taxeditor-store/src/main/java/eu/etaxonomy/taxeditor/store/CdmStore.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.store;
  11
  12 import java.util.ArrayList;
  13 import java.util.LinkedHashMap;
  14 import java.util.List;
  15 import java.util.Set;
  16 import java.util.SortedSet;
  17 import java.util.UUID;
  18
  19 import org.apache.log4j.Logger;
  20 import org.springframework.security.providers.ProviderManager;
  21
  22 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  23 import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
  24 import eu.etaxonomy.cdm.api.service.ILocationService;
  25 import eu.etaxonomy.cdm.api.service.INameService;
  26 import eu.etaxonomy.cdm.api.service.IReferenceService;
  27 import eu.etaxonomy.cdm.api.service.ITaxonService;
  28 import eu.etaxonomy.cdm.api.service.ITermService;
  29 import eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator;
  30 import eu.etaxonomy.cdm.api.service.config.impl.TaxonServiceConfiguratorImpl;
  31 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  32 import eu.etaxonomy.cdm.database.ICdmDataSource;
  33 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  34 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  35 import eu.etaxonomy.cdm.model.common.Language;
  36 import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
  37 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  38 import eu.etaxonomy.cdm.model.common.VocabularyEnum;
  39 import eu.etaxonomy.cdm.model.description.Feature;
  40 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
  41 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  42 import eu.etaxonomy.cdm.model.name.Rank;
  43 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  44 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  45 import eu.etaxonomy.cdm.model.reference.Article;
  46 import eu.etaxonomy.cdm.model.reference.Book;
  47 import eu.etaxonomy.cdm.model.reference.BookSection;
  48 import eu.etaxonomy.cdm.model.reference.Generic;
  49 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  50 import eu.etaxonomy.cdm.model.taxon.Taxon;
  51 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  52 import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;
  53 import eu.etaxonomy.cdm.persistence.query.MatchMode;
  54 import eu.etaxonomy.taxeditor.datasource.CdmDataSourceRepository;
  55
  56 /**
  57  * This implementation of ICdmDataRepository depends on hibernate sessions to store the data correctly
  58  * for the current session. No state is held in this class.
  59  *
  60  * Only methods that either get or manipulate data are exposed here. So this class acts as a facade
  61  * for the methods in cdmlib-service.
  62  *
  63  *
  64  * @author n.hoffmann
  65  * @created 17.03.2009
  66  * @version 1.0
  67  */
  68 public class CdmStore{
  69         private static final Logger logger = Logger.getLogger(CdmStore.class);
  70
  71         // FIXME change this to ClassPathResources as soon as it is included into the plugin
  72         private static String DEFAULT_APPLICATION_CONTEXT = null;
  73         private static DbSchemaValidation DEFAULT_DB_SCHEMA_VALIDATION = DbSchemaValidation.UPDATE;
  74
  75         private static CdmStore instance;
  76
  77         private CdmApplicationController applicationController;
  78
  79         private ConversationHolder globalReadOnlyConversation;
  80
  81         private static DbSchemaValidation dbSchemaValidation;
  82
  83         /**
  84          *
  85          * @return
  86          */
  87         public static CdmStore getDefault(){
  88                 return getDefault(DEFAULT_APPLICATION_CONTEXT);
  89         }
  90
  91         /**
  92          *
  93          * @param applicationContextBean
  94          * @return
  95          */
  96         public static CdmStore getDefault(String applicationContextBean){
  97                 if(instance == null){
  98                         logger.info("Initializing application context ...");
  99                         ICdmDataSource cdmDatasource = CdmDataSourceRepository.getDefault().
 100                                         getCurrentDataSource();
 101
 102                         instance = new CdmStore(cdmDatasource, getDbSchemaValidation(), applicationContextBean);
 103
 104                         logger.info("Application context initialized.");
 105                 }
 106                 return instance;
 107         }
 108
 109         /**
 110          * @return
 111          */
 112         private static DbSchemaValidation getDbSchemaValidation() {
 113                 return (dbSchemaValidation == null) ? DEFAULT_DB_SCHEMA_VALIDATION : dbSchemaValidation;
 114         }
 115
 116         /**
 117          *
 118          */
 119         private CdmStore(ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation, String applicationContextBean) {
 120                 // TODO application context bean is not honored by application controller at the moment.
 121                 // cdmDefaultApplicationController bean gets loaded per default always.
 122
 123                 try {
 124                         CdmStore.DEFAULT_APPLICATION_CONTEXT = applicationContextBean;
 125 //                      applicationController = CdmApplicationController.NewInstance(applicationContextBean, dataSource, dbSchemaValidation, false);
 126
 127 //                      logger.warn("OMITTING TERM LOADING FOR DEBUGGING");
 128 //                      applicationController = CdmApplicationController.NewInstance(dataSource, dbSchemaValidation, true);
 129                         applicationController = CdmApplicationController.NewInstance(dataSource, dbSchemaValidation);
 130                 } catch (Exception e) {
 131                         throw new RuntimeException(e);
 132                 }
 133         }
 134
 135         public Set<TaxonRelationshipType> getConceptRelationshipTypes() {
 136                 Set<TaxonRelationshipType> conceptRelationshipTypes = getTaxonRelationshipTypes().getTerms();
 137                 // remove these two relations as they are considered standard taxon relations
 138                 conceptRelationshipTypes.remove(TaxonRelationshipType.MISAPPLIED_NAME_FOR());
 139                 conceptRelationshipTypes.remove(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN());
 140
 141                 return conceptRelationshipTypes;
 142         }
 143
 144         public ReferenceBase<?> getDefaultSec() {
 145                 // TODO why is this returning null? and of course, replace w the real deal
 146                 return applicationController.getReferenceService().getReferenceByUuid(
 147                                 UUID.fromString("f3593c18-a8d2-4e51-bdad-0befbf8fb2d1"));
 148         }
 149
 150         private TermVocabulary<Feature> getFeaturesInternal() {
 151                 return applicationController.getTermService().getVocabulary(VocabularyEnum.Feature);
 152         }
 153
 154         public static SortedSet<Feature> getFeatures() {
 155                 return getDefault().getFeaturesInternal().getTermsOrderedByLabels(getDefaultLanguage());
 156         }
 157
 158         public SortedSet<NameRelationshipType> getNameRelationshipTypes() {
 159                 return applicationController.getTermService().getVocabulary(VocabularyEnum.NameRelationshipType).getTermsOrderedByLabels(Language.DEFAULT());
 160         }
 161
 162         public TermVocabulary<NomenclaturalStatusType> getNomenclaturalStatusTypesInternal() {
 163                 return applicationController.getTermService().getVocabulary(VocabularyEnum.NomenclaturalStatusType);
 164         }
 165
 166         public static Set<NomenclaturalStatusType> getNomenclaturalStatusTypes(){
 167                 // TODO sort types
 168                 return getDefault().getNomenclaturalStatusTypesInternal().getTerms();
 169         }
 170
 171         private OrderedTermVocabulary<Rank> getRanksInternal(){
 172                 TermVocabulary<Rank> vocabulary = applicationController.getTermService().getVocabulary(VocabularyEnum.Rank);
 173                 return HibernateProxyHelper.deproxy(vocabulary, OrderedTermVocabulary.class);
 174         }
 175
 176         public static SortedSet<Rank> getRanks(){
 177                 return getDefault().getRanksInternal().getOrderedTerms(null);
 178         }
 179
 180         public List<Taxon> getRootTaxa() {
 181                 boolean onlyWithChildren = false;
 182                 boolean withMisapplications = true;
 183
 184                 return applicationController.getTaxonService().getRootTaxa(
 185                                 getDefaultSec(), onlyWithChildren, withMisapplications);
 186         }
 187
 188         /**
 189          * @return
 190          */
 191         public List<TaxonomicTree> getTaxonomicTrees() {
 192                 return applicationController.getTaxonService().getAllTaxonomicTrees(10000, 0);
 193         }
 194
 195         public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypes() {
 196                 TermVocabulary vocabulary = HibernateProxyHelper.deproxy
 197                                 (applicationController.getTermService().getVocabulary(VocabularyEnum.TaxonRelationshipType), TermVocabulary.class);
 198                 return (OrderedTermVocabulary<TaxonRelationshipType>) vocabulary;
 199         }
 200
 201         public TermVocabulary<SpecimenTypeDesignationStatus> getSpecimenTypeDesignationStatus() {
 202                 return applicationController.getTermService().getVocabulary(VocabularyEnum.SpecimenTypeDesignationStatus);
 203         }
 204
 205
 206         public UUID saveTaxon(Taxon taxon) {
 207                 return applicationController.getTaxonService().save(taxon);
 208         }
 209
 210         public void setApplicationController(
 211                         CdmApplicationController applicationController) {
 212                 this.applicationController = applicationController;
 213         }
 214
 215         public CdmApplicationController getApplicationController(){
 216                 return applicationController;
 217         }
 218
 219
 220         /**
 221          * Create a new conversation and bind resources to it
 222          *
 223          * @return
 224          */
 225         public static ConversationHolder NewConversation(){
 226
 227                 CdmStore store = getDefault();
 228                 CdmApplicationController controller = store.getApplicationController();
 229
 230                 ConversationHolder conversation = controller.NewConversation();
 231
 232                 return conversation;
 233         }
 234
 235         /**
 236          * Creates a new conversation, binds resources to the conversation and
 237          * start a transaction for this conversation.
 238          *
 239          * @return
 240          */
 241         public static ConversationHolder NewTransactionalConversation() {
 242                 ConversationHolder conversation = NewConversation();
 243
 244                 conversation.startTransaction();
 245                 return conversation;
 246         }
 247
 248
 249         private ConversationHolder getGlobalReadOnlyConversation() {
 250                 ConversationHolder conversation = globalReadOnlyConversation == null
 251                                 ? NewConversation()
 252                                 : globalReadOnlyConversation;
 253                 conversation.bind();
 254                 return conversation;
 255         }
 256
 257         public static ConversationHolder getGlobalConversation(){
 258                 return getDefault().getGlobalReadOnlyConversation();
 259         }
 260
 261         public static ITaxonService getTaxonService(){
 262                 return getDefault().getApplicationController().getTaxonService();
 263         }
 264
 265         public static INameService getNameService(){
 266                 return getDefault().getApplicationController().getNameService();
 267         }
 268
 269         public static IReferenceService getReferenceService(){
 270                 return getDefault().getApplicationController().getReferenceService();
 271         }
 272
 273         public static ILocationService getLocationService(){
 274                 return getDefault().getApplicationController().getLocationService();
 275         }
 276
 277         public static ProviderManager getAuthenticationManager() {
 278                 return getDefault().getApplicationController().getAuthenticationManager();
 279         }
 280
 281
 282         /**
 283          * @param searchText
 284          * @return
 285          */
 286         @SuppressWarnings("unchecked")
 287         public static List<TaxonNameBase> searchNameString(String searchText) {
 288                 List<TaxonNameBase> resultSet = new ArrayList<TaxonNameBase>();
 289                 resultSet.addAll(getNameService()
 290                                 .getNamesByName(searchText.replace("*", "%")));
 291                 return resultSet;
 292         }
 293
 294         private List<IdentifiableEntity> findTaxaByName(String queryString, boolean restrictToTaxonObjs) {
 295
 296                 ITaxonServiceConfigurator configurator = new TaxonServiceConfiguratorImpl();
 297
 298                 configurator.setSearchString(queryString);
 299                 configurator.setDoTaxa(true);
 300                 configurator.setMatchMode(MatchMode.BEGINNING);
 301                 if (restrictToTaxonObjs) {
 302                         configurator.setDoNamesWithoutTaxa(false);
 303                         configurator.setDoSynonyms(false);
 304                 } else {
 305                         configurator.setDoNamesWithoutTaxa(true);
 306                         configurator.setDoSynonyms(true);
 307                 }
 308                 configurator.setReferenceBase(null);
 309                 configurator.setPageNumber(0);
 310                 // TODO currently limit results to 1000
 311                 configurator.setPageSize(1000);
 312
 313                 List<IdentifiableEntity> result = getTaxonService().findTaxaAndNames(configurator).getRecords();
 314
 315                 return result;
 316         }
 317
 318         public static List<IdentifiableEntity> searchTaxaByName(String queryString){
 319                 return getDefault().findTaxaByName(queryString, false);
 320         }
 321
 322         public static List<IdentifiableEntity> searchTaxaByName(String queryString, boolean restrictToTaxonObjs){
 323                 return getDefault().findTaxaByName(queryString, restrictToTaxonObjs);
 324         }
 325
 326         /**
 327          * Searches for references by string. "%" is used as a wildcard.
 328          *
 329          * @param text
 330          * @return
 331          */
 332         public static List<ReferenceBase> getReferencesByTitle(String reference) {
 333
 334                 reference = reference.replace("*", "%");
 335                 List<ReferenceBase> resultsList = null;
 336                 try {
 337                         resultsList = getReferenceService().getReferencesByTitle(reference);
 338                 } catch (RuntimeException e) {
 339 //                      MessageDialog.openError(GlobalController.getShell(), "Search reference error",
 340 //                                      "Reference search returned an error. This could be a Hibernate concurrency problem. " +
 341 //                                      "Please try saving your work, then searching again.");
 342                         e.printStackTrace();
 343                 }
 344                 return resultsList;
 345         }
 346
 347
 348         public static List<Language> getLanguages() {
 349                 ITermService termService = getDefault().getApplicationController().getTermService();
 350                 ArrayList<Language> languages = new ArrayList<Language>();
 351                 for (Language language : termService.getLanguageVocabulary()) {
 352                         languages.add(language);
 353                 }
 354
 355                 // TODO sort languages
 356
 357 //              languages.add(Language.ENGLISH());
 358 //              languages.add(Language.GERMAN());
 359                 return languages;
 360         }
 361
 362         /**
 363          * FIXME mock
 364          *
 365          * @return
 366          */
 367         public static Language getDefaultLanguage(){
 368                 return Language.ENGLISH();
 369         }
 370
 371         /**
 372          * @return
 373          */
 374         private static String getApplicationContextBean() {
 375                 return DEFAULT_APPLICATION_CONTEXT;
 376         }
 377
 378         /**
 379          * @return
 380          */
 381         public static LinkedHashMap<Class<?>, String> getReferenceTypes() {
 382                 LinkedHashMap<Class<?>, String> nomReferenceTypeMap = new LinkedHashMap<Class<?>, String>();
 383
 384 //              referenceTypeMap.put(BibtexReference.class, "BibTeX Reference");
 385                 nomReferenceTypeMap.put(Article.class, "Article");
 386                 nomReferenceTypeMap.put(Generic.class, "Generic");
 387                 nomReferenceTypeMap.put(Book.class, "Book");
 388                 nomReferenceTypeMap.put(BookSection.class, "Book Section");
 389
 390                 return nomReferenceTypeMap;
 391         }
 392
 393         /**
 394          * @param feature
 395          */
 396         public static void saveFeature(Feature feature) {
 397                 TermVocabulary<Feature> vocabulary = getDefault().getFeaturesInternal();
 398
 399                 vocabulary.addTerm(feature);
 400
 401                 getDefault().getApplicationController().getTermService().saveTermVocabulary(vocabulary);
 402         }
 403
 404         /**
 405          * TODO make this more generic
 406          *
 407          * @param feature
 408          */
 409         public static void updateFeature(Feature feature) {
 410                 TermVocabulary<Feature> vocabulary = getDefault().getFeaturesInternal();
 411
 412                 getDefault().getApplicationController().getTermService().saveTermVocabulary(vocabulary);
 413         }
 414 }