eclipseprojects/eu.etaxonomy.taxeditor/src/eu/etaxonomy/taxeditor/TaxEditorPlugin.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;
  11
  12 import java.net.URL;
  13 import java.util.Collection;
  14 import java.util.HashMap;
  15 import java.util.HashSet;
  16 import java.util.Map;
  17 import java.util.ResourceBundle;
  18 import java.util.Set;
  19 import java.util.UUID;
  20
  21 import org.apache.log4j.Logger;
  22 import org.eclipse.core.databinding.observable.Realm;
  23 import org.eclipse.core.databinding.observable.list.WritableList;
  24 import org.eclipse.core.databinding.observable.set.IObservableSet;
  25 import org.eclipse.core.databinding.observable.set.WritableSet;
  26 import org.eclipse.core.runtime.FileLocator;
  27 import org.eclipse.core.runtime.IPath;
  28 import org.eclipse.core.runtime.Path;
  29 import org.eclipse.jface.databinding.swt.SWTObservables;
  30 import org.eclipse.jface.preference.IPreferenceStore;
  31 import org.eclipse.jface.resource.FontRegistry;
  32 import org.eclipse.jface.resource.ImageDescriptor;
  33 import org.eclipse.jface.resource.ImageRegistry;
  34 import org.eclipse.swt.SWT;
  35 import org.eclipse.swt.graphics.Color;
  36 import org.eclipse.swt.graphics.Font;
  37 import org.eclipse.swt.graphics.FontData;
  38 import org.eclipse.swt.graphics.Image;
  39 import org.eclipse.swt.widgets.Display;
  40 import org.eclipse.ui.forms.FormColors;
  41 import org.eclipse.ui.plugin.AbstractUIPlugin;
  42 import org.osgi.framework.BundleContext;
  43 import org.springframework.transaction.TransactionStatus;
  44
  45 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  46 import eu.etaxonomy.cdm.api.service.IDescriptionService;
  47 import eu.etaxonomy.cdm.api.service.INameService;
  48 import eu.etaxonomy.cdm.api.service.ITaxonService;
  49 import eu.etaxonomy.cdm.database.CdmDataSource;
  50 import eu.etaxonomy.cdm.database.DataSourceNotFoundException;
  51 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  52 import eu.etaxonomy.cdm.database.ICdmDataSource;
  53 import eu.etaxonomy.cdm.model.agent.Person;
  54 import eu.etaxonomy.cdm.model.common.Language;
  55 import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
  56 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  57 import eu.etaxonomy.cdm.model.common.init.TermNotFoundException;
  58 import eu.etaxonomy.cdm.model.description.Feature;
  59 import eu.etaxonomy.cdm.model.name.BotanicalName;
  60 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
  61 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  62 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  63 import eu.etaxonomy.cdm.model.name.Rank;
  64 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  65 import eu.etaxonomy.cdm.model.taxon.Taxon;
  66 import eu.etaxonomy.taxeditor.model.CdmUtil;
  67 import eu.etaxonomy.taxeditor.navigation.TaxonomicTreeView;
  68
  69 /**
  70  * The class controlling the plug-in life cycle.
  71  * </p>
  72  * <ul>
  73  *      <li>Initializes datastore as necessary.</li>
  74  *      <li>Initializes default preferences.</li>
  75  *      <li>Gateway to CDM service layer.</li>
  76  *      <li>Stores taxa for application session.</li>
  77  *      <li>Stores registries for colors, fonts, images.</li>
  78  * </ul>
  79  *
  80  * @author p.ciardelli
  81  * @created 15.05.2008
  82  * @version 1.0
  83  */
  84 public class TaxEditorPlugin extends AbstractUIPlugin {
  85         private static final Logger logger = Logger
  86                         .getLogger(TaxEditorPlugin.class);
  87
  88         /**
  89          * The plug-in ID
  90          */
  91         public static final String PLUGIN_ID = "eu.etaxonomy.taxeditor.plugin";
  92         /**
  93          * The shared instance
  94          */
  95         private static TaxEditorPlugin plugin;
  96
  97 //      private DbSchemaValidation dbSchemaValidation = DbSchemaValidation.VALIDATE;
  98         private DbSchemaValidation dbSchemaValidation = DbSchemaValidation.UPDATE;
  99
 100         /**
 101          * The constructor
 102          */
 103         public TaxEditorPlugin() {
 104                 logger.fatal("Fatal");
 105                 logger.error("Error");
 106                 logger.debug("Debug");
 107                 logger.info("Info");
 108                 logger.warn("Warn");
 109                 logger.trace("Trace");
 110         }
 111
 112         /*
 113          * (non-Javadoc)
 114          *
 115          * @see org.eclipse.ui.plugin.AbstractUIPlugin#start(org.osgi.framework.BundleContext)
 116          */
 117         public void start(BundleContext context) throws Exception {
 118                 super.start(context);
 119                 plugin = this;
 120
 121                 boolean initDatastore = false;
 122
 123                 // If the preferences INITIALIZED has not been set, the IF clause
 124                 // will return false, i.e. datastore will be initialized first
 125                 // time the application is run after being installed.
 126                 boolean initialized = getPreferenceStore()
 127                                 .getBoolean(ITaxEditorConstants.INITIALIZED);
 128
 129 //              initialized = false; // to re-init db, uncomment this line
 130                 if (!initialized) {
 131                         logger.warn("Initializing datastore");
 132                         initDatastore = true;
 133
 134                         getPreferenceStore()
 135                                         .setValue(ITaxEditorConstants.INITIALIZED, true);
 136                 } else {
 137                         logger.warn("Datastore already initialized");
 138                 }
 139
 140                 if (initDatastore) {
 141                         dbSchemaValidation = DbSchemaValidation.CREATE;
 142                         initDatastore();
 143                 }
 144
 145                 cdmApp = getCdmApp();
 146
 147 //              if (initDatastore) {
 148 //                      initDatastore();
 149 //              }
 150
 151         }
 152
 153         /*
 154          * (non-Javadoc)
 155          *
 156          * @see org.eclipse.ui.plugin.AbstractUIPlugin#stop(org.osgi.framework.BundleContext)
 157          */
 158         public void stop(BundleContext context) throws Exception {
 159                 stopTransaction();
 160                 plugin = null;
 161                 super.stop(context);
 162
 163                 disposeColors();
 164         }
 165
 166         void initDatastore() {
 167
 168                 boolean useSoraya = true;
 169                 // useSoraya = false;
 170                 Taxon genusTaxon;
 171                 if (useSoraya) {
 172                         genusTaxon = getSorayasGenusTaxon();
 173                 } else {
 174
 175                         BotanicalName botanicalName = BotanicalName.NewInstance(Rank
 176                                         .GENUS());
 177                         botanicalName.setTitleCache("Hieracium L.");
 178                         botanicalName.setGenusOrUninomial("Hieracium");
 179                         botanicalName.setCombinationAuthorTeam(Person.NewInstance());
 180                         botanicalName.getCombinationAuthorTeam()
 181                                         .setNomenclaturalTitle("L.");
 182                         genusTaxon = Taxon.NewInstance(botanicalName, CdmUtil
 183                                         .getSessionDefaultSec());
 184
 185                         BotanicalName botSpecies = BotanicalName
 186                                         .NewInstance(Rank.SPECIES());
 187                         botSpecies.setTitleCache("Hieracium asturianum Pau");
 188                         botSpecies.setGenusOrUninomial("Hieracium");
 189                         botSpecies.setSpecificEpithet("asturianum");
 190                         botSpecies.setCombinationAuthorTeam(Person.NewInstance());
 191                         botSpecies.getCombinationAuthorTeam().setNomenclaturalTitle("Pau");
 192                         Taxon childTaxon = Taxon.NewInstance(botSpecies, null);
 193                         childTaxon.setTaxonomicParent(genusTaxon, null, null);
 194
 195                         BotanicalName botSpecies2 = BotanicalName.NewInstance(Rank
 196                                         .SPECIES());
 197                         botSpecies2.setTitleCache("Hieracium wolffii Zahn");
 198                         botSpecies2.setGenusOrUninomial("Hieracium");
 199                         botSpecies2.setSpecificEpithet("wolffii");
 200                         botSpecies2.setCombinationAuthorTeam(Person.NewInstance());
 201                         botSpecies2.getCombinationAuthorTeam()
 202                                         .setNomenclaturalTitle("Zahn");
 203                         Taxon childTaxon2 = Taxon.NewInstance(botSpecies2, CdmUtil
 204                                         .getSessionDefaultSec());
 205                         // childTaxon2.setName(botSpecies2);
 206                         // childTaxon2.setSec(null);
 207                         childTaxon2.setTaxonomicParent(genusTaxon, null, null);
 208
 209                         // Add some name relations to botSpecies2
 210                         botSpecies2.addRelationshipFromName(botSpecies,
 211                                         NameRelationshipType.BASIONYM(), null);
 212                         botSpecies2.addRelationshipToName(botSpecies, NameRelationshipType
 213                                         .REPLACED_SYNONYM(), null);
 214                         logger.warn("Name relations created");
 215
 216                         // Add name status to botSpecies2
 217                         botSpecies2.addStatus(NomenclaturalStatus
 218                                         .NewInstance(NomenclaturalStatusType.NOVUM()));
 219                         logger.warn("Nom. status created");
 220                 }
 221
 222                 getCdmApp().getTaxonService().saveTaxon(genusTaxon);
 223
 224                 // System.exit(-1);
 225         }
 226
 227         /**
 228          * Returns the shared instance
 229          *
 230          * @return the shared instance
 231          */
 232         public static TaxEditorPlugin getDefault() {
 233                 return plugin;
 234         }
 235
 236         /***************************************************************************
 237          * CDM SERVICES
 238          **************************************************************************/
 239         /**
 240          * All CDM services are called via the application controller
 241          */
 242         private CdmApplicationController cdmApp;
 243         private TransactionStatus txStatus;
 244
 245         public CdmApplicationController getCdmApp() {
 246                 if (cdmApp == null) {
 247                         try {
 248                                  ICdmDataSource ds =
 249                                          CdmDataSource.NewH2EmbeddedInstance("cdm", "sa", "");
 250 //                                       CdmDataSource.NewMySqlInstance("192.168.2.10", "cdm_test_andreasM2", "edit", "wp5");
 251
 252                                  // Is this the problem?
 253                                  cdmApp = CdmApplicationController
 254                                                 .NewInstance(ds, dbSchemaValidation);
 255
 256
 257 //                              cdmApp = CdmApplicationController
 258 //                                              .NewInstance(dbSchemaValidation);
 259
 260                                 startTransaction();
 261                                  Object txStatus = cdmApp.startTransaction();
 262                                 // cdmApp.commitTransaction((TransactionStatus) txStatus);
 263
 264                         } catch (DataSourceNotFoundException e) {
 265                                 // TODO Auto-generated catch block
 266                                 e.printStackTrace();
 267                         } catch (TermNotFoundException e) {
 268                                 // TODO Auto-generated catch block
 269                                 e.printStackTrace();
 270                         }
 271                 }
 272                 return cdmApp;
 273         }
 274
 275         public void startTransaction() {
 276                 if (cdmApp != null) {
 277                         txStatus = cdmApp.startTransaction();
 278                 }
 279         }
 280
 281         public void stopTransaction() {
 282                 if (txStatus != null) {
 283                         cdmApp.commitTransaction(txStatus);
 284                         txStatus = null;
 285                 }
 286         }
 287
 288         private ITaxonService taxonService;
 289
 290         public ITaxonService getTaxonService() {
 291                 if (taxonService == null) {
 292                         taxonService = getCdmApp().getTaxonService();
 293                 }
 294                 return taxonService;
 295         }
 296
 297         private INameService nameService;
 298
 299         public INameService getNameService() {
 300                 if (nameService == null) {
 301                         nameService = getCdmApp().getNameService();
 302                 }
 303                 return nameService;
 304         }
 305
 306         private IDescriptionService descriptionService;
 307
 308         public IDescriptionService getDescriptionService() {
 309                 if (descriptionService == null) {
 310                         descriptionService = getCdmApp().getDescriptionService();
 311                 }
 312                 return descriptionService;
 313
 314         }
 315
 316         /***************************************************************************
 317          * OBSERVABLE LISTS
 318          **************************************************************************/
 319
 320         private WritableList observableRecentNamesList = null;
 321         private WritableList observableFavoritesList = null;
 322
 323         public WritableList getObservableRecentNamesList() {
 324                 if (observableRecentNamesList == null) {
 325                         observableRecentNamesList = new WritableList();
 326                 }
 327                 return observableRecentNamesList;
 328         }
 329
 330         public WritableList getObservableFavoritesList() {
 331                 if (observableFavoritesList == null) {
 332                         observableFavoritesList = new WritableList();
 333                 }
 334                 return observableFavoritesList;
 335         }
 336
 337         /***************************************************************************
 338          * IMAGE REGISTRY
 339          **************************************************************************/
 340         public ImageDescriptor getImageDescriptor(String key) {
 341                 return getImageRegistry().getDescriptor(key);
 342         }
 343
 344         public Image getImage(String key) {
 345                 return getImageRegistry().get(key);
 346         }
 347
 348         // Resource bundle.
 349         private ResourceBundle resourceBundle;
 350         private FormColors formColors;
 351
 352         protected void initializeImageRegistry(ImageRegistry registry) {
 353                 registerImage(registry, ITaxEditorConstants.EDIT_ICON, "edit_16x16.ico");
 354                 registerImage(registry, ITaxEditorConstants.WARNING_ICON,
 355                                 "warn_tsk.gif");
 356                 registerImage(registry, ITaxEditorConstants.BLACK_SQUARE_ICON,
 357                                 "accepted_small.gif");
 358                 registerImage(registry, ITaxEditorConstants.HOMOTYPIC_SYN_ICON,
 359                                 "homosyn_no_bg.gif");
 360                 registerImage(registry,
 361                                 ITaxEditorConstants.HOMOTYPIC_SYN_ORIGINAL_ICON,
 362                                 "homosyn_original_no_bg.gif");
 363                 registerImage(registry, ITaxEditorConstants.HETEROTYPIC_SYN_ICON,
 364                                 "heterosyn_no_bg.gif");
 365                 registerImage(registry,
 366                                 ITaxEditorConstants.HETEROTYPIC_SYN_ORIGINAL_ICON,
 367                                 "heterosyn_original_no_bg.gif");
 368                 registerImage(registry, ITaxEditorConstants.MISAPPLIED_NAME_ICON,
 369                                 "misapplied_no_bg.gif");
 370                 registerImage(registry, ITaxEditorConstants.AUTONYM_ICON,
 371                                 "autonym_no_bg.gif");
 372                 registerImage(registry, ITaxEditorConstants.BASIONYM_ICON,
 373                                 "basionym_no_bg.gif");
 374                 registerImage(registry, ITaxEditorConstants.ORTHOGRAPHIC_VARIANT_ICON,
 375                                 "orthovariant_no_bg.gif");
 376                 registerImage(registry, ITaxEditorConstants.DB_ICON, "db.gif");
 377                 registerImage(registry, ITaxEditorConstants.MOVE_ICON,
 378                                 "correction_change.gif");
 379                 registerImage(registry, ITaxEditorConstants.ACTIVE_DELETE_ICON,
 380                                 "delete_edit.gif");
 381                 registerImage(registry, ITaxEditorConstants.SYNONYM_TO_TAXON_ICON,
 382                                 "change.gif");
 383                 registerImage(registry, ITaxEditorConstants.OPEN_TAXON_ICON, "open.gif");
 384                 registerImage(registry, ITaxEditorConstants.ADD_CHILD_TAXON_ICON,
 385                                 "new_child.gif");
 386                 registerImage(registry,
 387                                 ITaxEditorConstants.SWAP_SYNONYM_AND_TAXON_ICON, "swap2.gif");
 388                 registerImage(registry, ITaxEditorConstants.QUICK_ADD_ICON,
 389                                 "quick_add.gif");
 390                 registerImage(registry, ITaxEditorConstants.TAXON_TO_SYNONYM_ICON,
 391                                 "tax_to_syn.gif");
 392         }
 393
 394         private void registerImage(ImageRegistry registry, String key,
 395                         String fileName) {
 396                 try {
 397                         IPath path = new Path("icons/" + fileName); //$NON-NLS-1$
 398                         URL url = FileLocator.find(getBundle(), path, null);
 399                         if (url != null) {
 400                                 ImageDescriptor desc = ImageDescriptor.createFromURL(url);
 401                                 registry.put(key, desc);
 402                         }
 403                 } catch (Exception e) {
 404                 }
 405         }
 406
 407         /***************************************************************************
 408          * FONT REGISTRY
 409          **************************************************************************/
 410         private FontRegistry fontRegistry;
 411
 412         private FontRegistry getFontRegistry() {
 413                 if (fontRegistry == null) {
 414                         fontRegistry = new FontRegistry(Display.getCurrent());
 415
 416                         fontRegistry.put(ITaxEditorConstants.DATASOURCE_FONT,
 417                                         new FontData[] { new FontData("Arial", 8, SWT.NONE) });
 418                         fontRegistry.put(ITaxEditorConstants.MENU_ITEM_ITALICS_FONT,
 419                                         new FontData[] { new FontData("Arial", 9, SWT.ITALIC) });
 420                         fontRegistry.put(ITaxEditorConstants.ACCEPTED_TAXON_FONT,
 421                                         new FontData[] { new FontData("Georgia", 12, SWT.NONE) });
 422                         fontRegistry.put(ITaxEditorConstants.SYNONYM_FONT,
 423                                         new FontData[] { new FontData("Georgia", 10, SWT.NONE) });
 424                         fontRegistry.put(ITaxEditorConstants.MISAPPLIEDNAME_FONT,
 425                                         new FontData[] { new FontData("Georgia", 10, SWT.NONE) });
 426                         fontRegistry.put(ITaxEditorConstants.CHOOSE_NAME_TEXT_FONT,
 427                                         new FontData[] { new FontData("Arial", 12, SWT.BOLD) });
 428                         fontRegistry.put(ITaxEditorConstants.DEFAULT_PROMPT_FONT,
 429                                         new FontData[] { new FontData("Georgia", 10, SWT.ITALIC) });
 430                 }
 431                 return fontRegistry;
 432         }
 433
 434         public Font getFont(String key) {
 435                 return getFontRegistry().get(key);
 436         }
 437
 438         /***************************************************************************
 439          * COLOR MAP
 440          **************************************************************************/
 441         private static HashMap<String, Color> colorMap;
 442
 443         public Color getColor(String key) {
 444                 return getColorMap().get(key);
 445         }
 446
 447         private HashMap<String, Color> getColorMap() {
 448                 if (colorMap == null) {
 449                          colorMap = new HashMap<String, Color>();
 450
 451                          colorMap.put(ITaxEditorConstants.GROUP_GRAY_BKG_COLOR,
 452                                          new Color(null, 246, 246, 246));
 453                 }
 454                 return colorMap;
 455         }
 456
 457         private void disposeColors() {
 458         for (Color color : colorMap.values()) {
 459                 color.dispose();
 460         }
 461         colorMap.clear();
 462         }
 463
 464         /***************************************************************************
 465          * PREFERENCES
 466          **************************************************************************/
 467         /* (non-Javadoc)
 468          * @see org.eclipse.ui.plugin.AbstractUIPlugin#initializeDefaultPreferences(org.eclipse.jface.preference.IPreferenceStore)
 469          */
 470         protected void initializeDefaultPreferences(IPreferenceStore store) {
 471                 // Platform.getPreferencesService().getBoolean(qualifier, key,
 472                 // defaultValue, contexts)
 473                 store.setDefault(ITaxEditorConstants.CODE_PREFERENCE,
 474                                 ITaxEditorConstants.DEFAULT_CODE_PREFERENCE);
 475
 476                 // Set preferences to display all features
 477                 TermVocabulary<Feature> features = descriptionService.getDefaultFeatureVocabulary();
 478                 for (Feature feature : features) {
 479                         String preferenceKey = ITaxEditorConstants.FEATURE_PREFERENCE
 480                                 . concat(".")
 481                                 . concat(feature.getUuid().toString());
 482                         store.setDefault(preferenceKey, true);
 483                 }
 484
 485         }
 486
 487         /***************************************************************************
 488          * TAXONOMIC TREE
 489          **************************************************************************/
 490
 491         public ReferenceBase getSec() {
 492                 return getCdmApp().getReferenceService().getReferenceByUuid(
 493                                 UUID.fromString("f3593c18-a8d2-4e51-bdad-0befbf8fb2d1"));
 494         }
 495
 496         private Set<Taxon> sessionRootTaxa;
 497         /**
 498          * The taxonomic tree content provider observes this set for changes, and
 499          * makes the appropriate changes to the tree.
 500          */
 501         private IObservableSet observableSessionTaxonSet;
 502         /**
 503          * This map of taxa to their taxonomic children is used by
 504          * NameTreeContentProvider's getChildren method.
 505          *
 506          * key = taxon, value = key's child taxa Note that a map can have a key ==
 507          * null, i.e. no parent taxon
 508          */
 509         private HashMap<Taxon, Set<Taxon>> sessionTaxonomicChildrenMap;
 510
 511         public Set<Taxon> getSessionRootTaxa() {
 512                 if (sessionRootTaxa == null) {
 513                         sessionRootTaxa = new HashSet<Taxon>();
 514 //                      sessionRootTaxa.addAll(getCdmApp().getTaxonService().getRootTaxa(
 515 //                                      getSec(), null, false));
 516                         sessionRootTaxa.addAll(getCdmApp().getTaxonService().getRootTaxa(
 517                                         getSec(), null, true));
 518                         addSessionTaxa(sessionRootTaxa);
 519                 }
 520                 return sessionRootTaxa;
 521         }
 522
 523         private Map<Taxon, Set<Taxon>> getTaxonomicChildrenMap() {
 524                 if (sessionTaxonomicChildrenMap == null) {
 525                         sessionTaxonomicChildrenMap = new HashMap<Taxon, Set<Taxon>>();
 526                 }
 527                 return sessionTaxonomicChildrenMap;
 528         }
 529
 530         /**
 531          * Returns a set of any child taxa for this taxon that have already been
 532          * requested during this session.
 533          *
 534          * @param parentTaxon
 535          * @return
 536          */
 537         public Set<Taxon> getSessionTaxonomicChildren(Taxon parentTaxon) {
 538                 if (!getTaxonomicChildrenMap().containsKey(parentTaxon)) {
 539                         if (parentTaxon == null) {
 540                                 getTaxonomicChildrenMap().put(parentTaxon, getSessionRootTaxa());
 541                         } else {
 542
 543                                 // BUG deleted taxon were re-appearing as NULL children
 544                                 Set<Taxon> childTaxa = new HashSet<Taxon>();
 545                                 for (Taxon taxon : parentTaxon.getTaxonomicChildren()) {
 546                                         if (taxon != null) {
 547                                                 childTaxa.add(taxon);
 548                                         }
 549                                 }
 550                                 getTaxonomicChildrenMap().put(parentTaxon, childTaxa);
 551                         }
 552                 }
 553                 return getTaxonomicChildrenMap().get(parentTaxon);
 554         }
 555
 556         /**
 557          * @return
 558          */
 559         public IObservableSet getObservableSessionTaxa() {
 560                 if (observableSessionTaxonSet == null) {
 561                         Realm realm = SWTObservables.getRealm(Display.getDefault());
 562                         observableSessionTaxonSet = new WritableSet(realm);
 563                 }
 564                 return observableSessionTaxonSet;
 565         }
 566
 567         /**
 568          * Recursive function to clear the hashmap of a taxon's children used in
 569          * this session, and the childrens' children, etc.
 570          *
 571          * @param taxon
 572          */
 573         private void clearTaxonomicChildren(Taxon taxon) {
 574                 Set<Taxon> children = getSessionTaxonomicChildren(taxon);
 575                 if (children != null) {
 576                         for (Taxon child : children) {
 577                                 clearTaxonomicChildren(child);
 578                         }
 579                         getTaxonomicChildrenMap().remove(taxon);
 580                         getObservableSessionTaxa().removeAll(children);
 581                 }
 582         }
 583
 584         /**
 585          * Remove taxon from all session collections
 586          *
 587          * @param taxon
 588          */
 589         public void removeSessionTaxon(Taxon taxon) {
 590
 591                 // Recursively remove all children, children's children, etc.
 592                 clearTaxonomicChildren(taxon);
 593
 594                 Taxon parentTaxon = taxon.getTaxonomicParent();
 595
 596                 // Remove from parent's child map, or from root taxa
 597                 if (parentTaxon == null) {
 598                         getSessionRootTaxa().remove(taxon);
 599                 } else {
 600                         getSessionTaxonomicChildren(parentTaxon).remove(taxon);
 601                 }
 602
 603                 // Remove from session taxa
 604                 getObservableSessionTaxa().remove(taxon);
 605
 606                 UiUtil.getTreeViewer().remove(taxon);
 607         }
 608
 609         public void addSessionTaxa(Collection<Taxon> taxa) {
 610                 for (Taxon taxon : taxa) {
 611                         addSessionTaxon(taxon);
 612                 }
 613         }
 614
 615         /**
 616          * Whenever a taxon is opened, either for editing or for display in the
 617          * taxonomic tree, it should be added to the collections of taxa used during
 618          * this session.
 619          *
 620          * @param taxon
 621          */
 622         public void addSessionTaxon(Taxon taxon) {
 623
 624                 // Add taxon to session taxa if not already there
 625                 if (!(getObservableSessionTaxa().contains(taxon))) {
 626                         getObservableSessionTaxa().add(taxon);
 627                 }
 628
 629                 Taxon parentTaxon = taxon.getTaxonomicParent();
 630
 631                 // If taxon has no parent, add it to root taxa
 632                 if (parentTaxon == null) {
 633                         if (!(getSessionRootTaxa().contains(taxon))) {
 634                                 getSessionRootTaxa().add(taxon);
 635                         }
 636                 }
 637
 638                 // Add taxon to its parent's child map
 639                 getSessionTaxonomicChildren(parentTaxon).add(taxon);
 640
 641                 if (taxonomicTreeView != null) {
 642
 643                         UiUtil.getTreeViewer().remove(taxon);
 644
 645                         if (parentTaxon == null) {
 646                                 UiUtil.getTreeViewer().setInput(getSessionRootTaxa());
 647                         } else {
 648                                 UiUtil.getTreeViewer().add(parentTaxon, taxon);
 649                         }
 650
 651                 }
 652         }
 653
 654
 655         private TaxonomicTreeView taxonomicTreeView;
 656
 657         public void setTaxonomicTree(TaxonomicTreeView taxonomicTreeView) {
 658                 this.taxonomicTreeView = taxonomicTreeView;
 659         }
 660
 661         /***************************************************************************
 662          * RANKS
 663          **************************************************************************/
 664         OrderedTermVocabulary<Rank> rankVocabulary = null;
 665
 666         public OrderedTermVocabulary<Rank> getRankVocabulary() {
 667                 if (rankVocabulary == null) {
 668                         rankVocabulary = getCdmApp().getNameService().getRankVocabulary();
 669                 }
 670                 return rankVocabulary;
 671         }
 672
 673         /***************************************************************************
 674          * NOMENCLATURAL STATUS
 675          **************************************************************************/
 676         TermVocabulary<NomenclaturalStatusType> nomStatusVocabulary = null;
 677
 678         public TermVocabulary<NomenclaturalStatusType> getNomStatusVocabulary() {
 679                 if (nomStatusVocabulary == null) {
 680                         nomStatusVocabulary = getCdmApp().getNameService()
 681                                         .getStatusTypeVocabulary();
 682                 }
 683                 return nomStatusVocabulary;
 684         }
 685
 686         /***************************************************************************
 687          * NAME RELATIONS
 688          **************************************************************************/
 689         TermVocabulary<NameRelationshipType> nameRelationshipTypeVocabulary = null;
 690
 691         public TermVocabulary<NameRelationshipType> getNameRelationshipTypeVocabulary() {
 692                 if (nameRelationshipTypeVocabulary == null) {
 693                         nameRelationshipTypeVocabulary = getCdmApp().getNameService()
 694                                         .getNameRelationshipTypeVocabulary();
 695                 }
 696                 return nameRelationshipTypeVocabulary;
 697         }
 698
 699         public Set<NameRelationshipType> getSortedNameRelationshipTypes() {
 700                 return getNameRelationshipTypeVocabulary().getTermsOrderedByLabels(
 701                                 Language.DEFAULT());
 702         }
 703
 704         /***************************************************************************
 705          * SORAYA DATA
 706          **************************************************************************/
 707         private Taxon getSorayasGenusTaxon() {
 708
 709                 String[] children = new String[] {
 710                                 "Heterospathe annectens H.E.Moore",
 711                                 "Heterospathe arfakiana (Becc.) H.E.Moore",
 712                                 "Heterospathe brevicaulis Fernando",
 713                                 "Heterospathe cagayanensis Becc.",
 714                                 "Heterospathe califrons Fernando, Palms 45: 118 (2001).",
 715                                 "Heterospathe clemensiae (Burret) H.E.Moore",
 716                                 "Heterospathe delicatula H.E.Moore",
 717                                 "Heterospathe dransfieldii Fernando",
 718                                 "Heterospathe elata Scheff.",
 719                                 "Heterospathe elata var. elata.",
 720                                 "Heterospathe elata var. guamensis Becc.",
 721                                 "Heterospathe elata var. palauensis (Becc.) Becc.",
 722                                 "Heterospathe elegans (Becc.) Becc.",
 723                                 "Heterospathe elmeri Becc.",
 724                                 "Heterospathe glabra (Burret) H.E.Moore",
 725                                 "Heterospathe glauca (Scheff.) H.E.Moore",
 726                                 "Heterospathe humilis Becc.",
 727                                 "Heterospathe intermedia (Becc.) Fernando",
 728                                 "Heterospathe kajewskii Burret",
 729                                 "Heterospathe ledermanniana Becc.",
 730                                 "Heterospathe lepidota H.E.Moore",
 731                                 "Heterospathe longipes (H.E.Moore) Norup",
 732                                 "Heterospathe macgregorii (Becc.) H.E.Moore",
 733                                 "Heterospathe micrantha (Becc.) H.E.Moore",
 734                                 "Heterospathe minor Burret",
 735                                 "Heterospathe muelleriana (Becc.) Becc.",
 736                                 "Heterospathe negrosensis Becc.",
 737                                 "Heterospathe obriensis (Becc.) H.E.Moore",
 738                                 "Heterospathe palauensis Becc.",
 739                                 "Heterospathe parviflora Essig",
 740                                 "Heterospathe philippinensis (Becc.) Becc.",
 741                                 // "Heterospathe phillipsii D.Fuller & Dowe", // <--------------
 742                                 "Heterospathe pilosa (Burret) Burret",
 743                                 "Heterospathe pisifera (Gaertn.) Burret",
 744                                 "Heterospathe pulchra H.E.Moore",
 745                                 "Heterospathe ramulosa Burret",
 746                                 "Heterospathe salomonensis Becc.",
 747                                 "Heterospathe scitula Fernando", "Heterospathe sensisi Becc.",
 748                                 "Heterospathe sibuyanensis Becc.",
 749                                 "Heterospathe sphaerocarpa Burret",
 750                                 "Heterospathe trispatha Fernando",
 751                                 "Heterospathe uniformis Dowe",
 752                                 "Heterospathe versteegiana Becc.",
 753                                 "Heterospathe woodfordiana Becc." };
 754
 755                 BotanicalName genusName = BotanicalName
 756                                 .PARSED_NAME("Heterospathe Scheff.");
 757
 758                 Taxon genusTaxon = Taxon.NewInstance(genusName, CdmUtil
 759                                 .getSessionDefaultSec());
 760
 761                 for (String child : children) {
 762                         BotanicalName speciesName = BotanicalName.PARSED_NAME(child);
 763
 764                         Taxon childTaxon = Taxon.NewInstance(speciesName, CdmUtil
 765                                         .getSessionDefaultSec());
 766                         childTaxon.setTaxonomicParent(genusTaxon, null, null);
 767
 768                         if (child.equals("Heterospathe elegans (Becc.) Becc.")) {
 769                                 BotanicalName basionym = BotanicalName
 770                                                 .PARSED_NAME("Barkerwebbia elegans Becc.");
 771                                 speciesName.addRelationshipFromName(basionym,
 772                                                 NameRelationshipType.BASIONYM(), null);
 773                                 childTaxon.addHomotypicSynonymName(basionym, null, null);
 774                         }
 775
 776                         if (child.equals("Heterospathe humilis Becc.")) {
 777                                 BotanicalName synonymName = BotanicalName
 778                                                 .PARSED_NAME("Barkerwebbia humilis (Becc.) Becc. ex Martelli");
 779                                 childTaxon.addHomotypicSynonymName(synonymName, null, null);
 780                         }
 781                 }
 782
 783                 return genusTaxon;
 784         }
 785 }