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.ArrayList;
  14 import java.util.Collection;
  15 import java.util.HashMap;
  16 import java.util.HashSet;
  17 import java.util.List;
  18 import java.util.Locale;
  19 import java.util.Map;
  20 import java.util.ResourceBundle;
  21 import java.util.Set;
  22 import java.util.UUID;
  23
  24 import org.apache.log4j.Logger;
  25 import org.eclipse.core.databinding.observable.Realm;
  26 import org.eclipse.core.databinding.observable.list.WritableList;
  27 import org.eclipse.core.databinding.observable.set.IObservableSet;
  28 import org.eclipse.core.databinding.observable.set.WritableSet;
  29 import org.eclipse.core.runtime.FileLocator;
  30 import org.eclipse.core.runtime.IPath;
  31 import org.eclipse.core.runtime.Path;
  32 import org.eclipse.jface.databinding.swt.SWTObservables;
  33 import org.eclipse.jface.resource.FontRegistry;
  34 import org.eclipse.jface.resource.ImageDescriptor;
  35 import org.eclipse.jface.resource.ImageRegistry;
  36 import org.eclipse.swt.SWT;
  37 import org.eclipse.swt.graphics.Color;
  38 import org.eclipse.swt.graphics.Font;
  39 import org.eclipse.swt.graphics.FontData;
  40 import org.eclipse.swt.graphics.Image;
  41 import org.eclipse.swt.widgets.Display;
  42 import org.eclipse.swt.widgets.Tree;
  43 import org.eclipse.ui.forms.FormColors;
  44 import org.eclipse.ui.plugin.AbstractUIPlugin;
  45 import org.eclipse.ui.views.properties.PropertySheetPage;
  46 import org.osgi.framework.BundleContext;
  47 import org.springframework.transaction.TransactionStatus;
  48
  49 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  50 import eu.etaxonomy.cdm.api.service.IDescriptionService;
  51 import eu.etaxonomy.cdm.api.service.INameService;
  52 import eu.etaxonomy.cdm.api.service.IReferenceService;
  53 import eu.etaxonomy.cdm.api.service.ITaxonService;
  54 import eu.etaxonomy.cdm.database.CdmDataSource;
  55 import eu.etaxonomy.cdm.database.DataSourceNotFoundException;
  56 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  57 import eu.etaxonomy.cdm.database.ICdmDataSource;
  58 import eu.etaxonomy.cdm.model.agent.Person;
  59 import eu.etaxonomy.cdm.model.common.Language;
  60 import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
  61 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  62 import eu.etaxonomy.cdm.model.common.init.TermNotFoundException;
  63 import eu.etaxonomy.cdm.model.name.BotanicalName;
  64 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
  65 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  66 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  67 import eu.etaxonomy.cdm.model.name.Rank;
  68 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  69 import eu.etaxonomy.cdm.model.taxon.Taxon;
  70 import eu.etaxonomy.taxeditor.model.CdmUtil;
  71 import eu.etaxonomy.taxeditor.navigation.TaxonomicTreeViewer;
  72
  73 /**
  74  * The class controlling the plug-in life cycle.
  75  * </p>
  76  * <ul>
  77  *      <li>Initializes datastore as necessary.</li>
  78  *      <li>Initializes default preferences.</li>
  79  *      <li>Gateway to CDM service layer.</li>
  80  *      <li>Stores taxa for application session.</li>
  81  *      <li>Stores registries for colors, fonts, images.</li>
  82  * </ul>
  83  *
  84  * @author p.ciardelli
  85  * @created 15.05.2008
  86  * @version 1.0
  87  */
  88 public class TaxEditorPlugin extends AbstractUIPlugin {
  89         private static final Logger logger = Logger
  90                         .getLogger(TaxEditorPlugin.class);
  91
  92         /**
  93          * The plug-in ID
  94          */
  95         public static final String PLUGIN_ID = "eu.etaxonomy.taxeditor.plugin";
  96         /**
  97          * The shared instance
  98          */
  99         private static TaxEditorPlugin plugin;
 100
 101 //      private DbSchemaValidation dbSchemaValidation = DbSchemaValidation.VALIDATE;
 102         private DbSchemaValidation dbSchemaValidation = DbSchemaValidation.UPDATE;
 103
 104         /**
 105          * The constructor
 106          */
 107         public TaxEditorPlugin() {
 108 //              logger.fatal("Fatal");
 109 //              logger.error("Error");
 110 //              logger.debug("Debug");
 111 //              logger.info("Info");
 112 //              logger.warn("Warn");
 113 //              logger.trace("Trace");
 114         }
 115
 116         /*
 117          * (non-Javadoc)
 118          *
 119          * @see org.eclipse.ui.plugin.AbstractUIPlugin#start(org.osgi.framework.BundleContext)
 120          */
 121         public void start(BundleContext context) throws Exception {
 122                 super.start(context);
 123                 plugin = this;
 124
 125                 // If the preferences INITIALIZED has not been set, the IF clause
 126                 // will return false, i.e. datastore will be initialized first
 127                 // time the application is run after being installed.
 128                 boolean initialized = false;
 129                 if (getPreferenceStore()
 130                                 .contains(ITaxEditorConstants.INITIALIZED)) {
 131                         initialized = getPreferenceStore().getBoolean(
 132                                         ITaxEditorConstants.INITIALIZED);
 133                 }
 134
 135                 if (!initialized) {
 136
 137                         logger.warn("Initializing datastore");
 138
 139                         dbSchemaValidation = DbSchemaValidation.CREATE;
 140
 141                         if (getPreferenceStore().getBoolean(
 142                                         ITaxEditorConstants.INITIALIZE_W_TESTDATA)) {
 143                                 initDatastore();
 144                                 getPreferenceStore().setValue(
 145                                                 ITaxEditorConstants.INITIALIZE_W_TESTDATA, false);
 146                         }
 147
 148                         getPreferenceStore()
 149                                         .setValue(ITaxEditorConstants.INITIALIZED, true);
 150                 }
 151
 152                 cdmApp = getCdmApp();
 153
 154                 Locale locale = new Locale("en", "", "icbn");
 155                 Locale.setDefault(locale);
 156         }
 157
 158         /*
 159          * (non-Javadoc)
 160          *
 161          * @see org.eclipse.ui.plugin.AbstractUIPlugin#stop(org.osgi.framework.BundleContext)
 162          */
 163         public void stop(BundleContext context) throws Exception {
 164                 commitTransaction();
 165                 plugin = null;
 166                 super.stop(context);
 167
 168                 disposeColors();
 169         }
 170
 171         void initDatastore() {
 172
 173                 boolean useSoraya = true;
 174                 // useSoraya = false;
 175                 Taxon genusTaxon;
 176                 if (useSoraya) {
 177                         genusTaxon = getSorayasGenusTaxon();
 178                 } else {
 179
 180                         BotanicalName botanicalName = BotanicalName.NewInstance(Rank
 181                                         .GENUS());
 182                         botanicalName.setTitleCache("Hieracium L.");
 183                         botanicalName.setGenusOrUninomial("Hieracium");
 184                         botanicalName.setCombinationAuthorTeam(Person.NewInstance());
 185                         botanicalName.getCombinationAuthorTeam()
 186                                         .setNomenclaturalTitle("L.");
 187                         genusTaxon = Taxon.NewInstance(botanicalName, CdmUtil
 188                                         .getSessionDefaultSec());
 189
 190                         BotanicalName botSpecies = BotanicalName
 191                                         .NewInstance(Rank.SPECIES());
 192                         botSpecies.setTitleCache("Hieracium asturianum Pau");
 193                         botSpecies.setGenusOrUninomial("Hieracium");
 194                         botSpecies.setSpecificEpithet("asturianum");
 195                         botSpecies.setCombinationAuthorTeam(Person.NewInstance());
 196                         botSpecies.getCombinationAuthorTeam().setNomenclaturalTitle("Pau");
 197                         Taxon childTaxon = Taxon.NewInstance(botSpecies, null);
 198                         childTaxon.setTaxonomicParent(genusTaxon, null, null);
 199
 200                         BotanicalName botSpecies2 = BotanicalName.NewInstance(Rank
 201                                         .SPECIES());
 202                         botSpecies2.setTitleCache("Hieracium wolffii Zahn");
 203                         botSpecies2.setGenusOrUninomial("Hieracium");
 204                         botSpecies2.setSpecificEpithet("wolffii");
 205                         botSpecies2.setCombinationAuthorTeam(Person.NewInstance());
 206                         botSpecies2.getCombinationAuthorTeam()
 207                                         .setNomenclaturalTitle("Zahn");
 208                         Taxon childTaxon2 = Taxon.NewInstance(botSpecies2, CdmUtil
 209                                         .getSessionDefaultSec());
 210                         // childTaxon2.setName(botSpecies2);
 211                         // childTaxon2.setSec(null);
 212                         childTaxon2.setTaxonomicParent(genusTaxon, null, null);
 213
 214                         // Add some name relations to botSpecies2
 215                         botSpecies2.addRelationshipFromName(botSpecies,
 216                                         NameRelationshipType.BASIONYM(), null);
 217                         botSpecies2.addRelationshipToName(botSpecies, NameRelationshipType
 218                                         .REPLACED_SYNONYM(), null);
 219                         logger.warn("Name relations created");
 220
 221                         // Add name status to botSpecies2
 222                         botSpecies2.addStatus(NomenclaturalStatus
 223                                         .NewInstance(NomenclaturalStatusType.NOVUM()));
 224                         logger.warn("Nom. status created");
 225                 }
 226
 227                 getCdmApp().getTaxonService().saveTaxon(genusTaxon);
 228
 229                 // System.exit(-1);
 230         }
 231
 232         /**
 233          * Returns the shared instance
 234          *
 235          * @return the shared instance
 236          */
 237         public static TaxEditorPlugin getDefault() {
 238                 return plugin;
 239         }
 240
 241         /***************************************************************************
 242          * CDM SERVICES
 243          **************************************************************************/
 244         /**
 245          * All CDM services are called via the application controller
 246          */
 247         private CdmApplicationController cdmApp;
 248         private TransactionStatus txStatus;
 249
 250         public CdmApplicationController getCdmApp() {
 251                 if (cdmApp == null) {
 252                         try {
 253 //                              cdmApp.getDatabaseService().getDatabaseEnum();
 254 //                              cdmApp.getDatabaseService().saveDataSource(strDataSourceName, databaseTypeEnum, server, database, username, password)
 255
 256 //                              // Open ds by string
 257 //                              CdmPersistentDataSource ds = CdmPersistentDataSource.NewInstance(dataSourceName)
 258 //
 259 //                              // Open default instance
 260 //                              CdmPersistentDataSource ds = CdmPersistentDataSource.NewDefaultInstance();
 261 //
 262 //                              CdmPersistentDataSource.getAllDataSources();
 263 //
 264 //                              // Open CdmApp w default DB
 265 //                              CdmApplicationController.NewInstance(dbSchemaValidation);
 266
 267 //                              System.exit(-1);
 268
 269                                 cdmDatasource =
 270                                                 CdmDataSource.NewH2EmbeddedInstance("cdm", "sa", "");
 271 ////                                            CdmDataSource.NewMySqlInstance("192.168.2.10", "cdm_editor_test1", "edit", "wp5");
 272 ////                                            CdmPersistentDataSource.NewLocalHsqlInstance();
 273                                 cdmApp = CdmApplicationController
 274                                                 .NewInstance(cdmDatasource, dbSchemaValidation);
 275
 276 //                              cdmApp = CdmApplicationController.NewInstance(dbSchemaValidation);
 277
 278                                 startTransaction();
 279
 280                                 // cdmApp.commitTransaction((TransactionStatus) txStatus);
 281
 282                         } catch (DataSourceNotFoundException e) {
 283                                 // TODO Auto-generated catch block
 284                                 e.printStackTrace();
 285                         } catch (TermNotFoundException e) {
 286                                 // TODO Auto-generated catch block
 287                                 e.printStackTrace();
 288                         }
 289                 }
 290                 return cdmApp;
 291         }
 292
 293         public void startTransaction() {
 294                 if (cdmApp != null) {
 295                         txStatus = cdmApp.startTransaction();
 296                 }
 297         }
 298
 299         public void commitTransaction() {
 300                 if (txStatus != null) {
 301                         cdmApp.commitTransaction(txStatus);
 302                         txStatus = null;
 303                 }
 304         }
 305
 306         private ITaxonService taxonService;
 307
 308         public ITaxonService getTaxonService() {
 309                 if (taxonService == null) {
 310                         taxonService = getCdmApp().getTaxonService();
 311                 }
 312                 return taxonService;
 313         }
 314
 315         private INameService nameService;
 316
 317         public INameService getNameService() {
 318                 if (nameService == null) {
 319                         nameService = getCdmApp().getNameService();
 320                 }
 321                 return nameService;
 322         }
 323
 324         private IDescriptionService descriptionService;
 325
 326         public IDescriptionService getDescriptionService() {
 327                 if (descriptionService == null) {
 328                         descriptionService = getCdmApp().getDescriptionService();
 329                 }
 330                 return descriptionService;
 331         }
 332
 333         private IReferenceService referenceService;
 334
 335         public IReferenceService getReferenceService() {
 336                 if (referenceService == null) {
 337                         referenceService = getCdmApp().getReferenceService();
 338                 }
 339                 return referenceService;
 340         }
 341
 342         private List<ICdmDataSource> dataSources;
 343
 344         public List<ICdmDataSource> getDataSources() {
 345                 if (dataSources == null) {
 346                         dataSources = new ArrayList<ICdmDataSource>();
 347                         dataSources.add(CdmDataSource.
 348                                         NewH2EmbeddedInstance("cdm", "sa", ""));
 349                         dataSources.add(CdmDataSource.
 350                                         NewMySqlInstance("192.168.2.10", "cdm_editor_test1",
 351                                                         "edit", "wp5"));
 352                 }
 353                 return dataSources;
 354         }
 355
 356         private ICdmDataSource cdmDatasource;
 357
 358         public ICdmDataSource getCdmDataSource() {
 359                 return cdmDatasource;
 360         }
 361
 362         /***************************************************************************
 363          * OBSERVABLE LISTS
 364          **************************************************************************/
 365
 366         private WritableList observableRecentNamesList = null;
 367         private WritableList observableFavoritesList = null;
 368
 369         public WritableList getObservableRecentNamesList() {
 370                 if (observableRecentNamesList == null) {
 371                         observableRecentNamesList = new WritableList();
 372                 }
 373                 return observableRecentNamesList;
 374         }
 375
 376         public WritableList getObservableFavoritesList() {
 377                 if (observableFavoritesList == null) {
 378                         observableFavoritesList = new WritableList();
 379                 }
 380                 return observableFavoritesList;
 381         }
 382
 383         /***************************************************************************
 384          * IMAGE REGISTRY
 385          **************************************************************************/
 386         public ImageDescriptor getImageDescriptor(String key) {
 387                 return getImageRegistry().getDescriptor(key);
 388         }
 389
 390         public Image getImage(String key) {
 391                 return getImageRegistry().get(key);
 392         }
 393
 394         // Resource bundle.
 395         private ResourceBundle resourceBundle;
 396         private FormColors formColors;
 397
 398         protected void initializeImageRegistry(ImageRegistry registry) {
 399                 registerImage(registry, ITaxEditorConstants.EDIT_ICON, "edit_16x16.ico");
 400                 registerImage(registry, ITaxEditorConstants.WARNING_ICON,
 401                                 "warn_tsk.gif");
 402                 registerImage(registry, ITaxEditorConstants.BLACK_SQUARE_ICON,
 403                                 "accepted_small.gif");
 404                 registerImage(registry, ITaxEditorConstants.HOMOTYPIC_SYN_ICON,
 405                                 "homosyn_no_bg.gif");
 406                 registerImage(registry,
 407                                 ITaxEditorConstants.HOMOTYPIC_SYN_ORIGINAL_ICON,
 408                                 "homosyn_original_no_bg.gif");
 409                 registerImage(registry, ITaxEditorConstants.HETEROTYPIC_SYN_ICON,
 410                                 "heterosyn_no_bg.gif");
 411                 registerImage(registry,
 412                                 ITaxEditorConstants.HETEROTYPIC_SYN_ORIGINAL_ICON,
 413                                 "heterosyn_original_no_bg.gif");
 414                 registerImage(registry, ITaxEditorConstants.MISAPPLIED_NAME_ICON,
 415                                 "misapplied_no_bg.gif");
 416                 registerImage(registry, ITaxEditorConstants.AUTONYM_ICON,
 417                                 "autonym_no_bg.gif");
 418                 registerImage(registry, ITaxEditorConstants.BASIONYM_ICON,
 419                                 "basionym_no_bg.gif");
 420                 registerImage(registry, ITaxEditorConstants.ORTHOGRAPHIC_VARIANT_ICON,
 421                                 "orthovariant_no_bg.gif");
 422                 registerImage(registry, ITaxEditorConstants.DB_ICON, "db.gif");
 423                 registerImage(registry, ITaxEditorConstants.MOVE_ICON,
 424                                 "correction_change.gif");
 425                 registerImage(registry, ITaxEditorConstants.ACTIVE_DELETE_ICON,
 426                                 "delete_edit.gif");
 427                 registerImage(registry, ITaxEditorConstants.SYNONYM_TO_TAXON_ICON,
 428                                 "change.gif");
 429                 registerImage(registry, ITaxEditorConstants.OPEN_TAXON_ICON, "open.gif");
 430                 registerImage(registry, ITaxEditorConstants.ADD_CHILD_TAXON_ICON,
 431                                 "new_child.gif");
 432                 registerImage(registry,
 433                                 ITaxEditorConstants.SWAP_SYNONYM_AND_TAXON_ICON, "swap2.gif");
 434                 registerImage(registry, ITaxEditorConstants.QUICK_ADD_ICON,
 435                                 "quick_add.gif");
 436                 registerImage(registry, ITaxEditorConstants.TAXON_TO_SYNONYM_ICON,
 437                                 "tax_to_syn.gif");
 438         }
 439
 440         private void registerImage(ImageRegistry registry, String key,
 441                         String fileName) {
 442                 try {
 443                         IPath path = new Path("icons/" + fileName); //$NON-NLS-1$
 444                         URL url = FileLocator.find(getBundle(), path, null);
 445                         if (url != null) {
 446                                 ImageDescriptor desc = ImageDescriptor.createFromURL(url);
 447                                 registry.put(key, desc);
 448                         }
 449                 } catch (Exception e) {
 450                 }
 451         }
 452
 453         /***************************************************************************
 454          * FONT REGISTRY
 455          **************************************************************************/
 456         private FontRegistry fontRegistry;
 457
 458         private FontRegistry getFontRegistry() {
 459                 if (fontRegistry == null) {
 460                         fontRegistry = new FontRegistry(Display.getCurrent());
 461
 462                         fontRegistry.put(ITaxEditorConstants.DATASOURCE_FONT,
 463                                         new FontData[] { new FontData("Arial", 8, SWT.NONE) });
 464                         fontRegistry.put(ITaxEditorConstants.MENU_ITEM_ITALICS_FONT,
 465                                         new FontData[] { new FontData("Arial", 9, SWT.ITALIC) });
 466                         fontRegistry.put(ITaxEditorConstants.ACCEPTED_TAXON_FONT,
 467                                         new FontData[] { new FontData("Georgia", 12, SWT.NONE) });
 468                         fontRegistry.put(ITaxEditorConstants.SYNONYM_FONT,
 469                                         new FontData[] { new FontData("Georgia", 10, SWT.NONE) });
 470                         fontRegistry.put(ITaxEditorConstants.MISAPPLIEDNAME_FONT,
 471                                         new FontData[] { new FontData("Georgia", 10, SWT.NONE) });
 472                         fontRegistry.put(ITaxEditorConstants.CHOOSE_NAME_TEXT_FONT,
 473                                         new FontData[] { new FontData("Arial", 12, SWT.BOLD) });
 474                         fontRegistry.put(ITaxEditorConstants.DEFAULT_PROMPT_FONT,
 475                                         new FontData[] { new FontData("Georgia", 10, SWT.ITALIC) });
 476                 }
 477                 return fontRegistry;
 478         }
 479
 480         public Font getFont(String key) {
 481                 return getFontRegistry().get(key);
 482         }
 483
 484         /***************************************************************************
 485          * COLOR MAP
 486          **************************************************************************/
 487         private static HashMap<String, Color> colorMap;
 488
 489         public Color getColor(String key) {
 490                 return getColorMap().get(key);
 491         }
 492
 493         private HashMap<String, Color> getColorMap() {
 494                 if (colorMap == null) {
 495                          colorMap = new HashMap<String, Color>();
 496
 497                          colorMap.put(ITaxEditorConstants.GROUP_GRAY_BKG_COLOR,
 498                                          new Color(null, 240, 240, 240));
 499                          colorMap.put(ITaxEditorConstants.PROP_SHEET_RED,
 500                                          new Color(null, 255, 0, 0));
 501                 }
 502                 return colorMap;
 503         }
 504
 505         private void disposeColors() {
 506                 if (colorMap == null) {
 507                         return;
 508                 }
 509         for (Color color : colorMap.values()) {
 510                 color.dispose();
 511         }
 512         colorMap.clear();
 513         }
 514
 515         /***************************************************************************
 516          * TAXONOMIC TREE
 517          **************************************************************************/
 518
 519         public ReferenceBase getSec() {
 520                 return getCdmApp().getReferenceService().getReferenceByUuid(
 521                                 UUID.fromString("f3593c18-a8d2-4e51-bdad-0befbf8fb2d1"));
 522         }
 523
 524         private Set<Taxon> sessionRootTaxa;
 525         /**
 526          * The taxonomic tree content provider observes this set for changes, and
 527          * makes the appropriate changes to the tree.
 528          */
 529         private IObservableSet observableSessionTaxonSet;
 530         /**
 531          * This map of taxa to their taxonomic children is used by
 532          * NameTreeContentProvider's getChildren method.
 533          *
 534          * key = taxon, value = key's child taxa Note that a map can have a key ==
 535          * null, i.e. no parent taxon
 536          */
 537         private HashMap<Taxon, Set<Taxon>> sessionTaxonomicChildrenMap;
 538
 539         public Set<Taxon> getSessionRootTaxa() {
 540                 if (sessionRootTaxa == null) {
 541
 542                         sessionRootTaxa = new HashSet<Taxon>();
 543 //                      sessionRootTaxa.addAll(getCdmApp().getTaxonService().getRootTaxa(
 544 //                                      getSec(), null, false));
 545                         sessionRootTaxa.addAll(getCdmApp().getTaxonService().getRootTaxa(
 546                                         getSec(), null, true));
 547                         addSessionTaxa(sessionRootTaxa);
 548
 549                 }
 550                 return sessionRootTaxa;
 551         }
 552
 553         private Map<Taxon, Set<Taxon>> getTaxonomicChildrenMap() {
 554                 if (sessionTaxonomicChildrenMap == null) {
 555                         sessionTaxonomicChildrenMap = new HashMap<Taxon, Set<Taxon>>();
 556                 }
 557                 return sessionTaxonomicChildrenMap;
 558         }
 559
 560         /**
 561          * Returns a set of any child taxa for this taxon that have already been
 562          * requested during this session.
 563          *
 564          * @param parentTaxon
 565          * @return
 566          */
 567         public Set<Taxon> getSessionTaxonomicChildren(Taxon parentTaxon) {
 568                 if (!getTaxonomicChildrenMap().containsKey(parentTaxon)) {
 569                         if (parentTaxon == null) {
 570                                 getTaxonomicChildrenMap().put(parentTaxon, getSessionRootTaxa());
 571                         } else {
 572
 573                                 // BUG deleted taxon were re-appearing as NULL children
 574                                 Set<Taxon> childTaxa = new HashSet<Taxon>();
 575
 576 //                              TransactionStatus tx = getCdmApp().startTransaction();
 577 //                              getCdmApp().getTaxonService().saveTaxon(parentTaxon);
 578                                 for (Taxon taxon : parentTaxon.getTaxonomicChildren()) {
 579                                         if (taxon != null) {
 580                                                 childTaxa.add(taxon);
 581                                         }
 582                                 }
 583 //                              getCdmApp().commitTransaction(tx);
 584
 585                                 getTaxonomicChildrenMap().put(parentTaxon, childTaxa);
 586                         }
 587                 }
 588                 return getTaxonomicChildrenMap().get(parentTaxon);
 589         }
 590
 591         /**
 592          * @return
 593          */
 594         public IObservableSet getObservableSessionTaxa() {
 595                 if (observableSessionTaxonSet == null) {
 596                         Realm realm = SWTObservables.getRealm(Display.getDefault());
 597                         observableSessionTaxonSet = new WritableSet(realm);
 598                 }
 599                 return observableSessionTaxonSet;
 600         }
 601
 602         /**
 603          * Recursive function to clear the hashmap of a taxon's children used in
 604          * this session, and the childrens' children, etc.
 605          *
 606          * @param taxon
 607          */
 608         private void clearTaxonomicChildren(Taxon taxon) {
 609                 Set<Taxon> children = getSessionTaxonomicChildren(taxon);
 610                 if (children != null) {
 611                         for (Taxon child : children) {
 612                                 clearTaxonomicChildren(child);
 613                         }
 614                         getTaxonomicChildrenMap().remove(taxon);
 615                         getObservableSessionTaxa().removeAll(children);
 616                 }
 617         }
 618
 619         /**
 620          * Remove taxon from all session collections
 621          *
 622          * @param taxon
 623          */
 624         public void removeSessionTaxon(Taxon taxon) {
 625
 626                 // Recursively remove all children, children's children, etc.
 627                 clearTaxonomicChildren(taxon);
 628
 629                 Taxon parentTaxon = taxon.getTaxonomicParent();
 630
 631                 // Remove from parent's child map, or from root taxa
 632                 if (parentTaxon == null) {
 633                         getSessionRootTaxa().remove(taxon);
 634                 } else {
 635                         getSessionTaxonomicChildren(parentTaxon).remove(taxon);
 636                 }
 637
 638                 // Remove from session taxa
 639                 getObservableSessionTaxa().remove(taxon);
 640
 641                 UiUtil.getTreeViewer().remove(taxon);
 642         }
 643
 644         public void addSessionTaxa(Collection<Taxon> taxa) {
 645                 for (Taxon taxon : taxa) {
 646                         addSessionTaxon(taxon);
 647                 }
 648         }
 649
 650         /**
 651          * Whenever a taxon is opened, either for editing or for display in the
 652          * taxonomic tree, it should be added to the collections of taxa used during
 653          * this session.
 654          *
 655          * @param taxon
 656          */
 657         public void addSessionTaxon(Taxon taxon) {
 658
 659                 // Add taxon to session taxa if not already there
 660                 if (!(getObservableSessionTaxa().contains(taxon))) {
 661                         getObservableSessionTaxa().add(taxon);
 662                 }
 663
 664                 Taxon parentTaxon = taxon.getTaxonomicParent();
 665
 666                 // If taxon has no parent, add it to root taxa
 667                 if (parentTaxon == null) {
 668                         if (!(getSessionRootTaxa().contains(taxon))) {
 669                                 getSessionRootTaxa().add(taxon);
 670                         }
 671                 }
 672
 673                 // Add taxon to its parent's child map
 674                 getSessionTaxonomicChildren(parentTaxon).add(taxon);
 675
 676                 TaxonomicTreeViewer viewer = UiUtil.getTreeViewer();
 677
 678                 if (viewer != null) {
 679
 680                         if (parentTaxon == null) {
 681                                 viewer.setInput(getSessionRootTaxa());
 682                         } else {
 683                                 viewer.add(parentTaxon, taxon);
 684                         }
 685
 686                 }
 687         }
 688
 689
 690 //      private TaxonomicTreeView taxonomicTreeView;
 691 //
 692 //      public void setTaxonomicTree(TaxonomicTreeView taxonomicTreeView) {
 693 //              this.taxonomicTreeView = taxonomicTreeView;
 694 //      }
 695
 696         /***************************************************************************
 697          * RANKS
 698          **************************************************************************/
 699         OrderedTermVocabulary<Rank> rankVocabulary = null;
 700
 701         public OrderedTermVocabulary<Rank> getRankVocabulary() {
 702                 if (rankVocabulary == null) {
 703                         rankVocabulary = getCdmApp().getNameService().getRankVocabulary();
 704                 }
 705                 return rankVocabulary;
 706         }
 707
 708         /***************************************************************************
 709          * NOMENCLATURAL STATUS
 710          **************************************************************************/
 711         TermVocabulary<NomenclaturalStatusType> nomStatusVocabulary = null;
 712
 713         public TermVocabulary<NomenclaturalStatusType> getNomStatusVocabulary() {
 714                 if (nomStatusVocabulary == null) {
 715                         nomStatusVocabulary = getCdmApp().getNameService()
 716                                         .getStatusTypeVocabulary();
 717                 }
 718                 return nomStatusVocabulary;
 719         }
 720
 721         /***************************************************************************
 722          * NAME RELATIONS
 723          **************************************************************************/
 724         TermVocabulary<NameRelationshipType> nameRelationshipTypeVocabulary = null;
 725
 726         public TermVocabulary<NameRelationshipType> getNameRelationshipTypeVocabulary() {
 727                 if (nameRelationshipTypeVocabulary == null) {
 728                         nameRelationshipTypeVocabulary = getCdmApp().getNameService()
 729                                         .getNameRelationshipTypeVocabulary();
 730                 }
 731                 return nameRelationshipTypeVocabulary;
 732         }
 733
 734         public Set<NameRelationshipType> getSortedNameRelationshipTypes() {
 735                 return getNameRelationshipTypeVocabulary().getTermsOrderedByLabels(
 736                                 Language.DEFAULT());
 737         }
 738
 739         /***************************************************************************
 740          * SORAYA DATA
 741          **************************************************************************/
 742         private Taxon getSorayasGenusTaxon() {
 743
 744                 String[] children = new String[] {
 745                                 "Heterospathe annectens H.E.Moore",
 746                                 "Heterospathe arfakiana (Becc.) H.E.Moore",
 747                                 "Heterospathe brevicaulis Fernando",
 748                                 "Heterospathe cagayanensis Becc.",
 749                                 "Heterospathe califrons Fernando, Palms 45: 118 (2001).",
 750                                 "Heterospathe clemensiae (Burret) H.E.Moore",
 751                                 "Heterospathe delicatula H.E.Moore",
 752                                 "Heterospathe dransfieldii Fernando",
 753                                 "Heterospathe elata Scheff.",
 754                                 "Heterospathe elata var. elata.",
 755                                 "Heterospathe elata var. guamensis Becc.",
 756                                 "Heterospathe elata var. palauensis (Becc.) Becc.",
 757                                 "Heterospathe elegans (Becc.) Becc.",
 758                                 "Heterospathe elmeri Becc.",
 759                                 "Heterospathe glabra (Burret) H.E.Moore",
 760                                 "Heterospathe glauca (Scheff.) H.E.Moore",
 761                                 "Heterospathe humilis Becc.",
 762                                 "Heterospathe intermedia (Becc.) Fernando",
 763                                 "Heterospathe kajewskii Burret",
 764                                 "Heterospathe ledermanniana Becc.",
 765                                 "Heterospathe lepidota H.E.Moore",
 766                                 "Heterospathe longipes (H.E.Moore) Norup",
 767                                 "Heterospathe macgregorii (Becc.) H.E.Moore",
 768                                 "Heterospathe micrantha (Becc.) H.E.Moore",
 769                                 "Heterospathe minor Burret",
 770                                 "Heterospathe muelleriana (Becc.) Becc.",
 771                                 "Heterospathe negrosensis Becc.",
 772                                 "Heterospathe obriensis (Becc.) H.E.Moore",
 773                                 "Heterospathe palauensis Becc.",
 774                                 "Heterospathe parviflora Essig",
 775                                 "Heterospathe philippinensis (Becc.) Becc.",
 776                                 // "Heterospathe phillipsii D.Fuller & Dowe", // <--------------
 777                                 "Heterospathe pilosa (Burret) Burret",
 778                                 "Heterospathe pisifera (Gaertn.) Burret",
 779                                 "Heterospathe pulchra H.E.Moore",
 780                                 "Heterospathe ramulosa Burret",
 781                                 "Heterospathe salomonensis Becc.",
 782                                 "Heterospathe scitula Fernando", "Heterospathe sensisi Becc.",
 783                                 "Heterospathe sibuyanensis Becc.",
 784                                 "Heterospathe sphaerocarpa Burret",
 785                                 "Heterospathe trispatha Fernando",
 786                                 "Heterospathe uniformis Dowe",
 787                                 "Heterospathe versteegiana Becc.",
 788                                 "Heterospathe woodfordiana Becc." };
 789
 790                 BotanicalName genusName = BotanicalName
 791                                 .PARSED_NAME("Heterospathe Scheff.");
 792
 793                 Taxon genusTaxon = Taxon.NewInstance(genusName, CdmUtil
 794                                 .getSessionDefaultSec());
 795
 796                 for (String child : children) {
 797                         BotanicalName speciesName = BotanicalName.PARSED_NAME(child);
 798
 799                         Taxon childTaxon = Taxon.NewInstance(speciesName, CdmUtil
 800                                         .getSessionDefaultSec());
 801                         childTaxon.setTaxonomicParent(genusTaxon, null, null);
 802
 803                         if (child.equals("Heterospathe elegans (Becc.) Becc.")) {
 804                                 BotanicalName basionym = BotanicalName
 805                                                 .PARSED_NAME("Barkerwebbia elegans Becc.");
 806                                 speciesName.addRelationshipFromName(basionym,
 807                                                 NameRelationshipType.BASIONYM(), null);
 808                                 childTaxon.addHomotypicSynonymName(basionym, null, null);
 809                         }
 810
 811                         if (child.equals("Heterospathe humilis Becc.")) {
 812                                 BotanicalName synonymName = BotanicalName
 813                                                 .PARSED_NAME("Barkerwebbia humilis (Becc.) Becc. ex Martelli");
 814                                 childTaxon.addHomotypicSynonymName(synonymName, null, null);
 815                         }
 816                 }
 817
 818                 return genusTaxon;
 819         }
 820
 821         /***************************************************************************
 822          * PROPERTY SHEET
 823          **************************************************************************/
 824
 825         private Tree propertySheetTree;
 826
 827         public void setPropertySheetTree(Tree tree) {
 828                 this.propertySheetTree = tree;
 829         }
 830
 831         public Tree getPropertySheetTree() {
 832                 return propertySheetTree;
 833         }
 834
 835         private PropertySheetPage propertySheetPage;
 836
 837         public void setPropertySheetPage(PropertySheetPage page) {
 838                 this.propertySheetPage = page;
 839         }
 840
 841         public PropertySheetPage getPropertySheetPage() {
 842                 return propertySheetPage;
 843         }
 844 }