src/main/java/eu/etaxonomy/cdm/vaadin/view/distributionStatus/DistributionTablePresenter.java

   1 /**
   2 * Copyright (C) 2017 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 package eu.etaxonomy.cdm.vaadin.view.distributionStatus;
  10
  11 import java.sql.SQLException;
  12 import java.util.ArrayList;
  13 import java.util.Arrays;
  14 import java.util.Collections;
  15 import java.util.Comparator;
  16 import java.util.HashMap;
  17 import java.util.HashSet;
  18 import java.util.List;
  19 import java.util.Set;
  20 import java.util.UUID;
  21 import java.util.stream.Collectors;
  22
  23 import org.springframework.beans.factory.annotation.Autowired;
  24 import org.springframework.beans.factory.annotation.Qualifier;
  25 import org.springframework.transaction.TransactionStatus;
  26 import org.vaadin.addons.lazyquerycontainer.LazyQueryContainer;
  27 import org.vaadin.addons.lazyquerycontainer.QueryDefinition;
  28 import org.vaadin.addons.lazyquerycontainer.QueryFactory;
  29 import org.vaadin.spring.events.EventBus.ViewEventBus;
  30
  31 import com.vaadin.server.VaadinSession;
  32 import com.vaadin.spring.annotation.SpringComponent;
  33 import com.vaadin.spring.annotation.ViewScope;
  34 import com.vaadin.ui.Notification;
  35
  36 import eu.etaxonomy.cdm.api.application.CdmRepository;
  37 import eu.etaxonomy.cdm.api.util.UserHelper;
  38 import eu.etaxonomy.cdm.i18n.Messages;
  39 import eu.etaxonomy.cdm.model.common.CdmBase;
  40 import eu.etaxonomy.cdm.model.common.Language;
  41 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  42 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  43 import eu.etaxonomy.cdm.model.description.Distribution;
  44 import eu.etaxonomy.cdm.model.description.Feature;
  45 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  46 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  47 import eu.etaxonomy.cdm.model.location.NamedArea;
  48 import eu.etaxonomy.cdm.model.taxon.Classification;
  49 import eu.etaxonomy.cdm.model.taxon.Taxon;
  50 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  51 import eu.etaxonomy.cdm.model.term.DefinedTermBase;
  52 import eu.etaxonomy.cdm.model.term.OrderedTermVocabulary;
  53 import eu.etaxonomy.cdm.model.term.Representation;
  54 import eu.etaxonomy.cdm.model.term.TermVocabulary;
  55 import eu.etaxonomy.cdm.vaadin.container.CdmSQLContainer;
  56 import eu.etaxonomy.cdm.vaadin.container.PresenceAbsenceTermContainer;
  57 import eu.etaxonomy.cdm.vaadin.util.CdmQueryFactory;
  58 import eu.etaxonomy.cdm.vaadin.util.CdmSpringContextHelper;
  59 import eu.etaxonomy.cdm.vaadin.util.DistributionEditorUtil;
  60 import eu.etaxonomy.cdm.vaadin.util.DistributionStatusQueryDefinition;
  61 import eu.etaxonomy.cdm.vaadin.util.DistributionStatusQueryFactory;
  62 import eu.etaxonomy.vaadin.mvp.AbstractPresenter;
  63
  64 /**
  65  * The presenter of the distribution status editor.
  66  */
  67 @SpringComponent
  68 @ViewScope
  69 public class DistributionTablePresenter
  70         extends AbstractPresenter<DistributionTablePresenter,IDistributionTableView> {
  71
  72         private static final long serialVersionUID = 3313043335587777217L;
  73
  74     @Autowired
  75     private UserHelper userHelper;
  76
  77     @Autowired
  78     @Qualifier("cdmRepository")
  79     private CdmRepository repo; // TODO remove, since this is already in the super class
  80
  81     @Override
  82     protected void eventViewBusSubscription(ViewEventBus viewEventBus) {
  83         // no point subscribing
  84     }
  85
  86     /**
  87      * Changes the distribution status of the given {@link Taxon} for the given {@link NamedArea} to the sepcified {@link PresenceAbsenceTerm}.
  88      * @param area The area to update the distribution status for.
  89      * @param distributionStatus The distribution status to update the taxon with.
  90      * @param taxon The taxon to be updated.
  91      * @return
  92      * {@code 0} if the update was successful.
  93      * {@code 1} if the distributionStatus was null and the {@link DescriptionElementBase} was deleted successfully.
  94      * {@code -1} if an error occurred.
  95      */
  96     public int updateDistributionField(NamedArea area, PresenceAbsenceTerm distributionStatus, Taxon taxon) {
  97             TransactionStatus tx = repo.startTransaction();
  98             taxon = (Taxon)repo.getTaxonService().find(taxon.getUuid());
  99             if(area==null){
 100                 Notification.show(Messages.getLocalizedString(Messages.DistributionTablePresenter_ERROR_UPDATE_DISTRIBUTION_TERM));
 101                 repo.commitTransaction(tx);
 102                 return -1;
 103             }
 104             List<Distribution> distributions = getDistributions(taxon);
 105             Distribution distribution = null;
 106             for(Distribution dist : distributions){
 107                 if(dist.getArea()!=null && dist.getArea().equals(area)){
 108                     distribution = dist;
 109                     break;
 110                 }
 111             }
 112             if(distribution==null){
 113                 //create new distribution
 114                 distribution = Distribution.NewInstance(area, distributionStatus);
 115                         Set<TaxonDescription> descriptions = taxon.getDescriptions();
 116                         if (descriptions != null && !descriptions.isEmpty()) {
 117                             for (TaxonDescription desc : descriptions) {
 118                                 // add to first taxon description
 119                                 desc.addElement(distribution);
 120                                 repo.commitTransaction(tx);
 121                                 return 0;
 122                             }
 123                         } else {// there are no TaxonDescription yet.
 124                             TaxonDescription taxonDescription = TaxonDescription.NewInstance(taxon);
 125                             taxonDescription.addElement(distribution);
 126                             repo.commitTransaction(tx);
 127                             return 0;
 128                         }
 129             }
 130             else if(distributionStatus == null){//delete descriptionElementBase
 131                 DescriptionBase<?> desc = distribution.getInDescription();
 132                 desc.removeElement(distribution);
 133                 repo.commitTransaction(tx);
 134             return 1;
 135             }
 136             else{//update distribution
 137            distribution.setStatus(distributionStatus);
 138            repo.getCommonService().saveOrUpdate(distribution);
 139            repo.commitTransaction(tx);
 140            return 0;
 141         }
 142             repo.commitTransaction(tx);
 143             return -1;
 144         }
 145
 146     /**
 147      * Returns a {@link CdmSQLContainer} containing the distribution status information
 148      * for the chosen {@link TaxonNode}s and {@link NamedArea}s.
 149      * @return  {@link CdmSQLContainer} containing the distribution status information
 150      *  for the chosen {@link TaxonNode}s and {@link NamedArea}s.
 151      * @throws SQLException
 152      */
 153     public CdmSQLContainer getSQLContainer() throws SQLException{
 154          List<Integer> nodeIds = new ArrayList<>();
 155          for (TaxonNode taxonNode : getAllNodes()) {
 156              nodeIds.add(taxonNode.getId());
 157          }
 158          List<NamedArea> namedAreas = getChosenAreas();
 159          if(namedAreas!=null){
 160              return new CdmSQLContainer(CdmQueryFactory.generateTaxonDistributionQuery(nodeIds, namedAreas));
 161          }
 162          return null;
 163     }
 164
 165     /**
 166      * Returns a {@link PresenceAbsenceTermContainer} containing all allowed and chosen {@link PresenceAbsenceTerm}s.
 167      * @return {@link PresenceAbsenceTermContainer} containing all allowed and chosen {@link PresenceAbsenceTerm}s.
 168      */
 169     public PresenceAbsenceTermContainer getPresenceAbsenceTermContainer() {
 170         return PresenceAbsenceTermContainer.getInstance();
 171     }
 172
 173     /**
 174      * Returns a list of {@link DescriptionElementBase}s for the specified {@link Taxon} and {@link Feature} set.
 175      * @param taxon The {@link Taxon} to get the descriptions for.
 176      * @param setFeature The features to get the descriptions for.
 177      * @return List of {@link DescriptionElementBase}s for the specified {@link Taxon} and {@link Feature} set.
 178      */
 179     public List<DescriptionElementBase> listDescriptionElementsForTaxon(Taxon taxon, Set<Feature> setFeature){
 180
 181         boolean includeUnpublished = true;
 182         List<DescriptionElementBase> listDescriptionElementsForTaxon = CdmSpringContextHelper.getDescriptionService().listDescriptionElementsForTaxon(
 183                 taxon, setFeature, null, includeUnpublished, null, null, DESCRIPTION_INIT_STRATEGY);
 184         sort(listDescriptionElementsForTaxon);
 185         return listDescriptionElementsForTaxon;
 186     }
 187
 188     /**
 189      * Returns the list of {@link NamedArea}s for which the distribution status can't be updated.
 190      * @return List of {@link NamedArea}s for which the distribution status can't be updated.
 191      */
 192     public List<NamedArea> getReadOnlyAreas(){
 193         List<NamedArea> readonly = new ArrayList<>();
 194         // TODO: HACK FOR RL 2017: Remove as soon as possible by receiving read only areas from cdm preferences
 195         readonly.add(this.getAreaFromString("Deutschland"));
 196         return readonly;
 197     }
 198
 199     /**
 200      * Returns the {@link NamedArea} referred to by the given {@code areaString}.
 201      * @param areaString An string referring to a {@link NamedArea}.
 202      * @return The {@link NamedArea} referred to by the given {@code areaString}.
 203      */
 204     public NamedArea getAreaFromString(String areaString){
 205         List<NamedArea> namedAreas = getChosenAreas();
 206         NamedArea area = null;
 207         for(NamedArea namedArea:namedAreas){
 208             Representation representation = namedArea.getRepresentation(Language.DEFAULT());
 209             if(representation!=null){
 210                 if(DistributionEditorUtil.isAbbreviatedLabels()){
 211                     String label = representation.getLabel();
 212                     String abbreviatedLabel = representation.getAbbreviatedLabel();
 213                     if(abbreviatedLabel!=null && abbreviatedLabel.equalsIgnoreCase(areaString)){
 214                         area = namedArea;
 215                         break;
 216                     }
 217                     else if(label!=null && label.equalsIgnoreCase(areaString)){
 218                         area = namedArea;
 219                         break;
 220                     }
 221                 }
 222             }
 223             if(namedArea.getTitleCache().equalsIgnoreCase(areaString)){
 224                 area = namedArea;
 225                 break;
 226             }
 227         }
 228         return area;
 229     }
 230
 231     /**
 232      * Returns the {@link Distribution} of the given {@link Taxon}.
 233      * @param taxon Taxon to get the {@link Distribution} of.
 234      * @return {@link Distribution} of the given {@link Taxon}.
 235      */
 236     private List<Distribution> getDistributions(Taxon taxon) {
 237
 238         boolean includeUnpublished = true;
 239         Set<Feature> setFeature = new HashSet<>(Arrays.asList(Feature.DISTRIBUTION()));
 240         List<Distribution> listTaxonDescription = CdmSpringContextHelper.getDescriptionService()
 241                 .listDescriptionElementsForTaxon(taxon, setFeature, null, includeUnpublished,
 242                         null, null, DESCRIPTION_INIT_STRATEGY);
 243         return listTaxonDescription;
 244     }
 245
 246     /**
 247      * Returns the list of chosen {@link NamedArea}s defined in the
 248      * related vaadin session attribute {@link DistributionEditorUtil#SATTR_SELECTED_AREAS}.
 249      * If this vaadin session attribute is not set, all allowed {@link NamedArea}s of the
 250      * chosen {@link TermVocabulary} defined by the vaadin session attribute
 251      * {@link DistributionEditorUtil#SATTR_SELECTED_AREA_VOCABULARY_UUID} are returned.
 252      * @return List of chosen {@link NamedArea}s defined in the
 253      * related vaadin session attribute {@link DistributionEditorUtil#SATTR_SELECTED_AREAS}.
 254      * If this vaadin session attribute is not set, all allowed {@link NamedArea}s of the
 255      * chosen {@link TermVocabulary} defined by the vaadin session attribute
 256      * {@link DistributionEditorUtil#SATTR_SELECTED_AREA_VOCABULARY_UUID}.
 257      */
 258         private List<NamedArea> getChosenAreas(){
 259             List<NamedArea> namedAreas = (List<NamedArea>)VaadinSession.getCurrent().getAttribute(DistributionEditorUtil.SATTR_SELECTED_AREAS);
 260             if(namedAreas!=null && namedAreas.isEmpty()){
 261                 return getChosenAreasFromVoc();
 262             }
 263             return namedAreas;
 264         }
 265
 266         /**
 267          * Returns all {@link NamedArea}s of the {@link TermVocabulary} defined
 268          * by the vaadin session attribute {@link DistributionEditorUtil#SATTR_SELECTED_AREA_VOCABULARY_UUID}
 269          * ordered by labels.
 270          * @return all {@link NamedArea}s of the {@link TermVocabulary} defined
 271          * by the vaadin session attribute {@link DistributionEditorUtil#SATTR_SELECTED_AREA_VOCABULARY_UUID}
 272          * ordered by labels..
 273          */
 274         private List<NamedArea> getChosenAreasFromVoc(){
 275             VaadinSession session = VaadinSession.getCurrent();
 276             UUID vocUUID = (UUID) session.getAttribute(DistributionEditorUtil.SATTR_SELECTED_AREA_VOCABULARY_UUID);
 277             TermVocabulary<NamedArea> vocabulary = CdmSpringContextHelper.getVocabularyService().load(vocUUID, Arrays.asList("terms")); //$NON-NLS-1$
 278             vocabulary = CdmBase.deproxy(vocabulary, TermVocabulary.class);
 279             if (vocabulary instanceof OrderedTermVocabulary) {
 280                 List<NamedArea> list = new ArrayList<>(((OrderedTermVocabulary)vocabulary).getOrderedTerms());
 281                 Collections.reverse(list);
 282                 return list;
 283             }else {
 284                 return vocabulary.getTermsOrderedByLabels(Language.DEFAULT()).stream().collect(Collectors.toCollection(ArrayList::new));
 285             }
 286
 287         }
 288
 289         /**
 290          * Returns all {@link TaxonNode}s defined by the
 291          * vaadin session attribute {@link DistributionEditorUtil#SATTR_TAXON_NODES_UUID}.
 292          * If this session attribute is not set, all {@link TaxonNode}s of the chosen
 293          * classification defined by the vaadin session attribute
 294          * {@link DistributionEditorUtil#SATTR_CLASSIFICATION} are returned.
 295          * @return All {@link TaxonNode}s defined by the
 296          * vaadin session attribute {@link DistributionEditorUtil#SATTR_TAXON_NODES_UUID}.
 297          * If this session attribute is not set, all {@link TaxonNode}s of the chosen
 298          * classification defined by the vaadin session attribute
 299          * {@link DistributionEditorUtil#SATTR_CLASSIFICATION}.
 300          */
 301         private List<TaxonNode> getChosenTaxonNodes() {
 302                 VaadinSession session = VaadinSession.getCurrent();
 303         List<UUID> taxonNodeUUIDs = (List<UUID>) session.getAttribute(DistributionEditorUtil.SATTR_TAXON_NODES_UUID);
 304         UUID classificationUuid = (UUID)session.getAttribute(DistributionEditorUtil.SATTR_CLASSIFICATION);
 305         if((taxonNodeUUIDs==null || taxonNodeUUIDs.isEmpty()) && classificationUuid!=null){
 306             Classification classification = CdmSpringContextHelper.getClassificationService().load(classificationUuid);
 307             if(classification!=null){
 308                 taxonNodeUUIDs = Collections.singletonList(classification.getRootNode().getUuid());
 309             }
 310         }
 311         List<TaxonNode> loadedNodes = CdmSpringContextHelper.getTaxonNodeService().load(taxonNodeUUIDs, null);
 312         if(loadedNodes!=null){
 313             return loadedNodes;
 314         }
 315         return Collections.emptyList();
 316     }
 317
 318         /**
 319          * Returns the list of chosen {@link TaxonNode}s returned by {@link #getChosenTaxonNodes()}
 320          * and adds their children to it.
 321          * @return List of chosen {@link TaxonNode}s returned by {@link #getChosenTaxonNodes()}
 322          * and their children.
 323          */
 324         private List<TaxonNode> getAllNodes(){
 325             boolean includeUnpublished = DistributionEditorUtil.INCLUDE_UNPUBLISHED;
 326
 327             List<TaxonNode> allNodes = new ArrayList<>();
 328
 329                 List<TaxonNode> taxonNodes = getChosenTaxonNodes();
 330                 for (TaxonNode taxonNode : taxonNodes) {
 331                         if(taxonNode.getTaxon()!=null){
 332                                 allNodes.add(taxonNode);
 333                         }
 334                         allNodes.addAll(CdmSpringContextHelper.getTaxonNodeService().loadChildNodesOfTaxonNode(taxonNode, null, true, includeUnpublished, null));
 335                 }
 336                 return allNodes;
 337         }
 338
 339         protected static final List<String> DESCRIPTION_INIT_STRATEGY = Arrays.asList(new String []{
 340             "$", //$NON-NLS-1$
 341 "elements.*", //$NON-NLS-1$
 342 "elements.sources.citation.authorship.$", //$NON-NLS-1$
 343 "elements.sources.nameUsedInSource.originalInfo", //$NON-NLS-1$
 344 "elements.area.level", //$NON-NLS-1$
 345 "elements.modifyingText", //$NON-NLS-1$
 346 "elements.states.*", //$NON-NLS-1$
 347 "elements.media", //$NON-NLS-1$
 348 "elements.multilanguageText", //$NON-NLS-1$
 349 "multilanguageText", //$NON-NLS-1$
 350 "stateData.$", //$NON-NLS-1$
 351 "annotations", //$NON-NLS-1$
 352 "markers", //$NON-NLS-1$
 353 "sources.citation.authorship", //$NON-NLS-1$
 354 "sources.nameUsedInSource", //$NON-NLS-1$
 355 "multilanguageText", //$NON-NLS-1$
 356 "media", //$NON-NLS-1$
 357 "name.$", //$NON-NLS-1$
 358 "name.rank", //$NON-NLS-1$
 359 "name.status.type", //$NON-NLS-1$
 360 "taxon2.name", //$NON-NLS-1$
 361 });
 362
 363 /**Helper Methods*/
 364 private void sort(List<DescriptionElementBase> list){
 365         Collections.sort(list, new Comparator<DescriptionElementBase>() {
 366
 367                 @Override
 368                 public int compare(DescriptionElementBase o1, DescriptionElementBase o2) {
 369                         String feature1 = o1.getFeature().getTitleCache();
 370                         String feature2 = o2.getFeature().getTitleCache();
 371                         if(feature1 !=null && feature2 !=null){
 372                                 return feature1.compareTo(feature2);
 373                         }else{
 374                                 return 0;
 375
 376                         }
 377                 }
 378         });
 379 }
 380
 381 /**
 382  *
 383  * {@inheritDoc}
 384  */
 385 @Override
 386 protected void onPresenterReady() {
 387     /*
 388  * The area and taxon settings window should only be displayed after login
 389  * and only when no classification and areas are chosen yet.
 390  */
 391     VaadinSession vaadinSession = VaadinSession.getCurrent();
 392     if(userHelper.userIsAutheticated()
 393             && !userHelper.userIsAnnonymous()
 394             && (vaadinSession.getAttribute(DistributionEditorUtil.SATTR_CLASSIFICATION) == null
 395             || vaadinSession.getAttribute(DistributionEditorUtil.SATTR_SELECTED_AREA_VOCABULARY_UUID) == null
 396             || vaadinSession.getAttribute(DistributionEditorUtil.SATTR_SELECTED_AREAS) == null)) {
 397         getView().openAreaAndTaxonSettings();
 398     }
 399 }
 400
 401 /**Unused Methods*/
 402 // TODO: Currently unused. Remove?
 403 private List<String> getAbbreviatedNamedAreas() {
 404     List<NamedArea> terms = getChosenAreasFromVoc();
 405     List<String> list = new ArrayList<>();
 406     for(DefinedTermBase<?> dtb: terms){
 407         for(Representation r : dtb.getRepresentations()){
 408             list.add(r.getAbbreviatedLabel());
 409         }
 410     }
 411     return list;
 412 }
 413
 414 // TODO: Currently unused. Remove?
 415 private HashMap<DescriptionElementBase, Distribution> getDistribution(DefinedTermBase dt, Taxon taxon) {
 416
 417     boolean includeUnpublished = true;
 418     Set<Feature> setFeature = new HashSet<>(Arrays.asList(Feature.DISTRIBUTION()));
 419     List<DescriptionElementBase> listTaxonDescription = CdmSpringContextHelper.getDescriptionService()
 420             .listDescriptionElementsForTaxon(taxon, setFeature, null, includeUnpublished, null, null, DESCRIPTION_INIT_STRATEGY);
 421     HashMap<DescriptionElementBase, Distribution> map = null;
 422     for(DescriptionElementBase deb : listTaxonDescription){
 423         if(deb instanceof Distribution){
 424             Distribution db = (Distribution)deb;
 425             String titleCache = dt.getTitleCache();
 426             if(db.getArea().getTitleCache().equalsIgnoreCase(titleCache)){
 427                 map = new HashMap<DescriptionElementBase, Distribution>();
 428                 map.put(deb, db);
 429             }
 430         }
 431     }
 432     return map;
 433 }
 434
 435 public LazyQueryContainer getAreaDistributionStatusContainer() {
 436     List<UUID> nodeUuids = getAllNodes().stream().map(n -> n.getUuid()).collect(Collectors.toCollection(ArrayList::new));
 437     List<NamedArea> namedAreas = getChosenAreas();
 438     if(namedAreas!=null){
 439         QueryFactory factory = new DistributionStatusQueryFactory(this.repo, nodeUuids, namedAreas);
 440         QueryDefinition defintion = new DistributionStatusQueryDefinition(namedAreas, true, 50);
 441         return new LazyQueryContainer(defintion, factory);
 442     }
 443     return null;
 444 }
 445 }