType, Boolean> getEditMarkerTypePreferences() {
 774                 List<MarkerType> markerTypes = CdmStore.getTermManager()
 775                                 .getPreferredTerms(MarkerType.class);
 776
 777                 Map<MarkerType, Boolean> result = new HashMap<MarkerType, Boolean>();
 778
 779                 for (MarkerType markerType : markerTypes) {
 780                         String name = getMarkerTypeEditingPreferenceKey(markerType);
 781                         Boolean value = getPreferenceStore().getBoolean(name);
 782
 783                         result.put(markerType, value);
 784                 }
 785
 786                 return result;
 787         }
 788
 789         /**
 790          * @param markerTypeEditingMap
 791          */
 792         public static void setEditMarkerTypePreferences(
 793                         Map<MarkerType, Boolean> markerTypeEditingMap) {
 794                 for (MarkerType markerType : markerTypeEditingMap.keySet()) {
 795                         String name = getMarkerTypeEditingPreferenceKey(markerType);
 796                         getPreferenceStore().setValue(name,
 797                                         markerTypeEditingMap.get(markerType));
 798                 }
 799
 800         }
 801
 802         private static String getMarkerTypeEditingPreferenceKey(
 803                         MarkerType markerType) {
 804                 markerType = HibernateProxyHelper.deproxy(markerType);
 805                 return markerType.getClass().getName() + EDIT_MARKER_TYPE_PREFIX;
 806         }
 807
 808         /**
 809          * <p>
 810          * setEditMarkerTypePreference
 811          * </p>
 812          *
 813          * @param input
 814          *            a {@link org.eclipse.ui.IEditorInput} object.
 815          * @param markerType
 816          *            a {@link eu.etaxonomy.cdm.model.common.MarkerType} object.
 817          * @param edit
 818          *            a boolean.
 819          */
 820         public static void setEditMarkerTypePreference(MarkerType markerType,
 821                         boolean edit) {
 822                 getPreferenceStore().setValue(
 823                                 getMarkerTypeEditingPreferenceKey(markerType), edit);
 824         }
 825
 826         /**
 827          * @return
 828          */
 829         public static DerivedUnitFacadeConfigurator getDerivedUnitConfigurator() {
 830                 DerivedUnitFacadeConfigurator configurator = DerivedUnitFacadeConfigurator
 831                                 .NewInstance();
 832                 configurator.setMoveDerivedUnitMediaToGallery(true);
 833                 configurator.setMoveFieldObjectMediaToGallery(true);
 834                 return configurator;
 835         }
 836
 837         /**
 838          * This method will write language properties to the config.ini located in the configuration folder
 839          * of the Taxonomic Ediitor. <b>This method is only used to set the default language for Taxonomic Editor.</b>
 840          *
 841          * @param setLanguage 0 is for german and 1 for english.
 842          * @throws IOException
 843          */
 844     public void writePropertyToConfigFile(int setLanguage) throws IOException {
 845         File file = org.eclipse.core.runtime.preferences.ConfigurationScope.INSTANCE.getLocation().toFile();
 846         //give warning to user if the directory has no write access
 847         if(file == null){
 848             throw new IOException();
 849         }
 850         Properties properties = load(file.getAbsolutePath()+"/config.ini");
 851         switch(setLanguage){
 852         case 0:
 853             properties.setProperty("osgi.nl", "de");
 854             PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.DEFAULT_LANGUAGE_EDITOR, "de");
 855             break;
 856         case 1:
 857             properties.setProperty("osgi.nl", "en");
 858             PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.DEFAULT_LANGUAGE_EDITOR, "en");
 859             break;
 860         default:
 861             break;
 862         }
 863         save(file+"/config.ini", properties);
 864     }
 865
 866     /**
 867      * This method loads a property from a given file and returns it.
 868      *
 869      * @param filename
 870      * @return
 871      * @throws IOException
 872      */
 873     private Properties load(String filename) throws IOException {
 874         FileInputStream in = new FileInputStream(filename);
 875         Properties prop = new Properties();
 876         prop.load(in);
 877         in.close();
 878         return prop;
 879     }
 880
 881     /**
 882      * This method saves a property to the specified file.
 883      *
 884      * @param filename
 885      * @param properties
 886      * @throws IOException
 887      */
 888     private void save(String filename, Properties properties) throws IOException{
 889         FileOutputStream fos =  new FileOutputStream(filename);
 890         properties.store(fos, "");
 891         fos.close();
 892     }
 893
 894     /**
 895      * Saves a list of P2 Metadata Repositories as string with specified delimiters
 896      *
 897      * @param p2Repos
 898      */
 899     public static void setP2Repositories(List<MetadataRepositoryElement> p2Repos) {
 900         StringBuilder sb = new StringBuilder();
 901         for(MetadataRepositoryElement p2Repo : p2Repos) {
 902             sb.append(P2_REPOSITORIES_DELIM);
 903             if(p2Repo.getName() == null || p2Repo.getName().isEmpty()) {
 904                 sb.append("-");
 905             } else {
 906                 sb.append(p2Repo.getName());
 907             }
 908             sb.append(P2_REPOSITORY_FIELDS_DELIM);
 909             sb.append(p2Repo.getLocation().toString());
 910             sb.append(P2_REPOSITORY_FIELDS_DELIM);
 911             sb.append(String.valueOf(p2Repo.isEnabled()));
 912         }
 913         getPreferenceStore().setValue(P2_REPOSITORY_LIST, sb.toString());
 914     }
 915
 916
 917     /**
 918      * Retrieves a list of previously saved P2 repositories
 919      *
 920      * @return
 921      */
 922     public static List<MetadataRepositoryElement> getP2Repositories() {
 923         List<MetadataRepositoryElement> p2Repos = new ArrayList<MetadataRepositoryElement>();
 924         String p2ReposPref =  getPreferenceStore().getString(P2_REPOSITORY_LIST);
 925         if(p2ReposPref != null && !p2ReposPref.isEmpty()) {
 926             StringTokenizer p2ReposPrefST = new StringTokenizer(p2ReposPref,P2_REPOSITORIES_DELIM);
 927
 928             while(p2ReposPrefST.hasMoreTokens()) {
 929                 String p2RepoStr = p2ReposPrefST.nextToken();
 930                 StringTokenizer p2ReposStrST = new StringTokenizer(p2RepoStr,P2_REPOSITORY_FIELDS_DELIM);
 931                 if(p2ReposStrST.countTokens()==3) {
 932                     String nickname = p2ReposStrST.nextToken();
 933                     URI uri = null;
 934                     try {
 935                         uri = new URI(p2ReposStrST.nextToken());
 936                     } catch (URISyntaxException e) {
 937                         continue;
 938                     }
 939                     boolean enabled = Boolean.parseBoolean(p2ReposStrST.nextToken());
 940                     MetadataRepositoryElement mre = new MetadataRepositoryElement(null, uri, true);
 941                     mre.setNickname(nickname);
 942                     mre.setEnabled(enabled);
 943                     p2Repos.add(mre);
 944                 }
 945             }
 946         }
 947
 948         return p2Repos;
 949     }
 950
 951     /**
 952      * enables/disables nested composite. <br>
 953      *
 954      * @param ctrl - Composite to be en-/disabeld
 955      * @param enabled - boolean
 956      */
 957     public static void recursiveSetEnabled(Control ctrl, boolean enabled) {
 958         if (ctrl instanceof Composite) {
 959             Composite comp = (Composite) ctrl;
 960             for (Control c : comp.getChildren()) {
 961                 recursiveSetEnabled(c, enabled);
 962             }
 963         } else {
 964             ctrl.setEnabled(enabled);
 965         }
 966     }
 967
 968     /**
 969          * <p>
 970          * getSortRanksNaturally
 971          * </p>
 972          *
 973          * @return a boolean.
 974          */
 975         public static boolean getSortNodesNaturally() {
 976                 return getPreferenceStore().getBoolean(SORT_NODES_NATURALLY);
 977         }
 978
 979         /**
 980          * <p>
 981          * setSortRanksNaturally
 982          * </p>
 983          *
 984          * @param selection
 985          *            a boolean.
 986          */
 987         public static void setSortNodesNaturally(boolean selection) {
 988                 getPreferenceStore().setValue(SORT_NODES_NATURALLY, selection);
 989         }
 990
 991
 992         /**
 993          * <p>
 994          * getSortRanksNaturally
 995          * </p>
 996          *
 997          * @return a boolean.
 998          */
 999         public static boolean getSortNodesStrictlyAlphabetically() {
1000                 return getPreferenceStore().getBoolean(SORT_NODES_ALPHABETICALLY);
1001         }
1002
1003         /**
1004          * <p>
1005          * setSortRanksNaturally
1006          * </p>
1007          *
1008          * @param selection
1009          *            a boolean.
1010          */
1011         public static void setSortNodesStrictlyAlphabetically(boolean selection) {
1012                 getPreferenceStore().setValue(SORT_NODES_ALPHABETICALLY, selection);
1013         }
1014
1015         /**
1016          * <p>
1017          * setStoreNavigatorState
1018          * </p>
1019          *
1020          * @param selection
1021          *            a boolean.
1022          */
1023         public static boolean isStoreNavigatorState() {
1024                 return getPreferenceStore().getBoolean(RESTORE_NAVIGATOR_STATE);
1025
1026         }
1027
1028         /**
1029          * <p>
1030          * setStoreNavigatorState
1031          * </p>
1032          *
1033          * @param selection
1034          *            a boolean.
1035          */
1036         public static void setStoreNavigatorState(boolean selection) {
1037                 getPreferenceStore().setValue(RESTORE_NAVIGATOR_STATE, selection);
1038
1039         }
1040
1041     /**
1042      * @return
1043      */
1044     public static boolean isShowUpWidgetIsDisposedMessages() {
1045        return getPreferenceStore().getBoolean(IS_SHOW_UP_WIDGET_IS_DISPOSED);
1046     }
1047     public static void setShowUpWidgetIsDisposedMessages(boolean selection) {
1048         getPreferenceStore().setValue(IS_SHOW_UP_WIDGET_IS_DISPOSED, selection);
1049     }
1050
1051     /**
1052      * @return
1053      */
1054     public static boolean isShowIdInVocabularyInChecklistEditor() {
1055         String area_display = getPreferenceStore().getString(IPreferenceKeys.CHECKLIST_AREA_DISPLAY);
1056         if (area_display.equals(CHECKLIST_AREA_DISPLAY_ID_IN_VOCABULARY)) {
1057             return true;
1058         }else{
1059             return false;
1060         }
1061     }
1062     public static boolean isShowSymbol1InChecklistEditor() {
1063         String area_display = getPreferenceStore().getString(IPreferenceKeys.CHECKLIST_AREA_DISPLAY);
1064         if (area_display.equals(CHECKLIST_AREA_DISPLAY_SYMBOL1)) {
1065             return true;
1066         }else{
1067             return false;
1068         }
1069      }
1070     public static boolean isShowSymbol2InChecklistEditor() {
1071         String area_display = getPreferenceStore().getString(IPreferenceKeys.CHECKLIST_AREA_DISPLAY);
1072         if (area_display.equals(CHECKLIST_AREA_DISPLAY_SYMBOL2)) {
1073             return true;
1074         }else{
1075             return false;
1076         }
1077      }
1078     public static void setShowIdInVocabularyInChecklistEditor(String selection) {
1079         getPreferenceStore().setValue(CHECKLIST_AREA_DISPLAY, selection);
1080     }
1081
1082     /**
1083      * @return
1084      */
1085     public static boolean isShowSymbolInChecklistEditor() {
1086        return getPreferenceStore().getBoolean(IPreferenceKeys.CHECKLIST_SYMBOL);
1087     }
1088     public static void setShowSymbolInChecklistEditor(boolean selection) {
1089         getPreferenceStore().setValue(CHECKLIST_SYMBOL, selection);
1090     }
1091
1092     /**
1093      * @return
1094      */
1095     public static boolean isShowRankInChecklistEditor() {
1096         return getPreferenceStore().getBoolean(IPreferenceKeys.CHECKLIST_SHOW_RANK);
1097     }
1098     public static void setShowRankInChecklistEditor(boolean selection) {
1099         getPreferenceStore().setValue(CHECKLIST_SHOW_RANK, selection);
1100     }
1101
1102     /**
1103      * @param object
1104      * @param b
1105      * @return
1106      */
1107     public static NameDetailsConfigurator getPreferredNameDetailsConfiguration( boolean local) {
1108         NameDetailsConfigurator config = new NameDetailsConfigurator(true);
1109
1110         CdmPreference preference = null;
1111
1112         if (!local) {
1113             preference = getPreferenceFromDB(PreferencePredicate.NameDetailsView);
1114             if (preference == null){
1115                 return null;
1116             }
1117
1118             getPreferenceStore().setValue(ALLOW_OVERRIDE_NAME_DETAILS, preference.isAllowOverride());
1119
1120             //the preference value is build like this:
1121             //<section1>:true;<section2>:false....
1122
1123             String value = preference.getValue();
1124             String [] sections = value.split(";");
1125             Map<String, Boolean> sectionMap = new HashMap<String, Boolean>();
1126             String[] sectionValues;
1127             for (String sectionValue: sections){
1128                 sectionValues = sectionValue.split(":");
1129                 sectionMap.put(sectionValues[0], Boolean.valueOf(sectionValues[1]));
1130             }
1131             config.setAllowOverride(preference.isAllowOverride());
1132             config.setSimpleDetailsViewActivated(getValue(sectionMap, "simpleViewActivated"));
1133
1134     //        getPreferenceStore().setValue(SHOW_SIMPLE_NAME_DETAILS_TAXON,
1135     //                (getValue(sectionMap, "taxon")));
1136             config.setTaxonSectionActivated(getValue(sectionMap, "taxon"));
1137
1138     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_LSID,
1139     //                (getValue(sectionMap, "lsid")));
1140             config.setLSIDActivated(getValue(sectionMap, "lsid"));
1141
1142     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_CODE,
1143     //                (getValue(sectionMap, "nc")));
1144             config.setNomenclaturalCodeActived(getValue(sectionMap, "nc"));
1145
1146     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_APPENDED_PHRASE,
1147     //                (getValue(sectionMap, "ap")));
1148             config.setAppendedPhraseActivated(getValue(sectionMap, "ap"));
1149
1150     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_RANK,
1151     //                (getValue(sectionMap, "rank")));
1152             config.setRankActivated(getValue(sectionMap, "rank"));
1153
1154
1155     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_ATOMISED_EPITHETS,
1156     //                (getValue(sectionMap, "atomisedEpithets")));
1157             config.setAtomisedEpithetsActivated(getValue(sectionMap, "atomisedEpithets"));
1158
1159     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_AUTHORSHIP,
1160     //                (getValue(sectionMap,"author")));
1161             config.setAuthorshipSectionActivated(getValue(sectionMap,"author"));
1162
1163     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_REFERENCE,
1164     //                (getValue(sectionMap, "nomRef")));
1165             config.setNomenclaturalReferenceSectionActivated(sectionMap.get("nomRef"));
1166
1167     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_STATUS,
1168     //                (getValue(sectionMap, "nomStat")));
1169             config.setNomenclaturalStatusSectionActivated(getValue(sectionMap, "nomStat"));
1170
1171
1172     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_PROTOLOGUE,
1173     //                (getValue(sectionMap,"protologue")));
1174             config.setProtologueActivated(getValue(sectionMap,"protologue"));
1175
1176     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_TYPE_DESIGNATION,
1177     //                (getValue(sectionMap,"typeDes")));
1178             config.setTypeDesignationSectionActivated(getValue(sectionMap,"typeDes"));
1179
1180     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NAME_RELATIONSHIP,
1181     //                (getValue(sectionMap,"nameRelation")));
1182             config.setNameRelationsSectionActivated(getValue(sectionMap,"nameRelation"));
1183
1184     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_HYBRID,
1185     //                (getValue(sectionMap, "hybrid")));
1186             config.setHybridActivated(getValue(sectionMap,"hybrid"));
1187         }else{
1188             config.setSimpleDetailsViewActivated(getPreferenceStore().getBoolean(SHOW_SIMPLE_NAME_DETAILS_SECTION));
1189             config.setTaxonSectionActivated(getPreferenceStore().getBoolean(SHOW_SIMPLE_NAME_DETAILS_TAXON));
1190             config.setLSIDActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_LSID));
1191             config.setNomenclaturalCodeActived(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_CODE));
1192             config.setAppendedPhraseActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_APPENDED_PHRASE));
1193             config.setRankActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_RANK));
1194             config.setAtomisedEpithetsActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_ATOMISED_EPITHETS));
1195             config.setAuthorshipSectionActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_AUTHORSHIP));
1196             config.setNomenclaturalReferenceSectionActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_REFERENCE));
1197             config.setNomenclaturalStatusSectionActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_STATUS));
1198             config.setProtologueActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_PROTOLOGUE));
1199             config.setTypeDesignationSectionActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_TYPE_DESIGNATION));
1200             config.setNameRelationsSectionActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_NAME_RELATIONSHIP));
1201             config.setHybridActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_HYBRID));
1202         }
1203         return config;
1204     }
1205
1206     /**
1207      * @param object
1208      * @param b
1209      * @return
1210      */
1211     public static void setPreferredNameDetailsConfiguration(NameDetailsConfigurator config, boolean local) {
1212         CdmPreference preference = null;
1213
1214         if (!local) {
1215             preference = CdmPreference.NewInstance(PreferenceSubject.NewDatabaseInstance(), PreferencePredicate.NameDetailsView, config.toString());
1216
1217             setPreferenceToDB(preference);
1218         }
1219         //also add to local preferences
1220         getPreferenceStore().setValue(SHOW_SIMPLE_NAME_DETAILS_SECTION, config.isSimpleDetailsViewActivated());
1221         getPreferenceStore().setValue(SHOW_SIMPLE_NAME_DETAILS_TAXON, config.isTaxonSectionActivated());
1222         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_LSID, config.isLSIDActivated());
1223         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_CODE, config.isNomenclaturalCodeActived());
1224         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_APPENDED_PHRASE, config.isAppendedPhraseActivated());
1225         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_RANK, config.isRankActivated());
1226         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_ATOMISED_EPITHETS, config.isAtomisedEpithetsActivated());
1227         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_AUTHORSHIP, config.isAuthorshipSectionActivated());
1228         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_REFERENCE, config.isNomenclaturalReferenceSectionActivated());
1229         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_STATUS, config.isNomenclaturalStatusSectionActivated());
1230         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_PROTOLOGUE, config.isProtologueActivated());
1231         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_TYPE_DESIGNATION, config.isTypeDesignationSectionActivated());
1232         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NAME_RELATIONSHIP, config.isNameRelationsSectionActivated());
1233         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_HYBRID, config.isHybridActivated());
1234
1235     }
1236
1237     private static Boolean getValue(Map<String, Boolean> sectionMap, String string) {
1238                 if (sectionMap.containsKey(string)){
1239                         return sectionMap.get(string);
1240                 }else{
1241                         return true;
1242                 }
1243
1244         }
1245
1246
1247
1248     /**
1249      * <p>
1250      * setAbcdConfigurator
1251      * </p>
1252      *
1253      * @param preferredConfiguration
1254      *            a {@link eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator}
1255      *            object.
1256      */
1257     public static Abcd206ImportConfigurator getAbcdImportConfigurationPreference() {
1258
1259         Abcd206ImportConfigurator config = Abcd206ImportConfigurator.NewInstance(null,null);
1260         ICdmRepository controller;
1261         controller = CdmStore.getCurrentApplicationConfiguration();
1262         PrefKey key = CdmPreference.NewKey(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AbcdImportConfig);
1263         CdmPreference preference = null;
1264         if (controller == null){
1265             return null;
1266         }
1267         preference = controller.getPreferenceService().find(key);
1268         boolean allowOverride = true;
1269         if (preference != null && !preference.isAllowOverride()){
1270             allowOverride = false;
1271         }
1272         if (PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_OVERRIDE) && allowOverride){
1273
1274             config.setAddIndividualsAssociationsSuchAsSpecimenAndObservations(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_ADD_INDIVIDUALS_ASSOCIATIONS_SUCH_AS_SPECIMEN_AND_OBSERVATIONS));
1275
1276             config.setAddMediaAsMediaSpecimen(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_ADD_MEDIA_AS_MEDIASPECIMEN));
1277
1278             config.setAllowReuseOtherClassifications(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_ALLOW_REUSE_OTHER_CLASSIFICATIONS));
1279             config.setDeduplicateClassifications(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_DEDUPLICATE_CLASSIFICATIONS));
1280             config.setDeduplicateReferences(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_DEDUPLICATE_REFERENCES));
1281
1282             config.setGetSiblings(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_DO_SIBLINGS));
1283             config.setIgnoreAuthorship(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_IGNORE_AUTHORSHIP));
1284             config.setIgnoreImportOfExistingSpecimen(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_IGNORE_IMPORT_OF_EXISTING_SPECIMEN));
1285             config.setMapUnitIdToAccessionNumber(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_MAP_UNIT_ID_TO_ACCESSION_NUMBER));
1286             config.setMapUnitIdToBarcode(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_MAP_UNIT_ID_TO_BARCODE));
1287             config.setMapUnitIdToCatalogNumber(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_MAP_UNIT_ID_TOCATALOG_NUMBER));
1288             config.setMoveNewTaxaToDefaultClassification(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_MOVE_NEW_TAXA_TO_DEFAULT_CLASSIFICATION));
1289             config.setOverwriteExistingSpecimens(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_OVERWRITE_EXISTING_SPECIMEN));
1290             config.setReuseExistingDescriptiveGroups(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_REUSE_EXISTING_DESCRIPTIVE_GROUPS));
1291             config.setReuseExistingMetaData(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_REUSE_EXISTING_META_DATA));
1292             config.setReuseExistingTaxaWhenPossible(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_REUSE_EXISTING_TAXA_WHEN_POSSIBLE));
1293             config.setNomenclaturalCode(NomenclaturalCode.getByKey(PreferencesUtil.getPreferenceStore().getString(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_NOMENCLATURAL_CODE)));
1294             return config;
1295
1296         }
1297
1298             if (preference == null){
1299                 return config;
1300              } else{
1301              String configString = preference.getValue();
1302              String[] configArray = configString.split(";");
1303
1304              for (String configItem: configArray){
1305                  String[] keyValue = configItem.split(":");
1306                  String keyString = keyValue[0];
1307                  String valueString = keyValue[1];
1308                  if (keyString.equals("ignoreImportOfExistingSpecimen")){
1309                      config.setIgnoreImportOfExistingSpecimen(Boolean.valueOf(valueString));
1310                  }else if (keyString.equals("addIndividualsAssociationsSuchAsSpecimenAndObservations")){
1311                      config.setAddIndividualsAssociationsSuchAsSpecimenAndObservations(Boolean.valueOf(valueString));
1312                  }else if (keyString.equals("reuseExistingTaxaWhenPossible")){
1313                      config.setReuseExistingTaxaWhenPossible(Boolean.valueOf(valueString));
1314                  }else if (keyString.equals("ignoreAuthorship")){
1315                      config.setIgnoreAuthorship(Boolean.valueOf(valueString));
1316                  }else if (keyString.equals("addMediaAsMediaSpecimen")){
1317                      config.setAddMediaAsMediaSpecimen(Boolean.valueOf(valueString));
1318                  }else if (keyString.equals("reuseExistingMetaData")){
1319                      config.setReuseExistingMetaData(Boolean.valueOf(valueString));
1320                  }else if (keyString.equals("reuseExistingDescriptiveGroups")){
1321                      config.setReuseExistingDescriptiveGroups(Boolean.valueOf(valueString));
1322                  }else if (keyString.equals("allowReuseOtherClassifications")){
1323                      config.setAllowReuseOtherClassifications(Boolean.valueOf(valueString));
1324                  }else if (keyString.equals("deduplicateReferences")){
1325                      config.setDeduplicateReferences(Boolean.valueOf(valueString));
1326                  }else if (keyString.equals("deduplicateClassifications")){
1327                      config.setDeduplicateClassifications(Boolean.valueOf(valueString));
1328                  }else if (keyString.equals("moveNewTaxaToDefaultClassification")){
1329                      config.setMoveNewTaxaToDefaultClassification(Boolean.valueOf(valueString));
1330                  }else if (keyString.equals("mapUnitIdToCatalogNumber")){
1331                      config.setMapUnitIdToCatalogNumber(Boolean.valueOf(valueString));
1332                  }else if (keyString.equals("mapUnitIdToAccessionNumber")){
1333                      config.setMapUnitIdToAccessionNumber(Boolean.valueOf(valueString));
1334                  }else if (keyString.equals("mapUnitIdToBarcode")){
1335                      config.setMapUnitIdToBarcode(Boolean.valueOf(valueString));
1336                  }else if (keyString.equals("overwriteExistingSpecimens")){
1337                      config.setOverwriteExistingSpecimens(Boolean.valueOf(valueString));
1338                  }else if (keyString.equals("nomenclaturalCode")){
1339                          config.setNomenclaturalCode(NomenclaturalCode.fromString(valueString));
1340                  }else{
1341                      logger.debug("This key of the abcd configurator needs to be added to the transformer: " + keyString);
1342                  }
1343
1344             }
1345         }
1346         return config;
1347     }
1348
1349
1350     public static void updateAbcdImportConfigurationPreference() {
1351
1352         Abcd206ImportConfigurator config = Abcd206ImportConfigurator.NewInstance(null,null);
1353         ICdmRepository controller;
1354         controller = CdmStore.getCurrentApplicationConfiguration();
1355         PrefKey key = CdmPreference.NewKey(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AbcdImportConfig);
1356         CdmPreference preference = null;
1357         if (controller == null){
1358             return ;
1359         }
1360         preference = controller.getPreferenceService().find(key);
1361         boolean allowOverride = true;
1362         if (preference != null && !preference.isAllowOverride()){
1363             allowOverride = false;
1364         }
1365         if (!PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_OVERRIDE) || !allowOverride){
1366
1367             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_ADD_INDIVIDUALS_ASSOCIATIONS_SUCH_AS_SPECIMEN_AND_OBSERVATIONS, config.isAddIndividualsAssociationsSuchAsSpecimenAndObservations());
1368             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_ADD_MEDIA_AS_MEDIASPECIMEN, config.isAddMediaAsMediaSpecimen());
1369
1370             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_ALLOW_REUSE_OTHER_CLASSIFICATIONS, config.isAllowReuseOtherClassifications());
1371             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_DEDUPLICATE_CLASSIFICATIONS, config.isDeduplicateClassifications());
1372             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_DEDUPLICATE_REFERENCES, config.isDeduplicateReferences());
1373
1374             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_DO_SIBLINGS, config.isGetSiblings());
1375             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_IGNORE_AUTHORSHIP, config.isIgnoreAuthorship());
1376             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_IGNORE_IMPORT_OF_EXISTING_SPECIMEN, config.isIgnoreImportOfExistingSpecimen());
1377             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_MAP_UNIT_ID_TO_ACCESSION_NUMBER, config.isMapUnitIdToAccessionNumber());
1378             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_MAP_UNIT_ID_TO_BARCODE, config.isMapUnitIdToBarcode());
1379             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_MAP_UNIT_ID_TOCATALOG_NUMBER, config.isMapUnitIdToCatalogNumber());
1380             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_MOVE_NEW_TAXA_TO_DEFAULT_CLASSIFICATION, config.isMoveNewTaxaToDefaultClassification());
1381             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_OVERWRITE_EXISTING_SPECIMEN, config.isOverwriteExistingSpecimens());
1382             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_REUSE_EXISTING_DESCRIPTIVE_GROUPS, config.isReuseExistingDescriptiveGroups());
1383             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_REUSE_EXISTING_META_DATA, config.isReuseExistingMetaData());
1384             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_REUSE_EXISTING_TAXA_WHEN_POSSIBLE, config.isReuseExistingTaxaWhenPossible());
1385             if (config.getNomenclaturalCode() != null){
1386                 getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_NOMENCLATURAL_CODE, config.getNomenclaturalCode().getKey());
1387             }
1388         }
1389     }
1390
1391
1392     /**
1393     *
1394     */
1395    public NameDetailsConfigurator createLocalNameDetailsViewConfig(boolean local) {
1396        NameDetailsConfigurator config = new NameDetailsConfigurator(true);
1397        if (local){
1398           config.setSimpleDetailsViewActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_SIMPLE_NAME_DETAILS_SECTION));
1399           config.setAppendedPhraseActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_APPENDED_PHRASE));
1400           config.setAtomisedEpithetsActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_ATOMISED_EPITHETS));
1401           config.setAuthorshipSectionActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_AUTHORSHIP));
1402           config.setLSIDActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_LSID));
1403           config.setNameApprobiationActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NAME_APPROBATION));
1404           config.setNameCacheActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_CACHE));
1405           config.setNameRelationsSectionActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NAME_RELATIONSHIP));
1406           config.setNomenclaturalCodeActived(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_CODE));
1407           config.setNomenclaturalStatusSectionActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_STATUS));
1408           config.setNomenclaturalReferenceSectionActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_REFERENCE));
1409           config.setProtologueActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_PROTOLOGUE));
1410           config.setRankActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_RANK));
1411           config.setTaxonSectionActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_SIMPLE_NAME_DETAILS_TAXON));
1412           config.setTypeDesignationSectionActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_TYPE_DESIGNATION));
1413           config.setHybridActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_HYBRID));
1414        }else{
1415
1416        }
1417
1418       return config;
1419    }
1420
1421
1422    public static void saveConfigToPrefernceStore(NameDetailsConfigurator config) {
1423        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_SIMPLE_NAME_DETAILS_SECTION,
1424                config.isSimpleDetailsViewActivated());
1425        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_SIMPLE_NAME_DETAILS_TAXON, config.isTaxonSectionActivated());
1426        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_LSID, config.isLSIDActivated());
1427        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_CODE,
1428                config.isNomenclaturalCodeActived());
1429        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NAMECACHE,
1430                config.isNameCacheActivated());
1431        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_APPENDED_PHRASE,
1432                config.isAppendedPhraseActivated());
1433        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_RANK, config.isRankActivated());
1434        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_ATOMISED_EPITHETS,
1435                config.isAtomisedEpithetsActivated());
1436        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_AUTHORSHIP_CACHE,
1437                config.isAuthorCacheActivated());
1438        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_AUTHORSHIP,
1439                config.isAuthorshipSectionActivated());
1440        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_REFERENCE,
1441                config.isNomenclaturalReferenceSectionActivated());
1442        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_STATUS,
1443                config.isNomenclaturalStatusSectionActivated());
1444        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_PROTOLOGUE,
1445                config.isProtologueActivated());
1446        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_TYPE_DESIGNATION,
1447                config.isTypeDesignationSectionActivated());
1448        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NAME_RELATIONSHIP,
1449                config.isNameRelationsSectionActivated());
1450        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_HYBRID,
1451                config.isHybridActivated());
1452
1453    }
1454
1455 /**
1456  * @return
1457  */
1458 public static boolean isSortTaxaByRankAndName() {
1459
1460     return getPreferenceStore().getBoolean(IPreferenceKeys.SORT_TAXA_BY_RANK_AND_NAME);
1461 }
1462
1463 /**
1464  * @return
1465  */
1466 public static boolean isSortNamedAreaByOrderInVocabulary() {
1467
1468     return getPreferenceStore().getBoolean(IPreferenceKeys.SORT_NAMED_AREA_BY_VOCABULARY_ORDER);
1469 }
1470
1471 public static void setSortNamedAreasByOrderInVocabulary(boolean isSortByVocabularyOrder) {
1472     getPreferenceStore().setValue(IPreferenceKeys.SORT_NAMED_AREA_BY_VOCABULARY_ORDER, isSortByVocabularyOrder);
1473
1474 }
1475
1476 /**
1477  * <p>
1478  * setPreferredNamedAreasForDistributionEditor
1479  * </p>
1480  *
1481  * @param saveCheckedElements
1482  * @param saveGrayedElements
1483  */
1484 public static void setLastSelectedReference(
1485         List<String> lastSelectedReferences) {
1486
1487         IPreferenceStore preferenceStore = PreferencesUtil.getPreferenceStore();
1488         preferenceStore.setValue(PreferencesUtil.LAST_SELECTED_REFERENCES, lastSelectedReferences.toString());
1489     }
1490
1491 /**
1492  * <p>
1493  * setPreferredNamedAreasForDistributionEditor
1494  * </p>
1495  *
1496  * @param saveCheckedElements
1497  * @param saveGrayedElements
1498  */
1499 public static List<String> getLastSelectedReferences() {
1500
1501         IPreferenceStore preferenceStore = PreferencesUtil.getPreferenceStore();
1502         String lastSelected = preferenceStore.getString(PreferencesUtil.LAST_SELECTED_REFERENCES);
1503         List<String> result = new ArrayList<>();
1504         if (!StringUtils.isBlank(lastSelected)){
1505             Collections.addAll(result, lastSelected.substring(1,lastSelected.length()-1).split(", "));
1506         }
1507         return result;
1508     }
1509
1510
1511 /**
1512  * <p>
1513  * setPreferredNamedAreasForDistributionEditor
1514  * </p>
1515  *
1516  * @param saveCheckedElements
1517  * @param saveGrayedElements
1518  */
1519 public static void setPreferredNamedAreasForDistributionEditor(
1520         String saveCheckedElements, String saveGrayedElements, boolean local) {
1521     if (local){
1522         IPreferenceStore preferenceStore = PreferencesUtil.getPreferenceStore();
1523         preferenceStore.setValue(PreferencesUtil.DISTRIBUTION_AREA_OCCURENCE_STATUS, saveCheckedElements);
1524         preferenceStore.setValue(PreferencesUtil.DISTRIBUTION_AREA_OCCURENCE_STATUS_GRAYED, saveGrayedElements);
1525
1526     }
1527     else{
1528         CdmPreference preference = null;
1529
1530         if (saveCheckedElements == null){
1531             preference = getPreferenceFromDB(PreferencePredicate.AvailableDistributionAreaTerms);
1532
1533             if (preference == null){
1534                 return ;
1535             } else{
1536                 getPreferenceStore().setValue(DISTRIBUTION_AREA_OCCURENCE_STATUS,
1537                         saveCheckedElements);
1538                 preference = CdmPreference.NewInstance(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AvailableDistributionAreaTerms, saveCheckedElements);
1539                 setPreferenceToDB(preference);
1540
1541             }
1542         } else{
1543            preference = CdmPreference.NewInstance(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AvailableDistributionAreaTerms, saveCheckedElements);
1544            setPreferenceToDB(preference);
1545            getPreferenceStore().setValue(DISTRIBUTION_AREA_OCCURENCE_STATUS,
1546                     saveCheckedElements);
1547
1548         }
1549     }
1550
1551 }
1552
1553 /**
1554  * @param saveCheckedElements
1555  * @param saveCheckedElements2
1556  * @param b
1557  */
1558 public static void setPreferredVocabulariesForDistributionEditor(String saveCheckedElements,
1559         boolean local) {
1560     if (local){
1561         IPreferenceStore preferenceStore = PreferencesUtil.getPreferenceStore();
1562         preferenceStore.setValue(PreferencesUtil.DISTRIBUTION_VOCABULARIES, saveCheckedElements);
1563     }
1564     else{
1565         ICdmRepository controller;
1566         CdmPreference preference = null;
1567
1568         if (saveCheckedElements == null){
1569             preference = getPreferenceFromDB(PreferencePredicate.AvailableDistributionAreaVocabularies);
1570
1571             if (preference == null){
1572                 return ;
1573             } else{
1574                 getPreferenceStore().setValue(DISTRIBUTION_VOCABULARIES,
1575                         saveCheckedElements);
1576                 preference = CdmPreference.NewInstance(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AvailableDistributionAreaVocabularies, saveCheckedElements);
1577                 setPreferenceToDB(preference);
1578             }
1579         } else{
1580             preference = CdmPreference.NewInstance(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AvailableDistributionAreaVocabularies, saveCheckedElements);
1581             setPreferenceToDB(preference);
1582             getPreferenceStore().setValue(DISTRIBUTION_VOCABULARIES,
1583                     saveCheckedElements);
1584
1585         }
1586     }
1587 }
1588
1589
1590
1591
1592 /**
1593  * @param saveCheckedElements
1594  * @param saveCheckedElements2
1595  * @param b
1596  */
1597 public static String getPreferredVocabulariesForDistributionEditor(boolean local) {
1598     if (local){
1599         IPreferenceStore preferenceStore = PreferencesUtil.getPreferenceStore();
1600         String pref = preferenceStore.getString(DISTRIBUTION_VOCABULARIES);
1601         return pref;
1602     }
1603     else{
1604         CdmPreference preference = null;
1605         preference = getPreferenceFromDB(PreferencePredicate.AvailableDistributionAreaVocabularies);
1606         if (preference == null){
1607             return null;
1608         } else{
1609             return preference.getValue();
1610         }
1611
1612     }
1613
1614
1615
1616 }
1617
1618 public static boolean getFilterCommonNameReferences(){
1619     return getPreferenceStore().getBoolean(PreferencesUtil.FILTER_COMMON_NAME_REFERENCES);
1620 }
1621
1622 /**
1623  *
1624  */
1625 public static void updateDBPreferences() {
1626     CdmPreference preference = null;
1627     IPreferenceStore prefStore = getPreferenceStore();
1628
1629     //ABCD Configurator
1630
1631     updateAbcdImportConfigurationPreference();
1632
1633     preference = getPreferenceFromDB(PreferencePredicate.ShowImportExportMenu);
1634     if (preference != null){
1635         if(!prefStore.getBoolean(SHOW_IO_MENU) ||  !preference.isAllowOverride()){
1636             prefStore.setValue(SHOW_IO_MENU, preference.getValue());
1637         }
1638     }else{
1639         prefStore.setValue(SHOW_IO_MENU, true);
1640     }
1641
1642     preference = getPreferenceFromDB(PreferencePredicate.ShowMediaView);
1643     if (preference != null){
1644         if(!prefStore.getBoolean(SHOW_MEDIA) ||  !preference.isAllowOverride()){
1645             prefStore.setValue(SHOW_MEDIA, preference.getValue());
1646         }
1647     }else{
1648         prefStore.setValue(SHOW_MEDIA, true);
1649     }
1650
1651     preference = getPreferenceFromDB(PreferencePredicate.ShowChecklistPerspective);
1652     if (preference != null){
1653         if(!prefStore.getBoolean(SHOW_CHECKLIST_PERSPECTIVE) ||  !preference.isAllowOverride()){
1654             prefStore.setValue(SHOW_CHECKLIST_PERSPECTIVE, preference.getValue());
1655         }
1656     }else{
1657         prefStore.setValue(SHOW_CHECKLIST_PERSPECTIVE, false);
1658     }
1659
1660     //Specimen Details
1661     preference = getPreferenceFromDB(PreferencePredicate.ShowSpecimen);
1662     if (preference != null){
1663         if(!prefStore.getBoolean(SHOW_SPECIMEN) ||  !preference.isAllowOverride()){
1664             prefStore.setValue(SHOW_SPECIMEN, preference.getValue());
1665         }
1666     }else{
1667         prefStore.setValue(SHOW_SPECIMEN, true);
1668     }
1669
1670     preference = getPreferenceFromDB(PreferencePredicate.ShowTaxonAssociations);
1671     if (preference != null){
1672         if(!prefStore.getBoolean(SHOW_TAXON_ASSOCIATIONS_OVERRIDE) ||  !preference.isAllowOverride()){
1673             prefStore.setValue(SHOW_TAXON_ASSOCIATIONS, preference.getValue());
1674         }
1675     }
1676     preference = getPreferenceFromDB(PreferencePredicate.ShowCollectingAreasInGeneralSection);
1677     if (preference != null){
1678         if(!prefStore.getBoolean(SHOW_COLLECTING_AREAS_IN_GENERAL_SECTION_OVERRIDE) ||  !preference.isAllowOverride()){
1679             prefStore.setValue(SHOW_COLLECTING_AREAS_IN_GENERAL_SECTION, preference.getValue());
1680         }
1681     }
1682     preference = getPreferenceFromDB(PreferencePredicate.ShowLifeForm);
1683     if (preference != null){
1684         if(!prefStore.getBoolean(SHOW_LIFE_FORM_OVERRIDE) ||  !preference.isAllowOverride()){
1685             prefStore.setValue(SHOW_LIFE_FORM, preference.getValue());
1686         }
1687     }
1688     preference = getPreferenceFromDB(PreferencePredicate.DeterminationOnlyForFieldUnits);
1689     if (preference != null){
1690         if(!prefStore.getBoolean(DETERMINATION_ONLY_FOR_FIELD_UNITS_OVERRIDE) ||  !preference.isAllowOverride()){
1691             prefStore.setValue(DETERMINATION_ONLY_FOR_FIELD_UNITS, preference.getValue());
1692         }
1693     }
1694
1695
1696     //Name Details
1697     NameDetailsConfigurator config = getPreferredNameDetailsConfiguration(false);
1698     if (config != null ){
1699         if (!prefStore.getBoolean(OVERRIDE_NAME_DETAILS) ||  !prefStore.getBoolean(ALLOW_OVERRIDE_NAME_DETAILS)){
1700             setPreferredNameDetailsConfiguration(config, false);
1701         }
1702     }
1703
1704     //Distribution Editor
1705     preference = getPreferenceFromDB(PreferencePredicate.AvailableDistributionAreaVocabularies);
1706     if (preference != null){
1707         if (!prefStore.getBoolean(DISTRIBUTION_AREA_PREFRENCES_ACTIVE_OVERRIDE) ||  !preference.isAllowOverride()){
1708             prefStore.setValue(DISTRIBUTION_VOCABULARIES, preference.getValue());
1709         }
1710     }
1711
1712     preference = getPreferenceFromDB(PreferencePredicate.DistributionEditorActivated);
1713     if (preference != null){
1714         if (!prefStore.getBoolean(DISTRIBUTION_AREA_PREFRENCES_ACTIVE_OVERRIDE) || !preference.isAllowOverride()){
1715             prefStore.setValue(DISTRIBUTION_AREA_PREFRENCES_ACTIVE, preference.getValue());
1716         }
1717     }
1718
1719     preference = getPreferenceFromDB(PreferencePredicate.AvailableDistributionStatus);
1720     if (preference != null){
1721         if (!prefStore.getBoolean(DISTRIBUTION_STATUS_OVERRIDE) || !preference.isAllowOverride()){
1722             //get terms for the uuids... and add them to the termManager as preferred terms
1723             ITermService termService = CdmStore.getService(ITermService.class);
1724             String[] uuidArray = preference.getValue().split(";");
1725             List<UUID> uuidList = new ArrayList();
1726             for (String uuidString:uuidArray){
1727                 uuidList.add(UUID.fromString(uuidString));
1728             }
1729
1730             List<DefinedTermBase> definedTermBases = termService.load(uuidList, null);
1731             CdmStore.getTermManager().setPreferredTerms(definedTermBases, TermStore.getTerms(TermType.PresenceAbsenceTerm, null));
1732         }
1733     }
1734
1735     preference = getPreferenceFromDB(PreferencePredicate.CommonNameAreaVocabularies);
1736     if (preference != null){
1737         if (!prefStore.getBoolean(COMMON_NAME_AREA_VOCABULARIES_OVERRIDE) ||  !preference.isAllowOverride()){
1738             prefStore.setValue(COMMON_NAME_AREA_VOCABULARIES, preference.getValue());
1739         }
1740     }
1741
1742     preference = getPreferenceFromDB(PreferencePredicate.CommonNameReferencesWithMarker);
1743     if (preference != null){
1744         if (!prefStore.getBoolean(FILTER_COMMON_NAME_REFERENCES) ||  !preference.isAllowOverride()){
1745             prefStore.setValue(FILTER_COMMON_NAME_REFERENCES, preference.getValue());
1746         }
1747     }else{
1748         prefStore.setValue(FILTER_COMMON_NAME_REFERENCES, false);
1749     }
1750
1751
1752     preference = getPreferenceFromDB(PreferencePredicate.ShowTaxonNodeWizard);
1753     if (preference != null){
1754         if (!prefStore.getBoolean(SHOW_TAXONNODE_WIZARD) ||  !preference.isAllowOverride()){
1755             prefStore.setValue(SHOW_TAXONNODE_WIZARD, preference.getValue());
1756         }
1757     }else{
1758         prefStore.setValue(SHOW_TAXONNODE_WIZARD, true);
1759     }
1760
1761     preference = getPreferenceFromDB(PreferencePredicate.ShowIdInSource);
1762     if (preference != null){
1763         if (!prefStore.getBoolean(SHOW_ID_IN_SOURCE) ||  !preference.isAllowOverride()){
1764             prefStore.setValue(SHOW_ID_IN_SOURCE, preference.getValue());
1765         }
1766     }else{
1767         prefStore.setValue(SHOW_ID_IN_SOURCE, true);
1768     }
1769
1770     preference = getPreferenceFromDB(PreferencePredicate.ShowNameInSource);
1771     if (preference != null){
1772         if (!prefStore.getBoolean(SHOW_NAME_IN_SOURCE) ||  !preference.isAllowOverride()){
1773             prefStore.setValue(SHOW_NAME_IN_SOURCE, preference.getValue());
1774         }
1775     }else{
1776         prefStore.setValue(SHOW_NAME_IN_SOURCE, true);
1777     }
1778
1779     preference = getPreferenceFromDB(PreferencePredicate.DisableMultiClassification);
1780     if (preference != null){
1781         if (!prefStore.getBoolean(DISABLE_MULTI_CLASSIFICATION) ||  !preference.isAllowOverride()){
1782             prefStore.setValue(DISABLE_MULTI_CLASSIFICATION, preference.getValue());
1783         }
1784     }else{
1785         prefStore.setValue(DISABLE_MULTI_CLASSIFICATION, false);
1786     }
1787
1788 }
1789
1790
1791
1792
1793
1794
1795
1796 }