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