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, true);
 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                 getPreferenceStore().setDefault(DISABLE_SEC, false);
 610                 getPreferenceStore().setDefault(SHOW_SEC_DETAILS, true);
 611         }
 612
 613         /**
 614          * <p>
 615          * checkNomenclaturalCode
 616          * </p>
 617          */
 618         public static void checkNomenclaturalCode() {
 619                 // First time Editor is opened, no nomenclatural code has been set
 620                 if (PreferencesUtil.getPreferredNomenclaturalCode(true) == null) {
 621                         PreferencesUtil.setPreferredNomenclaturalCode(getPreferenceKey(NomenclaturalCode.ICNAFP), true);
 622                 }
 623
 624
 625
 626         }
 627         public static void setNomenclaturalCodePreferences(){
 628             ICdmRepository controller;
 629         controller = CdmStore.getCurrentApplicationConfiguration();
 630         PrefKey key = CdmPreference.NewKey(PreferenceSubject.NewDatabaseInstance(), PreferencePredicate.NomenclaturalCode);
 631         CdmPreference preference = null;
 632         if (controller == null){
 633             return ;
 634         }
 635         preference = controller.getPreferenceService().find(key);
 636         if (preference == null){
 637             return;
 638         }
 639         getPreferenceStore().setValue(ALLOW_OVERRIDE_NOMENCLATURAL_CODE_KEY, preference.isAllowOverride());
 640
 641         int index = StringUtils.lastIndexOf(preference.getValue(), ".");
 642         UUID uuid = UUID.fromString(preference.getValue().substring(index +1, preference.getValue().length()));
 643         NomenclaturalCode preferredCode = NomenclaturalCode.getByUuid(uuid);
 644
 645         getPreferenceStore().setValue(PREFERRED_NOMENCLATURAL_CODE_KEY,
 646                 getPreferenceKey(preferredCode));
 647
 648         }
 649
 650         public static void checkDefaultLanguage(){
 651             if(PreferencesUtil.getPreferredDefaultLangugae() == null){
 652                Shell shell = AbstractUtility.getShell();
 653                int open = new DefaultLanguageDialog(shell).open();
 654                if(open == Window.OK){
 655                    PlatformUI.getWorkbench().restart();
 656                }
 657             }else{
 658                 //TODO:In case of a reinstall, the config.ini will be overwritten
 659                 //     here you create config.ini with the stored key from preferences
 660             }
 661         }
 662
 663         /**
 664          * <p>
 665          * getMapServiceAccessPoint
 666          * </p>
 667          *
 668          * @return a {@link java.lang.String} object.
 669          */
 670         public static String getMapServiceAccessPoint() {
 671                 return getPreferenceStore().getString(EDIT_MAP_SERVICE_ACCES_POINT);
 672         }
 673
 674         /**
 675          * <p>
 676          * shouldConnectAtStartUp
 677          * </p>
 678          *
 679          * @return a boolean.
 680          */
 681         public static boolean shouldConnectAtStartUp() {
 682                 //FIXME :  force SHOULD_CONNECT_AT_STARTUP to false (ticket 3828) until resolution
 683                 //return getPreferenceStore().getBoolean(SHOULD_CONNECT_AT_STARTUP);
 684                 return false;
 685         }
 686
 687         /**
 688          * <p>
 689          * getDefaultFeatureTreeForTextualDescription
 690          * </p>
 691          *
 692          * @return a {@link eu.etaxonomy.cdm.model.description.FeatureTree} object.
 693          */
 694         public static FeatureTree getDefaultFeatureTreeForTextualDescription() {
 695                 String uuidString = getPreferenceStore().getString(
 696                                 FEATURE_TREE_DEFAULT_TEXT);
 697                 return CdmUtils.isEmpty(uuidString) ? null : CdmStore.getService(
 698                                 IFeatureTreeService.class).load(UUID.fromString(uuidString));
 699         }
 700
 701         /**
 702          * <p>
 703          * getDefaultFeatureTreeForStructuredDescription
 704          * </p>
 705          *
 706          * @return a {@link eu.etaxonomy.cdm.model.description.FeatureTree} object.
 707          */
 708         public static FeatureTree getDefaultFeatureTreeForStructuredDescription() {
 709                 String uuidString = getPreferenceStore().getString(
 710                                 FEATURE_TREE_DEFAULT_STRUCTURE);
 711                 return CdmUtils.isEmpty(uuidString) ? null : CdmStore.getService(
 712                                 IFeatureTreeService.class).load(UUID.fromString(uuidString));
 713         }
 714
 715         /**
 716          * <p>
 717          * setSortRanksHierarchichally
 718          * </p>
 719          *
 720          * @param selection
 721          *            a boolean.
 722          */
 723         public static void setSortRanksHierarchichally(boolean selection) {
 724                 getPreferenceStore().setValue(SORT_RANKS_HIERARCHICHALLY, selection);
 725         }
 726
 727         /**
 728          * <p>
 729          * getSortRanksHierarchichally
 730          * </p>
 731          *
 732          * @return a boolean.
 733          */
 734         public static boolean getSortRanksHierarchichally() {
 735                 return getPreferenceStore().getBoolean(SORT_RANKS_HIERARCHICHALLY);
 736         }
 737
 738         public static boolean isMultilanguageTextEditingCapability() {
 739                 return getPreferenceStore().getBoolean(
 740                                 MULTILANGUAGE_TEXT_EDITING_CAPABILITY);
 741         }
 742
 743         public static Language getGlobalLanguage() {
 744
 745
 746                 String languageUuidString = getPreferenceStore().getString(
 747                                 GLOBAL_LANGUAGE_UUID);
 748
 749                 if(!CdmStore.isActive()) {
 750             MessagingUtils.noDataSourceWarningDialog(languageUuidString);
 751             return null;
 752         }
 753
 754                 if (CdmUtils.isBlank(languageUuidString)) {
 755                         return Language.getDefaultLanguage();
 756                 }
 757
 758                 UUID languageUuid = UUID.fromString(languageUuidString);
 759                 return (Language) CdmStore.getService(ITermService.class).load(
 760                                 languageUuid);
 761         }
 762
 763         public static void setGlobalLanguage(Language language) {
 764             if(language != null) {
 765                 getPreferenceStore().setValue(GLOBAL_LANGUAGE_UUID,language.getUuid().toString());
 766                 CdmStore.setDefaultLanguage(language);
 767             }
 768
 769         }
 770
 771         /**
 772          * @return
 773          */
 774         public static Map<MarkerType, Boolean> getEditMarkerTypePreferences() {
 775                 List<MarkerType> markerTypes = CdmStore.getTermManager()
 776                                 .getPreferredTerms(MarkerType.class);
 777
 778                 Map<MarkerType, Boolean> result = new HashMap<MarkerType, Boolean>();
 779
 780                 for (MarkerType markerType : markerTypes) {
 781                         String name = getMarkerTypeEditingPreferenceKey(markerType);
 782                         Boolean value = getPreferenceStore().getBoolean(name);
 783
 784                         result.put(markerType, value);
 785                 }
 786
 787                 return result;
 788         }
 789
 790         /**
 791          * @param markerTypeEditingMap
 792          */
 793         public static void setEditMarkerTypePreferences(
 794                         Map<MarkerType, Boolean> markerTypeEditingMap) {
 795                 for (MarkerType markerType : markerTypeEditingMap.keySet()) {
 796                         String name = getMarkerTypeEditingPreferenceKey(markerType);
 797                         getPreferenceStore().setValue(name,
 798                                         markerTypeEditingMap.get(markerType));
 799                 }
 800
 801         }
 802
 803         private static String getMarkerTypeEditingPreferenceKey(
 804                         MarkerType markerType) {
 805                 markerType = HibernateProxyHelper.deproxy(markerType);
 806                 return markerType.getClass().getName() + EDIT_MARKER_TYPE_PREFIX;
 807         }
 808
 809         /**
 810          * <p>
 811          * setEditMarkerTypePreference
 812          * </p>
 813          *
 814          * @param input
 815          *            a {@link org.eclipse.ui.IEditorInput} object.
 816          * @param markerType
 817          *            a {@link eu.etaxonomy.cdm.model.common.MarkerType} object.
 818          * @param edit
 819          *            a boolean.
 820          */
 821         public static void setEditMarkerTypePreference(MarkerType markerType,
 822                         boolean edit) {
 823                 getPreferenceStore().setValue(
 824                                 getMarkerTypeEditingPreferenceKey(markerType), edit);
 825         }
 826
 827         /**
 828          * @return
 829          */
 830         public static DerivedUnitFacadeConfigurator getDerivedUnitConfigurator() {
 831                 DerivedUnitFacadeConfigurator configurator = DerivedUnitFacadeConfigurator
 832                                 .NewInstance();
 833                 configurator.setMoveDerivedUnitMediaToGallery(true);
 834                 configurator.setMoveFieldObjectMediaToGallery(true);
 835                 return configurator;
 836         }
 837
 838         /**
 839          * This method will write language properties to the config.ini located in the configuration folder
 840          * of the Taxonomic Ediitor. <b>This method is only used to set the default language for Taxonomic Editor.</b>
 841          *
 842          * @param setLanguage 0 is for german and 1 for english.
 843          * @throws IOException
 844          */
 845     public void writePropertyToConfigFile(int setLanguage) throws IOException {
 846         File file = org.eclipse.core.runtime.preferences.ConfigurationScope.INSTANCE.getLocation().toFile();
 847         //give warning to user if the directory has no write access
 848         if(file == null){
 849             throw new IOException();
 850         }
 851         Properties properties = load(file.getAbsolutePath()+"/config.ini");
 852         switch(setLanguage){
 853         case 0:
 854             properties.setProperty("osgi.nl", "de");
 855             PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.DEFAULT_LANGUAGE_EDITOR, "de");
 856             break;
 857         case 1:
 858             properties.setProperty("osgi.nl", "en");
 859             PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.DEFAULT_LANGUAGE_EDITOR, "en");
 860             break;
 861         default:
 862             break;
 863         }
 864         save(file+"/config.ini", properties);
 865     }
 866
 867     /**
 868      * This method loads a property from a given file and returns it.
 869      *
 870      * @param filename
 871      * @return
 872      * @throws IOException
 873      */
 874     private Properties load(String filename) throws IOException {
 875         FileInputStream in = new FileInputStream(filename);
 876         Properties prop = new Properties();
 877         prop.load(in);
 878         in.close();
 879         return prop;
 880     }
 881
 882     /**
 883      * This method saves a property to the specified file.
 884      *
 885      * @param filename
 886      * @param properties
 887      * @throws IOException
 888      */
 889     private void save(String filename, Properties properties) throws IOException{
 890         FileOutputStream fos =  new FileOutputStream(filename);
 891         properties.store(fos, "");
 892         fos.close();
 893     }
 894
 895     /**
 896      * Saves a list of P2 Metadata Repositories as string with specified delimiters
 897      *
 898      * @param p2Repos
 899      */
 900     public static void setP2Repositories(List<MetadataRepositoryElement> p2Repos) {
 901         StringBuilder sb = new StringBuilder();
 902         for(MetadataRepositoryElement p2Repo : p2Repos) {
 903             sb.append(P2_REPOSITORIES_DELIM);
 904             if(p2Repo.getName() == null || p2Repo.getName().isEmpty()) {
 905                 sb.append("-");
 906             } else {
 907                 sb.append(p2Repo.getName());
 908             }
 909             sb.append(P2_REPOSITORY_FIELDS_DELIM);
 910             sb.append(p2Repo.getLocation().toString());
 911             sb.append(P2_REPOSITORY_FIELDS_DELIM);
 912             sb.append(String.valueOf(p2Repo.isEnabled()));
 913         }
 914         getPreferenceStore().setValue(P2_REPOSITORY_LIST, sb.toString());
 915     }
 916
 917
 918     /**
 919      * Retrieves a list of previously saved P2 repositories
 920      *
 921      * @return
 922      */
 923     public static List<MetadataRepositoryElement> getP2Repositories() {
 924         List<MetadataRepositoryElement> p2Repos = new ArrayList<MetadataRepositoryElement>();
 925         String p2ReposPref =  getPreferenceStore().getString(P2_REPOSITORY_LIST);
 926         if(p2ReposPref != null && !p2ReposPref.isEmpty()) {
 927             StringTokenizer p2ReposPrefST = new StringTokenizer(p2ReposPref,P2_REPOSITORIES_DELIM);
 928
 929             while(p2ReposPrefST.hasMoreTokens()) {
 930                 String p2RepoStr = p2ReposPrefST.nextToken();
 931                 StringTokenizer p2ReposStrST = new StringTokenizer(p2RepoStr,P2_REPOSITORY_FIELDS_DELIM);
 932                 if(p2ReposStrST.countTokens()==3) {
 933                     String nickname = p2ReposStrST.nextToken();
 934                     URI uri = null;
 935                     try {
 936                         uri = new URI(p2ReposStrST.nextToken());
 937                     } catch (URISyntaxException e) {
 938                         continue;
 939                     }
 940                     boolean enabled = Boolean.parseBoolean(p2ReposStrST.nextToken());
 941                     MetadataRepositoryElement mre = new MetadataRepositoryElement(null, uri, true);
 942                     mre.setNickname(nickname);
 943                     mre.setEnabled(enabled);
 944                     p2Repos.add(mre);
 945                 }
 946             }
 947         }
 948
 949         return p2Repos;
 950     }
 951
 952     /**
 953      * enables/disables nested composite. <br>
 954      *
 955      * @param ctrl - Composite to be en-/disabeld
 956      * @param enabled - boolean
 957      */
 958     public static void recursiveSetEnabled(Control ctrl, boolean enabled) {
 959         if (ctrl instanceof Composite) {
 960             Composite comp = (Composite) ctrl;
 961             for (Control c : comp.getChildren()) {
 962                 recursiveSetEnabled(c, enabled);
 963             }
 964         } else {
 965             ctrl.setEnabled(enabled);
 966         }
 967     }
 968
 969     /**
 970          * <p>
 971          * getSortRanksNaturally
 972          * </p>
 973          *
 974          * @return a boolean.
 975          */
 976         public static boolean getSortNodesNaturally() {
 977                 return getPreferenceStore().getBoolean(SORT_NODES_NATURALLY);
 978         }
 979
 980         /**
 981          * <p>
 982          * setSortRanksNaturally
 983          * </p>
 984          *
 985          * @param selection
 986          *            a boolean.
 987          */
 988         public static void setSortNodesNaturally(boolean selection) {
 989                 getPreferenceStore().setValue(SORT_NODES_NATURALLY, selection);
 990         }
 991
 992
 993         /**
 994          * <p>
 995          * getSortRanksNaturally
 996          * </p>
 997          *
 998          * @return a boolean.
 999          */
1000         public static boolean getSortNodesStrictlyAlphabetically() {
1001                 return getPreferenceStore().getBoolean(SORT_NODES_ALPHABETICALLY);
1002         }
1003
1004         /**
1005          * <p>
1006          * setSortRanksNaturally
1007          * </p>
1008          *
1009          * @param selection
1010          *            a boolean.
1011          */
1012         public static void setSortNodesStrictlyAlphabetically(boolean selection) {
1013                 getPreferenceStore().setValue(SORT_NODES_ALPHABETICALLY, selection);
1014         }
1015
1016         /**
1017          * <p>
1018          * setStoreNavigatorState
1019          * </p>
1020          *
1021          * @param selection
1022          *            a boolean.
1023          */
1024         public static boolean isStoreNavigatorState() {
1025                 return getPreferenceStore().getBoolean(RESTORE_NAVIGATOR_STATE);
1026
1027         }
1028
1029         /**
1030          * <p>
1031          * setStoreNavigatorState
1032          * </p>
1033          *
1034          * @param selection
1035          *            a boolean.
1036          */
1037         public static void setStoreNavigatorState(boolean selection) {
1038                 getPreferenceStore().setValue(RESTORE_NAVIGATOR_STATE, selection);
1039
1040         }
1041
1042     /**
1043      * @return
1044      */
1045     public static boolean isShowUpWidgetIsDisposedMessages() {
1046        return getPreferenceStore().getBoolean(IS_SHOW_UP_WIDGET_IS_DISPOSED);
1047     }
1048     public static void setShowUpWidgetIsDisposedMessages(boolean selection) {
1049         getPreferenceStore().setValue(IS_SHOW_UP_WIDGET_IS_DISPOSED, selection);
1050     }
1051
1052     /**
1053      * @return
1054      */
1055     public static boolean isShowIdInVocabularyInChecklistEditor() {
1056         String area_display = getPreferenceStore().getString(IPreferenceKeys.CHECKLIST_AREA_DISPLAY);
1057         if (area_display.equals(CHECKLIST_AREA_DISPLAY_ID_IN_VOCABULARY)) {
1058             return true;
1059         }else{
1060             return false;
1061         }
1062     }
1063     public static boolean isShowSymbol1InChecklistEditor() {
1064         String area_display = getPreferenceStore().getString(IPreferenceKeys.CHECKLIST_AREA_DISPLAY);
1065         if (area_display.equals(CHECKLIST_AREA_DISPLAY_SYMBOL1)) {
1066             return true;
1067         }else{
1068             return false;
1069         }
1070      }
1071     public static boolean isShowSymbol2InChecklistEditor() {
1072         String area_display = getPreferenceStore().getString(IPreferenceKeys.CHECKLIST_AREA_DISPLAY);
1073         if (area_display.equals(CHECKLIST_AREA_DISPLAY_SYMBOL2)) {
1074             return true;
1075         }else{
1076             return false;
1077         }
1078      }
1079     public static void setShowIdInVocabularyInChecklistEditor(String selection) {
1080         getPreferenceStore().setValue(CHECKLIST_AREA_DISPLAY, selection);
1081     }
1082
1083     /**
1084      * @return
1085      */
1086     public static boolean isShowSymbolInChecklistEditor() {
1087        return getPreferenceStore().getBoolean(IPreferenceKeys.CHECKLIST_SYMBOL);
1088     }
1089     public static void setShowSymbolInChecklistEditor(boolean selection) {
1090         getPreferenceStore().setValue(CHECKLIST_SYMBOL, selection);
1091     }
1092
1093     /**
1094      * @return
1095      */
1096     public static boolean isShowRankInChecklistEditor() {
1097         return getPreferenceStore().getBoolean(IPreferenceKeys.CHECKLIST_SHOW_RANK);
1098     }
1099     public static void setShowRankInChecklistEditor(boolean selection) {
1100         getPreferenceStore().setValue(CHECKLIST_SHOW_RANK, selection);
1101     }
1102
1103     /**
1104      * @param object
1105      * @param b
1106      * @return
1107      */
1108     public static NameDetailsConfigurator getPreferredNameDetailsConfiguration( boolean local) {
1109         NameDetailsConfigurator config = new NameDetailsConfigurator(true);
1110
1111         CdmPreference preference = null;
1112
1113         if (!local) {
1114             preference = getPreferenceFromDB(PreferencePredicate.NameDetailsView);
1115             if (preference == null){
1116                 return null;
1117             }
1118
1119             getPreferenceStore().setValue(ALLOW_OVERRIDE_NAME_DETAILS, preference.isAllowOverride());
1120
1121             //the preference value is build like this:
1122             //<section1>:true;<section2>:false....
1123
1124             String value = preference.getValue();
1125             String [] sections = value.split(";");
1126             Map<String, Boolean> sectionMap = new HashMap<String, Boolean>();
1127             String[] sectionValues;
1128             for (String sectionValue: sections){
1129                 sectionValues = sectionValue.split(":");
1130                 sectionMap.put(sectionValues[0], Boolean.valueOf(sectionValues[1]));
1131             }
1132             config.setAllowOverride(preference.isAllowOverride());
1133             config.setSimpleDetailsViewActivated(getValue(sectionMap, "simpleViewActivated"));
1134
1135     //        getPreferenceStore().setValue(SHOW_SIMPLE_NAME_DETAILS_TAXON,
1136     //                (getValue(sectionMap, "taxon")));
1137             config.setTaxonSectionActivated(getValue(sectionMap, "taxon"));
1138
1139             config.setSecDetailsActivated(getValue(sectionMap, "taxon.SecEnabled"));
1140             config.setSecEnabled(getValue(sectionMap, "taxon.SecDetails"));
1141
1142     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_LSID,
1143     //                (getValue(sectionMap, "lsid")));
1144             config.setLSIDActivated(getValue(sectionMap, "lsid"));
1145
1146     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_CODE,
1147     //                (getValue(sectionMap, "nc")));
1148             config.setNomenclaturalCodeActived(getValue(sectionMap, "nc"));
1149
1150     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_APPENDED_PHRASE,
1151     //                (getValue(sectionMap, "ap")));
1152             config.setAppendedPhraseActivated(getValue(sectionMap, "ap"));
1153
1154     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_RANK,
1155     //                (getValue(sectionMap, "rank")));
1156             config.setRankActivated(getValue(sectionMap, "rank"));
1157
1158
1159     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_ATOMISED_EPITHETS,
1160     //                (getValue(sectionMap, "atomisedEpithets")));
1161             config.setAtomisedEpithetsActivated(getValue(sectionMap, "atomisedEpithets"));
1162
1163     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_AUTHORSHIP,
1164     //                (getValue(sectionMap,"author")));
1165             config.setAuthorshipSectionActivated(getValue(sectionMap,"author"));
1166
1167     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_REFERENCE,
1168     //                (getValue(sectionMap, "nomRef")));
1169             config.setNomenclaturalReferenceSectionActivated(sectionMap.get("nomRef"));
1170
1171     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_STATUS,
1172     //                (getValue(sectionMap, "nomStat")));
1173             config.setNomenclaturalStatusSectionActivated(getValue(sectionMap, "nomStat"));
1174
1175
1176     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_PROTOLOGUE,
1177     //                (getValue(sectionMap,"protologue")));
1178             config.setProtologueActivated(getValue(sectionMap,"protologue"));
1179
1180     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_TYPE_DESIGNATION,
1181     //                (getValue(sectionMap,"typeDes")));
1182             config.setTypeDesignationSectionActivated(getValue(sectionMap,"typeDes"));
1183
1184     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NAME_RELATIONSHIP,
1185     //                (getValue(sectionMap,"nameRelation")));
1186             config.setNameRelationsSectionActivated(getValue(sectionMap,"nameRelation"));
1187
1188     //        getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_HYBRID,
1189     //                (getValue(sectionMap, "hybrid")));
1190             config.setHybridActivated(getValue(sectionMap,"hybrid"));
1191         }else{
1192             config.setSimpleDetailsViewActivated(getPreferenceStore().getBoolean(SHOW_SIMPLE_NAME_DETAILS_SECTION));
1193             config.setTaxonSectionActivated(getPreferenceStore().getBoolean(SHOW_SIMPLE_NAME_DETAILS_TAXON));
1194             config.setSecDetailsActivated(getPreferenceStore().getBoolean(SHOW_SEC_DETAILS));
1195             config.setSecEnabled(getPreferenceStore().getBoolean(DISABLE_SEC));
1196             config.setLSIDActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_LSID));
1197             config.setNomenclaturalCodeActived(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_CODE));
1198             config.setAppendedPhraseActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_APPENDED_PHRASE));
1199             config.setRankActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_RANK));
1200             config.setAtomisedEpithetsActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_ATOMISED_EPITHETS));
1201             config.setAuthorshipSectionActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_AUTHORSHIP));
1202             config.setNomenclaturalReferenceSectionActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_REFERENCE));
1203             config.setNomenclaturalStatusSectionActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_STATUS));
1204             config.setProtologueActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_PROTOLOGUE));
1205             config.setTypeDesignationSectionActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_TYPE_DESIGNATION));
1206             config.setNameRelationsSectionActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_NAME_RELATIONSHIP));
1207             config.setHybridActivated(getPreferenceStore().getBoolean(SHOW_NAME_DETAILS_SECTION_HYBRID));
1208         }
1209         return config;
1210     }
1211
1212     /**
1213      * @param object
1214      * @param b
1215      * @return
1216      */
1217     public static void setPreferredNameDetailsConfiguration(NameDetailsConfigurator config, boolean local) {
1218         CdmPreference preference = null;
1219
1220         if (!local) {
1221             preference = CdmPreference.NewInstance(PreferenceSubject.NewDatabaseInstance(), PreferencePredicate.NameDetailsView, config.toString());
1222
1223             setPreferenceToDB(preference);
1224         }
1225         //also add to local preferences
1226         getPreferenceStore().setValue(SHOW_SIMPLE_NAME_DETAILS_SECTION, config.isSimpleDetailsViewActivated());
1227         getPreferenceStore().setValue(SHOW_SIMPLE_NAME_DETAILS_TAXON, config.isTaxonSectionActivated());
1228         getPreferenceStore().setValue(SHOW_SEC_DETAILS, config.isSecDetailsActivated());
1229         getPreferenceStore().setValue(DISABLE_SEC, config.isSecEnabled());
1230         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_LSID, config.isLSIDActivated());
1231         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_CODE, config.isNomenclaturalCodeActived());
1232         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_APPENDED_PHRASE, config.isAppendedPhraseActivated());
1233         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_RANK, config.isRankActivated());
1234         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_ATOMISED_EPITHETS, config.isAtomisedEpithetsActivated());
1235         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_AUTHORSHIP, config.isAuthorshipSectionActivated());
1236         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_REFERENCE, config.isNomenclaturalReferenceSectionActivated());
1237         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_STATUS, config.isNomenclaturalStatusSectionActivated());
1238         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_PROTOLOGUE, config.isProtologueActivated());
1239         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_TYPE_DESIGNATION, config.isTypeDesignationSectionActivated());
1240         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_NAME_RELATIONSHIP, config.isNameRelationsSectionActivated());
1241         getPreferenceStore().setValue(SHOW_NAME_DETAILS_SECTION_HYBRID, config.isHybridActivated());
1242
1243     }
1244
1245     private static Boolean getValue(Map<String, Boolean> sectionMap, String string) {
1246                 if (sectionMap.containsKey(string)){
1247                         return sectionMap.get(string);
1248                 }else{
1249                         return true;
1250                 }
1251
1252         }
1253
1254
1255
1256     /**
1257      * <p>
1258      * setAbcdConfigurator
1259      * </p>
1260      *
1261      * @param preferredConfiguration
1262      *            a {@link eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator}
1263      *            object.
1264      */
1265     public static Abcd206ImportConfigurator getAbcdImportConfigurationPreference() {
1266
1267         Abcd206ImportConfigurator config = Abcd206ImportConfigurator.NewInstance(null,null);
1268         ICdmRepository controller;
1269         controller = CdmStore.getCurrentApplicationConfiguration();
1270         PrefKey key = CdmPreference.NewKey(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AbcdImportConfig);
1271         CdmPreference preference = null;
1272         if (controller == null){
1273             return null;
1274         }
1275         preference = controller.getPreferenceService().find(key);
1276         boolean allowOverride = true;
1277         if (preference != null && !preference.isAllowOverride()){
1278             allowOverride = false;
1279         }
1280         if (PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_OVERRIDE) && allowOverride){
1281
1282             config.setAddIndividualsAssociationsSuchAsSpecimenAndObservations(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_ADD_INDIVIDUALS_ASSOCIATIONS_SUCH_AS_SPECIMEN_AND_OBSERVATIONS));
1283
1284             config.setAddMediaAsMediaSpecimen(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_ADD_MEDIA_AS_MEDIASPECIMEN));
1285
1286             config.setAllowReuseOtherClassifications(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_ALLOW_REUSE_OTHER_CLASSIFICATIONS));
1287             config.setDeduplicateClassifications(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_DEDUPLICATE_CLASSIFICATIONS));
1288             config.setDeduplicateReferences(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_DEDUPLICATE_REFERENCES));
1289
1290             config.setGetSiblings(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_DO_SIBLINGS));
1291             config.setIgnoreAuthorship(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_IGNORE_AUTHORSHIP));
1292             config.setIgnoreImportOfExistingSpecimen(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_IGNORE_IMPORT_OF_EXISTING_SPECIMEN));
1293             config.setMapUnitIdToAccessionNumber(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_MAP_UNIT_ID_TO_ACCESSION_NUMBER));
1294             config.setMapUnitIdToBarcode(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_MAP_UNIT_ID_TO_BARCODE));
1295             config.setMapUnitIdToCatalogNumber(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_MAP_UNIT_ID_TOCATALOG_NUMBER));
1296             config.setMoveNewTaxaToDefaultClassification(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_MOVE_NEW_TAXA_TO_DEFAULT_CLASSIFICATION));
1297             config.setOverwriteExistingSpecimens(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_OVERWRITE_EXISTING_SPECIMEN));
1298             config.setReuseExistingDescriptiveGroups(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_REUSE_EXISTING_DESCRIPTIVE_GROUPS));
1299             config.setReuseExistingMetaData(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_REUSE_EXISTING_META_DATA));
1300             config.setReuseExistingTaxaWhenPossible(PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_REUSE_EXISTING_TAXA_WHEN_POSSIBLE));
1301             config.setNomenclaturalCode(NomenclaturalCode.getByKey(PreferencesUtil.getPreferenceStore().getString(IPreferenceKeys.ABCD_IMPORT_CONFIGURATOR_NOMENCLATURAL_CODE)));
1302             return config;
1303
1304         }
1305
1306             if (preference == null){
1307                 return config;
1308              } else{
1309              String configString = preference.getValue();
1310              String[] configArray = configString.split(";");
1311
1312              for (String configItem: configArray){
1313                  String[] keyValue = configItem.split(":");
1314                  String keyString = keyValue[0];
1315                  String valueString = keyValue[1];
1316                  if (keyString.equals("ignoreImportOfExistingSpecimen")){
1317                      config.setIgnoreImportOfExistingSpecimen(Boolean.valueOf(valueString));
1318                  }else if (keyString.equals("addIndividualsAssociationsSuchAsSpecimenAndObservations")){
1319                      config.setAddIndividualsAssociationsSuchAsSpecimenAndObservations(Boolean.valueOf(valueString));
1320                  }else if (keyString.equals("reuseExistingTaxaWhenPossible")){
1321                      config.setReuseExistingTaxaWhenPossible(Boolean.valueOf(valueString));
1322                  }else if (keyString.equals("ignoreAuthorship")){
1323                      config.setIgnoreAuthorship(Boolean.valueOf(valueString));
1324                  }else if (keyString.equals("addMediaAsMediaSpecimen")){
1325                      config.setAddMediaAsMediaSpecimen(Boolean.valueOf(valueString));
1326                  }else if (keyString.equals("reuseExistingMetaData")){
1327                      config.setReuseExistingMetaData(Boolean.valueOf(valueString));
1328                  }else if (keyString.equals("reuseExistingDescriptiveGroups")){
1329                      config.setReuseExistingDescriptiveGroups(Boolean.valueOf(valueString));
1330                  }else if (keyString.equals("allowReuseOtherClassifications")){
1331                      config.setAllowReuseOtherClassifications(Boolean.valueOf(valueString));
1332                  }else if (keyString.equals("deduplicateReferences")){
1333                      config.setDeduplicateReferences(Boolean.valueOf(valueString));
1334                  }else if (keyString.equals("deduplicateClassifications")){
1335                      config.setDeduplicateClassifications(Boolean.valueOf(valueString));
1336                  }else if (keyString.equals("moveNewTaxaToDefaultClassification")){
1337                      config.setMoveNewTaxaToDefaultClassification(Boolean.valueOf(valueString));
1338                  }else if (keyString.equals("mapUnitIdToCatalogNumber")){
1339                      config.setMapUnitIdToCatalogNumber(Boolean.valueOf(valueString));
1340                  }else if (keyString.equals("mapUnitIdToAccessionNumber")){
1341                      config.setMapUnitIdToAccessionNumber(Boolean.valueOf(valueString));
1342                  }else if (keyString.equals("mapUnitIdToBarcode")){
1343                      config.setMapUnitIdToBarcode(Boolean.valueOf(valueString));
1344                  }else if (keyString.equals("overwriteExistingSpecimens")){
1345                      config.setOverwriteExistingSpecimens(Boolean.valueOf(valueString));
1346                  }else if (keyString.equals("nomenclaturalCode")){
1347                          config.setNomenclaturalCode(NomenclaturalCode.fromString(valueString));
1348                  }else{
1349                      logger.debug("This key of the abcd configurator needs to be added to the transformer: " + keyString);
1350                  }
1351
1352             }
1353         }
1354         return config;
1355     }
1356
1357
1358     public static void updateAbcdImportConfigurationPreference() {
1359
1360         Abcd206ImportConfigurator config = Abcd206ImportConfigurator.NewInstance(null,null);
1361         ICdmRepository controller;
1362         controller = CdmStore.getCurrentApplicationConfiguration();
1363         PrefKey key = CdmPreference.NewKey(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AbcdImportConfig);
1364         CdmPreference preference = null;
1365         if (controller == null){
1366             return ;
1367         }
1368         preference = controller.getPreferenceService().find(key);
1369         boolean allowOverride = true;
1370         if (preference != null && !preference.isAllowOverride()){
1371             allowOverride = false;
1372         }
1373         if (!PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.ABCD_IMPORT_OVERRIDE) || !allowOverride){
1374
1375             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_ADD_INDIVIDUALS_ASSOCIATIONS_SUCH_AS_SPECIMEN_AND_OBSERVATIONS, config.isAddIndividualsAssociationsSuchAsSpecimenAndObservations());
1376             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_ADD_MEDIA_AS_MEDIASPECIMEN, config.isAddMediaAsMediaSpecimen());
1377
1378             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_ALLOW_REUSE_OTHER_CLASSIFICATIONS, config.isAllowReuseOtherClassifications());
1379             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_DEDUPLICATE_CLASSIFICATIONS, config.isDeduplicateClassifications());
1380             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_DEDUPLICATE_REFERENCES, config.isDeduplicateReferences());
1381
1382             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_DO_SIBLINGS, config.isGetSiblings());
1383             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_IGNORE_AUTHORSHIP, config.isIgnoreAuthorship());
1384             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_IGNORE_IMPORT_OF_EXISTING_SPECIMEN, config.isIgnoreImportOfExistingSpecimen());
1385             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_MAP_UNIT_ID_TO_ACCESSION_NUMBER, config.isMapUnitIdToAccessionNumber());
1386             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_MAP_UNIT_ID_TO_BARCODE, config.isMapUnitIdToBarcode());
1387             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_MAP_UNIT_ID_TOCATALOG_NUMBER, config.isMapUnitIdToCatalogNumber());
1388             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_MOVE_NEW_TAXA_TO_DEFAULT_CLASSIFICATION, config.isMoveNewTaxaToDefaultClassification());
1389             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_OVERWRITE_EXISTING_SPECIMEN, config.isOverwriteExistingSpecimens());
1390             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_REUSE_EXISTING_DESCRIPTIVE_GROUPS, config.isReuseExistingDescriptiveGroups());
1391             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_REUSE_EXISTING_META_DATA, config.isReuseExistingMetaData());
1392             getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_REUSE_EXISTING_TAXA_WHEN_POSSIBLE, config.isReuseExistingTaxaWhenPossible());
1393             if (config.getNomenclaturalCode() != null){
1394                 getPreferenceStore().setValue(ABCD_IMPORT_CONFIGURATOR_NOMENCLATURAL_CODE, config.getNomenclaturalCode().getKey());
1395             }
1396         }
1397     }
1398
1399
1400     /**
1401     *
1402     */
1403    public NameDetailsConfigurator createLocalNameDetailsViewConfig(boolean local) {
1404        NameDetailsConfigurator config = new NameDetailsConfigurator(true);
1405        if (local){
1406           config.setSimpleDetailsViewActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_SIMPLE_NAME_DETAILS_SECTION));
1407           config.setAppendedPhraseActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_APPENDED_PHRASE));
1408           config.setAtomisedEpithetsActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_ATOMISED_EPITHETS));
1409           config.setAuthorshipSectionActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_AUTHORSHIP));
1410           config.setLSIDActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_LSID));
1411           config.setNameApprobiationActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NAME_APPROBATION));
1412           config.setNameCacheActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_CACHE));
1413           config.setNameRelationsSectionActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NAME_RELATIONSHIP));
1414           config.setNomenclaturalCodeActived(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_CODE));
1415           config.setNomenclaturalStatusSectionActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_STATUS));
1416           config.setNomenclaturalReferenceSectionActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_REFERENCE));
1417           config.setProtologueActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_PROTOLOGUE));
1418           config.setRankActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_RANK));
1419           config.setTaxonSectionActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_SIMPLE_NAME_DETAILS_TAXON));
1420           config.setTypeDesignationSectionActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_TYPE_DESIGNATION));
1421           config.setHybridActivated(getPreferenceStore().getBoolean(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_HYBRID));
1422        }else{
1423
1424        }
1425
1426       return config;
1427    }
1428
1429
1430    public static void saveConfigToPrefernceStore(NameDetailsConfigurator config) {
1431        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_SIMPLE_NAME_DETAILS_SECTION,
1432                config.isSimpleDetailsViewActivated());
1433        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_SIMPLE_NAME_DETAILS_TAXON, config.isTaxonSectionActivated());
1434        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_LSID, config.isLSIDActivated());
1435        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_CODE,
1436                config.isNomenclaturalCodeActived());
1437        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NAMECACHE,
1438                config.isNameCacheActivated());
1439        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_APPENDED_PHRASE,
1440                config.isAppendedPhraseActivated());
1441        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_RANK, config.isRankActivated());
1442        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_ATOMISED_EPITHETS,
1443                config.isAtomisedEpithetsActivated());
1444        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_AUTHORSHIP_CACHE,
1445                config.isAuthorCacheActivated());
1446        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_AUTHORSHIP,
1447                config.isAuthorshipSectionActivated());
1448        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_REFERENCE,
1449                config.isNomenclaturalReferenceSectionActivated());
1450        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NOMENCLATURAL_STATUS,
1451                config.isNomenclaturalStatusSectionActivated());
1452        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_PROTOLOGUE,
1453                config.isProtologueActivated());
1454        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_TYPE_DESIGNATION,
1455                config.isTypeDesignationSectionActivated());
1456        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_NAME_RELATIONSHIP,
1457                config.isNameRelationsSectionActivated());
1458        PreferencesUtil.getPreferenceStore().setValue(IPreferenceKeys.SHOW_NAME_DETAILS_SECTION_HYBRID,
1459                config.isHybridActivated());
1460
1461    }
1462
1463 /**
1464  * @return
1465  */
1466 public static boolean isSortTaxaByRankAndName() {
1467
1468     return getPreferenceStore().getBoolean(IPreferenceKeys.SORT_TAXA_BY_RANK_AND_NAME);
1469 }
1470
1471 /**
1472  * @return
1473  */
1474 public static boolean isSortNamedAreaByOrderInVocabulary() {
1475
1476     return getPreferenceStore().getBoolean(IPreferenceKeys.SORT_NAMED_AREA_BY_VOCABULARY_ORDER);
1477 }
1478
1479 public static void setSortNamedAreasByOrderInVocabulary(boolean isSortByVocabularyOrder) {
1480     getPreferenceStore().setValue(IPreferenceKeys.SORT_NAMED_AREA_BY_VOCABULARY_ORDER, isSortByVocabularyOrder);
1481
1482 }
1483
1484 /**
1485  * <p>
1486  * setPreferredNamedAreasForDistributionEditor
1487  * </p>
1488  *
1489  * @param saveCheckedElements
1490  * @param saveGrayedElements
1491  */
1492 public static void setLastSelectedReference(
1493         List<String> lastSelectedReferences) {
1494
1495         IPreferenceStore preferenceStore = PreferencesUtil.getPreferenceStore();
1496         preferenceStore.setValue(PreferencesUtil.LAST_SELECTED_REFERENCES, lastSelectedReferences.toString());
1497     }
1498
1499 /**
1500  * <p>
1501  * setPreferredNamedAreasForDistributionEditor
1502  * </p>
1503  *
1504  * @param saveCheckedElements
1505  * @param saveGrayedElements
1506  */
1507 public static List<String> getLastSelectedReferences() {
1508
1509         IPreferenceStore preferenceStore = PreferencesUtil.getPreferenceStore();
1510         String lastSelected = preferenceStore.getString(PreferencesUtil.LAST_SELECTED_REFERENCES);
1511         List<String> result = new ArrayList<>();
1512         if (!StringUtils.isBlank(lastSelected)){
1513             Collections.addAll(result, lastSelected.substring(1,lastSelected.length()-1).split(", "));
1514         }
1515         return result;
1516     }
1517
1518
1519 /**
1520  * <p>
1521  * setPreferredNamedAreasForDistributionEditor
1522  * </p>
1523  *
1524  * @param saveCheckedElements
1525  * @param saveGrayedElements
1526  */
1527 public static void setPreferredNamedAreasForDistributionEditor(
1528         String saveCheckedElements, String saveGrayedElements, boolean local) {
1529     if (local){
1530         IPreferenceStore preferenceStore = PreferencesUtil.getPreferenceStore();
1531         preferenceStore.setValue(PreferencesUtil.DISTRIBUTION_AREA_OCCURENCE_STATUS, saveCheckedElements);
1532         preferenceStore.setValue(PreferencesUtil.DISTRIBUTION_AREA_OCCURENCE_STATUS_GRAYED, saveGrayedElements);
1533
1534     }
1535     else{
1536         CdmPreference preference = null;
1537
1538         if (saveCheckedElements == null){
1539             preference = getPreferenceFromDB(PreferencePredicate.AvailableDistributionAreaTerms);
1540
1541             if (preference == null){
1542                 return ;
1543             } else{
1544                 getPreferenceStore().setValue(DISTRIBUTION_AREA_OCCURENCE_STATUS,
1545                         saveCheckedElements);
1546                 preference = CdmPreference.NewInstance(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AvailableDistributionAreaTerms, saveCheckedElements);
1547                 setPreferenceToDB(preference);
1548
1549             }
1550         } else{
1551            preference = CdmPreference.NewInstance(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AvailableDistributionAreaTerms, saveCheckedElements);
1552            setPreferenceToDB(preference);
1553            getPreferenceStore().setValue(DISTRIBUTION_AREA_OCCURENCE_STATUS,
1554                     saveCheckedElements);
1555
1556         }
1557     }
1558
1559 }
1560
1561 /**
1562  * @param saveCheckedElements
1563  * @param saveCheckedElements2
1564  * @param b
1565  */
1566 public static void setPreferredVocabulariesForDistributionEditor(String saveCheckedElements,
1567         boolean local) {
1568     if (local){
1569         IPreferenceStore preferenceStore = PreferencesUtil.getPreferenceStore();
1570         preferenceStore.setValue(PreferencesUtil.DISTRIBUTION_VOCABULARIES, saveCheckedElements);
1571     }
1572     else{
1573         ICdmRepository controller;
1574         CdmPreference preference = null;
1575
1576         if (saveCheckedElements == null){
1577             preference = getPreferenceFromDB(PreferencePredicate.AvailableDistributionAreaVocabularies);
1578
1579             if (preference == null){
1580                 return ;
1581             } else{
1582                 getPreferenceStore().setValue(DISTRIBUTION_VOCABULARIES,
1583                         saveCheckedElements);
1584                 preference = CdmPreference.NewInstance(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AvailableDistributionAreaVocabularies, saveCheckedElements);
1585                 setPreferenceToDB(preference);
1586             }
1587         } else{
1588             preference = CdmPreference.NewInstance(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AvailableDistributionAreaVocabularies, saveCheckedElements);
1589             setPreferenceToDB(preference);
1590             getPreferenceStore().setValue(DISTRIBUTION_VOCABULARIES,
1591                     saveCheckedElements);
1592
1593         }
1594     }
1595 }
1596
1597
1598
1599
1600 /**
1601  * @param saveCheckedElements
1602  * @param saveCheckedElements2
1603  * @param b
1604  */
1605 public static String getPreferredVocabulariesForDistributionEditor(boolean local) {
1606     if (local){
1607         IPreferenceStore preferenceStore = PreferencesUtil.getPreferenceStore();
1608         String pref = preferenceStore.getString(DISTRIBUTION_VOCABULARIES);
1609         return pref;
1610     }
1611     else{
1612         CdmPreference preference = null;
1613         preference = getPreferenceFromDB(PreferencePredicate.AvailableDistributionAreaVocabularies);
1614         if (preference == null){
1615             return null;
1616         } else{
1617             return preference.getValue();
1618         }
1619
1620     }
1621
1622
1623
1624 }
1625
1626 public static boolean getFilterCommonNameReferences(){
1627     return getPreferenceStore().getBoolean(PreferencesUtil.FILTER_COMMON_NAME_REFERENCES);
1628 }
1629
1630 /**
1631  *
1632  */
1633 public static void updateDBPreferences() {
1634     CdmPreference preference = null;
1635     IPreferenceStore prefStore = getPreferenceStore();
1636
1637     //ABCD Configurator
1638
1639     updateAbcdImportConfigurationPreference();
1640
1641     preference = getPreferenceFromDB(PreferencePredicate.ShowImportExportMenu);
1642     if (preference != null){
1643         if(!prefStore.getBoolean(SHOW_IO_MENU) ||  !preference.isAllowOverride()){
1644             prefStore.setValue(SHOW_IO_MENU, preference.getValue());
1645         }
1646     }else{
1647         prefStore.setValue(SHOW_IO_MENU, true);
1648     }
1649
1650     preference = getPreferenceFromDB(PreferencePredicate.ShowMediaView);
1651     if (preference != null){
1652         if(!prefStore.getBoolean(SHOW_MEDIA) ||  !preference.isAllowOverride()){
1653             prefStore.setValue(SHOW_MEDIA, preference.getValue());
1654         }
1655     }else{
1656         prefStore.setValue(SHOW_MEDIA, true);
1657     }
1658
1659     preference = getPreferenceFromDB(PreferencePredicate.ShowChecklistPerspective);
1660     if (preference != null){
1661         if(!prefStore.getBoolean(SHOW_CHECKLIST_PERSPECTIVE) ||  !preference.isAllowOverride()){
1662             prefStore.setValue(SHOW_CHECKLIST_PERSPECTIVE, preference.getValue());
1663         }
1664     }else{
1665         prefStore.setValue(SHOW_CHECKLIST_PERSPECTIVE, false);
1666     }
1667
1668     //Specimen Details
1669     preference = getPreferenceFromDB(PreferencePredicate.ShowSpecimen);
1670     if (preference != null){
1671         if(!prefStore.getBoolean(SHOW_SPECIMEN) ||  !preference.isAllowOverride()){
1672             prefStore.setValue(SHOW_SPECIMEN, preference.getValue());
1673         }
1674     }else{
1675         prefStore.setValue(SHOW_SPECIMEN, true);
1676     }
1677
1678     preference = getPreferenceFromDB(PreferencePredicate.ShowTaxonAssociations);
1679     if (preference != null){
1680         if(!prefStore.getBoolean(SHOW_TAXON_ASSOCIATIONS_OVERRIDE) ||  !preference.isAllowOverride()){
1681             prefStore.setValue(SHOW_TAXON_ASSOCIATIONS, preference.getValue());
1682         }
1683     }
1684     preference = getPreferenceFromDB(PreferencePredicate.ShowCollectingAreasInGeneralSection);
1685     if (preference != null){
1686         if(!prefStore.getBoolean(SHOW_COLLECTING_AREAS_IN_GENERAL_SECTION_OVERRIDE) ||  !preference.isAllowOverride()){
1687             prefStore.setValue(SHOW_COLLECTING_AREAS_IN_GENERAL_SECTION, preference.getValue());
1688         }
1689     }
1690     preference = getPreferenceFromDB(PreferencePredicate.ShowLifeForm);
1691     if (preference != null){
1692         if(!prefStore.getBoolean(SHOW_LIFE_FORM_OVERRIDE) ||  !preference.isAllowOverride()){
1693             prefStore.setValue(SHOW_LIFE_FORM, preference.getValue());
1694         }
1695     }
1696     preference = getPreferenceFromDB(PreferencePredicate.DeterminationOnlyForFieldUnits);
1697     if (preference != null){
1698         if(!prefStore.getBoolean(DETERMINATION_ONLY_FOR_FIELD_UNITS_OVERRIDE) ||  !preference.isAllowOverride()){
1699             prefStore.setValue(DETERMINATION_ONLY_FOR_FIELD_UNITS, preference.getValue());
1700         }
1701     }
1702
1703
1704     //Name Details
1705     NameDetailsConfigurator config = getPreferredNameDetailsConfiguration(false);
1706     if (config != null ){
1707         if (!prefStore.getBoolean(OVERRIDE_NAME_DETAILS) ||  !prefStore.getBoolean(ALLOW_OVERRIDE_NAME_DETAILS)){
1708             setPreferredNameDetailsConfiguration(config, false);
1709         }
1710     }
1711
1712     //Distribution Editor
1713     preference = getPreferenceFromDB(PreferencePredicate.AvailableDistributionAreaVocabularies);
1714     if (preference != null){
1715         if (!prefStore.getBoolean(DISTRIBUTION_VOCABULARIES_OVERRIDE) ||  !preference.isAllowOverride()){
1716             prefStore.setValue(DISTRIBUTION_VOCABULARIES, preference.getValue());
1717             prefStore.setValue(DISTRIBUTION_VOCABULARIES_ALLOW_OVERRIDE, preference.getValue());
1718         }
1719     }else{
1720         prefStore.setValue(DISTRIBUTION_VOCABULARIES_ALLOW_OVERRIDE,true);
1721         prefStore.setToDefault(DISTRIBUTION_VOCABULARIES);
1722     }
1723
1724     preference = getPreferenceFromDB(PreferencePredicate.DistributionEditorActivated);
1725     if (preference != null){
1726         if (!prefStore.getBoolean(DISTRIBUTION_AREA_PREFRENCES_ACTIVE_OVERRIDE) || !preference.isAllowOverride()){
1727             prefStore.setValue(DISTRIBUTION_AREA_PREFRENCES_ACTIVE, preference.getValue());
1728         }
1729     }
1730
1731     preference = getPreferenceFromDB(PreferencePredicate.AvailableDistributionStatus);
1732     if (preference != null){
1733         if (!prefStore.getBoolean(DISTRIBUTION_STATUS_OVERRIDE) || !preference.isAllowOverride()){
1734             //get terms for the uuids... and add them to the termManager as preferred terms
1735             ITermService termService = CdmStore.getService(ITermService.class);
1736             String[] uuidArray = preference.getValue().split(";");
1737             List<UUID> uuidList = new ArrayList();
1738             for (String uuidString:uuidArray){
1739                 uuidList.add(UUID.fromString(uuidString));
1740             }
1741
1742             List<DefinedTermBase> definedTermBases = termService.load(uuidList, null);
1743             CdmStore.getTermManager().setPreferredTerms(definedTermBases, TermStore.getTerms(TermType.PresenceAbsenceTerm, null));
1744         }
1745     }
1746
1747     preference = getPreferenceFromDB(PreferencePredicate.CommonNameAreaVocabularies);
1748     if (preference != null){
1749         if (!prefStore.getBoolean(COMMON_NAME_AREA_VOCABULARIES) ||  !preference.isAllowOverride()){
1750             prefStore.setValue(COMMON_NAME_AREA_VOCABULARIES, preference.getValue());
1751             prefStore.setValue(COMMON_NAME_AREA_VOCABULARIES_ALLOW_OVERRIDE, preference.isAllowOverride());
1752         }
1753     }else{
1754         prefStore.setToDefault(COMMON_NAME_AREA_VOCABULARIES);
1755         prefStore.setValue(COMMON_NAME_AREA_VOCABULARIES_ALLOW_OVERRIDE, true);
1756     }
1757
1758     preference = getPreferenceFromDB(PreferencePredicate.CommonNameReferencesWithMarker);
1759     if (preference != null){
1760         if (!prefStore.getBoolean(FILTER_COMMON_NAME_REFERENCES) ||  !preference.isAllowOverride()){
1761             prefStore.setValue(FILTER_COMMON_NAME_REFERENCES, preference.getValue());
1762         }
1763     }else{
1764         prefStore.setValue(FILTER_COMMON_NAME_REFERENCES, false);
1765     }
1766
1767
1768     preference = getPreferenceFromDB(PreferencePredicate.ShowTaxonNodeWizard);
1769     if (preference != null){
1770         if (!prefStore.getBoolean(SHOW_TAXONNODE_WIZARD) ||  !preference.isAllowOverride()){
1771             prefStore.setValue(SHOW_TAXONNODE_WIZARD, preference.getValue());
1772         }
1773     }else{
1774         prefStore.setValue(SHOW_TAXONNODE_WIZARD, true);
1775     }
1776
1777     preference = getPreferenceFromDB(PreferencePredicate.ShowIdInSource);
1778     if (preference != null){
1779         if (!prefStore.getBoolean(SHOW_ID_IN_SOURCE) ||  !preference.isAllowOverride()){
1780             prefStore.setValue(SHOW_ID_IN_SOURCE, preference.getValue());
1781         }
1782     }else{
1783         prefStore.setValue(SHOW_ID_IN_SOURCE, true);
1784     }
1785
1786     preference = getPreferenceFromDB(PreferencePredicate.ShowNameInSource);
1787     if (preference != null){
1788         if (!prefStore.getBoolean(SHOW_NAME_IN_SOURCE) ||  !preference.isAllowOverride()){
1789             prefStore.setValue(SHOW_NAME_IN_SOURCE, preference.getValue());
1790         }
1791     }else{
1792         prefStore.setValue(SHOW_NAME_IN_SOURCE, true);
1793     }
1794
1795     preference = getPreferenceFromDB(PreferencePredicate.DisableMultiClassification);
1796     if (preference != null){
1797         if (!prefStore.getBoolean(DISABLE_MULTI_CLASSIFICATION) ||  !preference.isAllowOverride()){
1798             prefStore.setValue(DISABLE_MULTI_CLASSIFICATION, preference.getValue());
1799         }
1800     }else{
1801         prefStore.setValue(DISABLE_MULTI_CLASSIFICATION, false);
1802     }
1803
1804 }
1805
1806
1807
1808
1809
1810
1811
1812 }