/ - Diff - EDIT - EDIT Project Management

src/main/java/eu/etaxonomy/cdm/i18n/Messages.java
14	14	import com.vaadin.server.VaadinSession;
15	15
16	16	/**
	17	* Internationalization class.
17	18	* @author freimeier
18	19	*
19	20	*/

     /**
+     *
      * @author pplitzner
      * A Configuration window for choosing distribution areas and taxa to work with.
+     *
      */
     public class AreaAndTaxonSettingsConfigWindow
                 extends SettingsDialogWindowBase<AreaAndTaxonSettingsPresenter>
                 implements ValueChangeListener, ClickListener, ExpandListener{
     	/**
+    	 *
     	 */
         private static final long serialVersionUID = 1439411115014088780L;
         private ComboBox classificationBox;
         private TextField taxonFilter;
-...
             super();
             this.distributionTableView = distributionTableView;
+        }
         /**
+         *
          * {@inheritDoc}
          */
         @Override
         protected void init() {
             //init classification
-...
             updateButtons();
+        }
         /**
+         *
          * {@inheritDoc}
          */
         @Override
         protected AbstractLayout buildMainLayout() {
-...
             return leftAndRightContainer;
+        }
         /**
+         *
          * {@inheritDoc}
          */
         @Override
         public void valueChange(ValueChangeEvent event) {
             Property<?> property = event.getProperty();
-...
             updateButtons();
+        }
         /**
+         *
          * {@inheritDoc}
          */
         @Override
         protected boolean isValid() {
             return classificationBox.getValue()!=null && distAreaBox.getValue()!=null;
+        }
         /**
+         *
          * {@inheritDoc}
          */
         @Override
         public void buttonClick(ClickEvent event) {
             Object source = event.getSource();
-...
+            }
+        }
         /**
+         *
          * {@inheritDoc}
          */
         @Override
         public void nodeExpand(ExpandEvent event) {
             UuidAndTitleCache<TaxonNode> parent = (UuidAndTitleCache<TaxonNode>) event.getItemId();
             ((TaxonNodeContainer) taxonTree.getContainerDataSource()).addChildItems(parent);
+        }
         /**
          * Starts a {@link TreeUpdater} thread to populate the {@link #taxonTree} with taxa of the classification specified by the given {@code rootNode}.
          * @param rootNode The root node of the classification whose taxa should be shown in the {@link #taxonTree}.
          */
         private void showClassificationTaxa(TaxonNode rootNode) {
             final Collection<UuidAndTitleCache<TaxonNode>> children = CdmSpringContextHelper.getTaxonNodeService().listChildNodesAsUuidAndTitleCache(rootNode);
             // Enable polling and set frequency to 0.5 seconds
-...
             taxonTree.setEnabled(false);
             taxonTree.removeAllItems();
             Notification.show(Messages.getLocalizedString(Messages.AreaAndTaxonSettingsConfigWindow_LOADING_TAXA));
             new TreeUpdater(children).start();
+        }
         /**
          * Returns the {@link UuidAndTitleCache} object of the classification specified by the given {@link RowId} of the {@link CdmSQLContainer} used in the {@link #classificationBox}.
          * @param classificationSelection
          * @return {@link UuidAndTitleCache} object of the given classification specified by {@code classificationSelection}
          */
         private UuidAndTitleCache<TaxonNode> getUuidAndTitleCacheFromRowId(Object classificationSelection) {
             String uuidString = (String) classificationBox.getContainerProperty(classificationSelection, "uuid").getValue(); //$NON-NLS-1$
             Property<Integer> rootNodeContainerProperty = null;
-...
             return new AreaAndTaxonSettingsPresenter();
+        }
         /**
          * Thread to populate {@link AreaAndTaxonSettingsConfigWindow#taxonTree}.
+         *
          */
         private class TreeUpdater extends Thread{
         	/**
         	 * The taxa to show.
         	 */
         	private Collection<UuidAndTitleCache<TaxonNode>> children;
         	/**
         	 * Creates a thread to show the given collection of taxa in {@link AreaAndTaxonSettingsConfigWindow#taxonTree}.
         	 * @param children {@link UuidAndTitleCache} of the taxa to show.
         	 */
     		public TreeUpdater(Collection<UuidAndTitleCache<TaxonNode>> children) {
     			this.children = children;
+    		}
     		/**
+    		 *
     		 * {@inheritDoc}
     		 */
     		@Override
         	public void run() {
     			UI.getCurrent().access(new Runnable() {
     				/**
+    				 *
     				 * {@inheritDoc}
     				 */
     				@Override
     				public void run() {
     					taxonTree.setContainerDataSource(new TaxonNodeContainer(children));

     import eu.etaxonomy.cdm.model.description.TextData;
     import eu.etaxonomy.cdm.model.taxon.Taxon;
     /**
      * A window to display details of a taxon.
+     *
      */
     @Scope("prototype")
     public class DetailWindow extends CustomComponent{
-...
     	private final Collection<DescriptionElementBase> listDescriptions;
     	private final Taxon taxon;
     	/**
     	 * Displays a window showing the given details of the given taxon.
     	 * @param taxon The taxon the details belong to.
     	 * @param listDescriptions The details to show.
     	 */
     	public DetailWindow(Taxon taxon, Collection<DescriptionElementBase> listDescriptions) {
     		this.taxon = taxon;
     		this.listDescriptions = listDescriptions;
+    	}
     	/**
     	 * Creates the detail window.
     	 * @return Window to be displayed.
     	 */
     	public Window createWindow(){
     		Window window = new Window();
     		window.setHeightUndefined();
-...
     			window.setContent(new Label(Messages.getLocalizedString(Messages.DetailWindow_NO_DESCRIPTIVE_DATA_FOUND)));
+    		}
     		else{
     			window.setContent(constructDescriptionTree(taxon));
     			window.setContent(constructDescriptionTree());
+    		}
     		return window;
+    	}
     	private Tree constructDescriptionTree(Taxon taxon){
     	/**
     	 * Creates a tree view of the details contained in {@link #listDescriptions}.
     	 * @return Tree of details contained in {@link #listDescriptions}.
     	 */
     	private Tree constructDescriptionTree(){
     		Tree tree = new Tree();
     		tree.setSizeUndefined();
     		String parent = "Descriptive Data"; //$NON-NLS-1$
-...
     		return tree;
+    	}
     	/**
     	 * Populates a given {@link Tree} with the details contained in {@code listDescriptions} and sets its root to {@code parent}.
     	 * @param tree The tree to populate.
     	 * @param listDescriptions The details to show.
     	 * @param parent The root of the tree.
     	 */
     	private void initDescriptionTree(Tree tree, Collection<DescriptionElementBase>listDescriptions, Object parent) {
     		//TODO: sorting List
     		for (DescriptionElementBase deb : listDescriptions){

     import eu.etaxonomy.cdm.vaadin.view.distributionStatus.settings.DistributionStatusSettingsPresenter;
     /**
      *A configuration window to set the available distribution status and toggle the usage of
      *abbreviated labels.
      * @author alex
      * @since 22.04.2015
+     *
-...
         	this.distributionTableView = distributionTableView;
+        }
         /**
+         *
          * {@inheritDoc}
          */
         @Override
         protected void init() {
             boxToggleAbbreviatedLabels.addValueChangeListener(this);
-...
             updateButtons();
+        }
         /**
+         *
          * {@inheritDoc}
          */
         @Override
         protected AbstractLayout buildMainLayout() {
-...
             return mainLayout;
+        }
         /**
+         *
          * {@inheritDoc}
          */
         @Override
         protected boolean isValid() {
         	return true;
+        }
         /**
+         *
          * {@inheritDoc}
          */
     	@Override
     	public void valueChange(ValueChangeEvent event) {
     		Property<?> property = event.getProperty();
-...
+    		}
+    	}
     	/**
+    	 *
     	 * {@inheritDoc}
     	 */
     	@Override
     	public void buttonClick(ClickEvent event) {
     		Object source = event.getSource();

     import eu.etaxonomy.vaadin.ui.navigation.NavigationEvent;
     import eu.etaxonomy.vaadin.ui.navigation.NavigationManager;
     /**
      * A toolbar for the distribution app. Displayed at the top of the screen.
      */
     @SpringComponent("distributionToolbar")
     @ViewScope
     public class DistributionToolbar extends HorizontalLayout implements Serializable{
-...
     //	private final Authentication authentication;
     //	private ExcelExporter exporter = new ExcelExporter();
     	/**
     	 * Constructs the toolbar.
     	 */
     	@PostConstruct
         public void init() {
     		setMargin(true);
-...
     		updateAuthenticationButtons();
+        }
     	/**
     	 * Called when authentication was successful. Updates the user menu buttons.
     	 * @param event
     	 */
     	@EventBusListenerMethod
         public void onAuthenticationSuccessEvent(org.vaadin.spring.events.Event<AuthenticationSuccessEvent> event){
             boolean isInitialized = userButton != null;
-...
+            }
+        }
         /**
          * @param event
          */
     	/**
     	 * Updates the user menu buttons on login and logout.
     	 */
         protected void updateAuthenticationButtons() {
             if(userHelper.userIsAutheticated() && !userHelper.userIsAnnonymous()){
                 userButton.setCaption(userHelper.userName());
-...
             uiEventBus.publish(this, new NavigationEvent("login", navigationManager.getCurrentViewName())); //$NON-NLS-1$
+        }
         /**
          * Logs the user out and closes the session.
          */
         private void performLogout() {
             userHelper.logout();
             updateAuthenticationButtons();
             navigationManager.reloadCurrentView();
+        }
         /**
          * The settings button.
          * @return
          */
         public Button getSettingsButton(){
             return settingsButton;
+        }
         /**
          * Button to open the {@link DistributionStatusSettingsConfigWindow}.
          * @return Button to display the {@link DistributionStatusSettingsConfigWindow}.
          */
         public Button getDistributionSettingsButton() {
     		return distributionSettingsButton;
+    	}
         /**
          * Unused.
          * @return
          */
     	public Button getEditButton() {
     		return editButton;
+    	}
     	/**
     	 * Unused.
     	 * @return
     	 */
     	public Button getSaveButton() {
     		return saveButton;
+    	}
     	/**
     	 * Button to open the {@link DetailWindow}.
     	 * @return  Button to open the {@link DetailWindow}.
     	 */
     	public Button getDetailButton() {
     		return detailButton;
+    	}
        public Button getHelpButton() {
             return helpButton;
+        }
     	/**
     	 * Button to open the {@link HelpWindow}.
     	 * @return Button to open the {@link HelpWindow}.
     	 */
     	public Button getHelpButton() {
     		return helpButton;
+    	}
+    }

     import eu.etaxonomy.cdm.vaadin.view.distributionStatus.IDistributionTableView;
     /**
      * A help window to display useful information on the usage of the distribution editor.
      * @author freimeier
      * @since 9 Mar 2018
+     *
-...
         private AbstractOrderedLayout mainLayout;
         private IDistributionTableView view;
         /**
          * Creates a new help window.
          * @param view The view the help window is related to.
          */
         public HelpWindow(IDistributionTableView view) {
             this.view = view;
             buildMainLayout();
+        }
         /**
          * Builds the layout of the help window and populates it with content.
          * @return Layout of the help window.
          */
         private AbstractLayout buildMainLayout() {
             mainLayout = new VerticalLayout();
             mainLayout.setSizeFull();
-...
             return mainLayout;
+        }
         /**
          * Creates the help window to display.
          * @param caption The caption of the window.
          * @return Help window to be displayed.
          */
         public Window createWindow(String caption) {
             window = new Window();
             window.setModal(true);

     import eu.etaxonomy.cdm.i18n.Messages;
     import eu.etaxonomy.cdm.vaadin.view.distributionStatus.settings.SettingsPresenterBase;
     /**
      * A base class for setting dialog windows.
+     *
      * @author fabreim
      * @since May 17, 2018
+     *
      * @param <P> The SettingsPresenterBase the SettingsDialog is used for.
      */
     @SuppressWarnings("serial")
     public abstract class SettingsDialogWindowBase<P extends SettingsPresenterBase> extends CustomComponent {
-...
             init();
+    	}
     	/**
     	 * Returns the presenter the settings window belongs to.
     	 * @return The presenter the settings window belongs to.
     	 */
         protected abstract P getPresenter();
         /**
          * Builds the layout of the settings window.
          * @return Layout of the settings window.
          */
         protected abstract AbstractLayout buildMainLayout();
         /**
          * Initializes the settings window and populates it with content.
          */
     	protected abstract void init();
     	protected HorizontalLayout createOkCancelButtons() {
-...
     		return buttonToolBar;
+    	}
     	/**
     	 * Creates the settings window and sets its caption.
     	 * @param caption The caption of the window.
     	 * @return The settings window to be displayed.
     	 */
     	public Window createWindow(String caption) {
     	    window = new Window();
     	    window.setModal(true);

     import eu.etaxonomy.cdm.model.common.TermVocabulary;
     import eu.etaxonomy.cdm.model.location.NamedArea;
     /**
      * A container containing the {@link NamedArea}s of a specified {@link TermVocabulary}.
      * @author fabreim
      * @since May 17, 2018
      */
     public class NamedAreaContainer extends BeanItemContainer<NamedArea> {
         private static final long serialVersionUID = 9150424479597481361L;
         /**
          * Creates a NamedAreaContainer containing all {@link NamedArea}s of the given {@code vocabulary}
          * in alphabetically ascending order.
          * @param vocabulary The vocabulary containing the {@link NamedArea}s to populate the container with.
          * @throws IllegalArgumentException
          */
     	public NamedAreaContainer(TermVocabulary<NamedArea> vocabulary)
     	        throws IllegalArgumentException {
     	    super(NamedArea.class);
-...
+    	    }
+    	}
     	/**
     	 * Comparator to sort the {@link NamedArea}s contained in {@link NamedAreaContainer}s.
+    	 *
     	 */
     	private class AlphabeticallyAscendingNamedAreaComparator implements Comparator<NamedArea>{
     		/**
+    		 *
     		 * {@inheritDoc}
     		 */
             @Override
             public int compare(NamedArea o1, NamedArea o2) {
                 return o2.compareTo(o1);

     	private static Collection<PresenceAbsenceTerm> defaultDistributionStatus;
     	/**
     	 * A comparator to sort {@link PresenceAbsenceTerm}s contained in {@link PresenceAbsenceTermContainer}s.
+    	 *
     	 */
         static class PresenceAbsenceTermComparator implements Comparator<PresenceAbsenceTerm> {
             @Override
             public int compare(PresenceAbsenceTerm pa1, PresenceAbsenceTerm pa2) {
-...
+        }
         /**
          * Creates and initializes a new {@link PresenceAbsenceTermContainer}.
          * @throws IllegalArgumentException
          */
     	private PresenceAbsenceTermContainer()
     			throws IllegalArgumentException {
     		super(PresenceAbsenceTerm.class);
     		initDataModel();
+    	}
     	/**
     	 * Initializes the data model of the container and adds all allowed {@link PresenceAbsenceTerm}s to the bean.
     	 */
         private void initDataModel() {
             Collection<PresenceAbsenceTerm> distributionStatus = getDistributionStatusList(TERMS_INIT_STRATEGY);
             defaultDistributionStatus = distributionStatus;
     		addAll(distributionStatus);
+        }
         /**
          * Gets an existing instance of the {@link PresenceAbsenceTermContainer} or creates a new one.
          * @return Instance of {@link PresenceAbsenceTermContainer}.
          */
     	public static PresenceAbsenceTermContainer getInstance(){
     	    if(instance == null){
     	        instance = new PresenceAbsenceTermContainer();
-...
     	    return instance;
+    	}
     	/**
     	 * Returns a list of all allowed {@link PresenceAbsenceTerm}s.
     	 * @param propertyPath The property path to use for calling {@link CdmSpringContextHelper} functions to load {@link PresenceAbsenceTerm}s.
     	 * @return List of all allowed {@link PresenceAbsenceTerm}s.
     	 */
         public static List<PresenceAbsenceTerm> getDistributionStatusList(List<String> propertyPath){
             CdmPreference statusPref = CdmSpringContextHelper.getPreferenceService().findVaadin(PreferencePredicate.AvailableDistributionStatus);
             List<PresenceAbsenceTerm> paList;

         @Autowired
         NavigationManagerBean navigator;
         /**
          * Sets the access AcessDeniedView for the UI.
          */
         protected void configureAccessDeniedView() {
             viewProvider.setAccessDeniedViewClass(RedirectToLoginView.class);
+        }
         /**
          * @return
          * Returns the state of the UI.
          * @return State of the UI.
          */
         private String pageFragmentAsState() {
             Page page = Page.getCurrent();
-...
         @Autowired
         UIEventBus uiEventBus;
         /**
          * Creates a new DistributionStatusUI.
          */
         public DistributionStatusUI() {
+        }
         /**
+         *
          * {@inheritDoc}
          */
     	@Override
     	protected void init(VaadinRequest request) {

     import eu.etaxonomy.cdm.model.common.TermVocabulary;
     import eu.etaxonomy.cdm.model.location.NamedArea;
     import eu.etaxonomy.cdm.model.taxon.Classification;
     import eu.etaxonomy.cdm.model.taxon.TaxonNode;
     import eu.etaxonomy.cdm.vaadin.view.distributionStatus.IDistributionTableView;
     /**
      * A utility class for the distribution status editor.
+     *
      */
     public class DistributionEditorUtil {
     	public static final String VIEW_TABLE = "table";
-...
         public static final String SEPARATOR = ";;";
         /**
          * Updates the vaadin session attributes related to the chosen
          * {@link TaxonNode}s, {@link NamedArea}s and {@link Classification}
          * and refreshes the given {@code distributionStatusTableView}.
          * @param distributionTableView The view to refresh after updating the session variables.
          * @param taxonNodes The taxa to be shown in the {@code distributionTableView}.
          * @param areaVoc The {@link TermVocabulary} of {@link NamedArea}s to be used.
          * @param selectedAreas The {@link NamedArea}s to be availbale in the {@code distributionTableView}.
          * @param classificationUuid The {@link UUID} of the {@link Classification} the {@code taxonNodes} belong to.
          */
         public static void updateDistributionView(IDistributionTableView distributionTableView, List<UUID> taxonNodes, TermVocabulary<NamedArea> areaVoc,
                 List<NamedArea> selectedAreas, UUID classificationUuid) {
     	    VaadinSession.getCurrent().setAttribute(SATTR_TAXON_NODES_UUID, taxonNodes);
-...
     	    distributionTableView.update();
+    	}
         /**
          * Clears the session attributes related to the chosen
          * {@link TaxonNode}s, {@link TermVocabulary} of {@link NamedArea}s,
          * {@link NamedArea}s and {@link Classification}.
          */
         public static void clearSessionAttributes(){
         	VaadinSession.getCurrent().setAttribute(SATTR_TAXON_NODES_UUID, null);
         	VaadinSession.getCurrent().setAttribute(SATTR_SELECTED_AREA_VOCABULARY_UUID, null);
-...
         	VaadinSession.getCurrent().setAttribute(SATTR_CLASSIFICATION, null);
+        }
         /**
          * Returns {@code true} if abbreviated labels should be used.
          * @return {@code true} if abbreviated labels should be used.
          */
         public static boolean isAbbreviatedLabels(){
         	Object isAbbreviated = VaadinSession.getCurrent().getAttribute(DistributionEditorUtil.SATTR_ABBREVIATED_LABELS);
     		return (isAbbreviated==null || (boolean) isAbbreviated);
+        }
         /**
          * Shows an {@link SQLException} to the user.
          * @param e The exception to show.
          */
     	public static void showSqlError(SQLException e) {
     		Notification.show("Error while accessing data base.","Cause: "+e.getMessage(), Type.ERROR_MESSAGE);
     		e.printStackTrace();

     import java.util.UUID;
     import org.springframework.transaction.TransactionStatus;
     import org.vaadin.addons.lazyquerycontainer.LazyQueryContainer;
     import org.vaadin.addons.lazyquerycontainer.Query;
     import org.vaadin.addons.lazyquerycontainer.QueryDefinition;
-...
     import eu.etaxonomy.cdm.model.taxon.TaxonNode;
     /**
      * A {@link Query} for populating a {@link LazyQueryContainer} with distribution status data.
      * Currently unused.
+     *
      * @author freimeier
      * @since 16.11.2017
+     *
      */
     public class DistributionStatusQuery implements Query{
         public static final String DTYPE_COLUMN = "DTYPE";
         public static final String ID_COLUMN = "id";
-...
         private List<UUID> nodeUuids;
         private List<NamedArea> namedAreas;
         /**
          * Creates a new DistributionStatusQuery which will return distribution status information
          * found in the specified {@link CdmRepository} for the {@link TaxonNode}s given by {@code nodeUuids} and the specified {@link NamedArea}s.
          * @param repo The repo to search for information.
          * @param nodeUuids The {@link UUID}s of {@link TaxonNode}s to search information for.
          * @param namedAreas The list of {@link NamedArea}s the distribution information should be related to.
          * @param definition The query definition to be used.
          */
         public DistributionStatusQuery(CdmRepository repo, List<UUID> nodeUuids, List<NamedArea> namedAreas, QueryDefinition definition) {
             this.repo = repo;
             this.nodeUuids = nodeUuids;
-...
             this.definition = definition;
+        }
         /* (non-Javadoc)
          * @see org.vaadin.addons.lazyquerycontainer.Query#constructItem()
         /**
+         *
          * {@inheritDoc}
          */
         @Override
         public Item constructItem() {
             return null;
+        }
         /* (non-Javadoc)
          * @see org.vaadin.addons.lazyquerycontainer.Query#deleteAllItems()
          */
        /**
+        *
         * {@inheritDoc}
         */
         @Override
         public boolean deleteAllItems() {
             return false;
+        }
         /* (non-Javadoc)
          * @see org.vaadin.addons.lazyquerycontainer.Query#loadItems(int, int)
          */
     	/**
+    	 *
     	 * {@inheritDoc}
     	 */
         @Override
         public List<Item> loadItems(int startIndex, int count) {
             List<Item> items = new ArrayList<>();
-...
             return items;
+        }
         /* (non-Javadoc)
          * @see org.vaadin.addons.lazyquerycontainer.Query#saveItems(java.util.List, java.util.List, java.util.List)
         /**
+         *
          * {@inheritDoc}
          */
         @Override
         public void saveItems(List<Item> addedItems, List<Item> modifiedItems, List<Item> removedItems) {
-...
+            }
+        }
         /* (non-Javadoc)
          * @see org.vaadin.addons.lazyquerycontainer.Query#size()
         /**
+         *
          * {@inheritDoc}
          */
         @Override
         public int size() {
             return this.nodeUuids.size();
+        }
         /**
          * Returns a map which maps {@link NamedArea}s to the related distribution status for the given {@code taxon}.
          * @param taxon The taxon the map should contain information for.
          * @return Map of {@link NamedArea}s and the related distribution status for the given {@code taxon}.
          */
         private Map<NamedArea, PresenceAbsenceTerm> getAreaToDistributionStatusMap(Taxon taxon) {
             Map<NamedArea, PresenceAbsenceTerm> distributionStatusMap = new HashMap<>();
-...
             return distributionStatusMap;
+        }
         /**
          * Updates the given taxon with the distribution information contained in {@code areaToDistributionStatusUuidMap}.
          * @param taxon The taxon to be updated.
          * @param areaToDistributionStatusUuidMap The information to update the taxon with.
          */
         private void updateDistributionStatus(Taxon taxon,  Map<NamedArea, UUID> areaToDistributionStatusUuidMap) {
             CdmRepository repo = this.repo;
             TransactionStatus tx = repo.startTransaction();
-...
             repo.commitTransaction(tx);
+        }
         /**
          * Returns the distribution information of the given {@code taxon}.
          * @param taxon The taxon to get the distribution information of.
          * @return The distribution information of the given {@code taxon}.
          */
         private List<Distribution> getDistributions(Taxon taxon) {
             Set<Feature> setFeature = new HashSet<>(Arrays.asList(Feature.DISTRIBUTION()));
             List<Distribution> listTaxonDescription = CdmSpringContextHelper.getDescriptionService()

     import eu.etaxonomy.cdm.model.location.NamedArea;
     /**
      * The {@link LazyQueryDefinition} to be used by {@link DistributionStatusQuery}.
      * @author freimeier
      * @since 22.11.2017
+     *
-...
         private List<NamedArea> namedAreas;
         /**
          * @param repo
          * @param nodeUuids
          * @param namedAreas
          * @param compositeItems
          * @param batchSize
          * @param idPropertyId
          * Creates a new {@link LazyQueryDefinition} to be used by {@link DistributionStatusQuery}.
          * @param namedAreas The {@link NamedArea}s to get distribution information for.
          * @param compositeItems True if native items should be wrapped to CompositeItems.
          * @param batchSize Value for batch size.
          */
         public DistributionStatusQueryDefinition(List<NamedArea> namedAreas,
                 boolean compositeItems, int batchSize) {

     import eu.etaxonomy.cdm.api.application.CdmRepository;
     import eu.etaxonomy.cdm.model.location.NamedArea;
     import eu.etaxonomy.cdm.model.taxon.TaxonNode;
     /**
      * The {@link QueryFactory} to generate {@link DistributionStatusQuery}.
      * @author freimeier
      * @since 16.11.2017
+     *
      */
     public class DistributionStatusQueryFactory implements QueryFactory{
         CdmRepository repo;
         List<UUID> nodeUuids;
         List<NamedArea> namedAreas;
         /**
          * Creates a new DistributionStatusQueryFactory which generates {@link DistributionStatusQuery}
          * which return distribution status information found in the specified {@link CdmRepository}
          * for the {@link TaxonNode}s given by {@code nodeUuids} and the specified {@link NamedArea}s.
          * @param repo The repo to search for information.
          * @param nodeUuids The {@link UUID}s of {@link TaxonNode}s to search information for.
          * @param namedAreas The list of {@link NamedArea}s the distribution information should be related to.
          */
         public DistributionStatusQueryFactory(CdmRepository repo, List<UUID> nodeUuids, List<NamedArea> namedAreas) {
             this.repo = repo;
             this.nodeUuids = nodeUuids;
             this.namedAreas = namedAreas;
+        }
         /* (non-Javadoc)
          * @see org.vaadin.addons.lazyquerycontainer.QueryFactory#constructQuery(org.vaadin.addons.lazyquerycontainer.QueryDefinition)
         /**
+         *
          * {@inheritDoc}
          */
         @Override
         public Query constructQuery(QueryDefinition definition) {

     import eu.etaxonomy.vaadin.mvp.AbstractPresenter;
     /**
      * @author freimeier
      * @since 18.10.2017
+     *
      * The presenter of the distribution status editor.
+     *
      */
     @SpringComponent
     @ViewScope
-...
             // no point subscribing
+        }
         /**
          * Changes the distribution status of the given {@link Taxon} for the given {@link NamedArea} to the sepcified {@link PresenceAbsenceTerm}.
          * @param area The area to update the distribution status for.
          * @param distributionStatus The distribution status to update the taxon with.
          * @param taxon The taxon to be updated.
          * @return
          * {@code 0} if the update was successful.
          * {@code 1} if the distributionStatus was null and the {@link DescriptionElementBase} was deleted successfully.
          * {@code -1} if an error occurred.
          */
         public int updateDistributionField(NamedArea area, PresenceAbsenceTerm distributionStatus, Taxon taxon) {
     	    TransactionStatus tx = repo.startTransaction();
     	    taxon = (Taxon)repo.getTaxonService().find(taxon.getUuid());
-...
     	    return -1;
+    	}
         /**
          * Returns a {@link CdmSQLContainer} containing the distribution status information
          * for the chosen {@link TaxonNode}s and {@link NamedArea}s.
          * @return  {@link CdmSQLContainer} containing the distribution status information
          *  for the chosen {@link TaxonNode}s and {@link NamedArea}s.
          * @throws SQLException
          */
         public CdmSQLContainer getSQLContainer() throws SQLException{
              List<Integer> nodeIds = new ArrayList<>();
              for (TaxonNode taxonNode : getAllNodes()) {
-...
              return null;
+        }
         /**
          * Returns a {@link PresenceAbsenceTermContainer} containing all allowed and chosen {@link PresenceAbsenceTerm}s.
          * @return {@link PresenceAbsenceTermContainer} containing all allowed and chosen {@link PresenceAbsenceTerm}s.
          */
         public PresenceAbsenceTermContainer getPresenceAbsenceTermContainer() {
             return PresenceAbsenceTermContainer.getInstance();
+        }
         /**
          * Returns a list of {@link DescriptionElementBase}s for the specified {@link Taxon} and {@link Feature} set.
          * @param taxon The {@link Taxon} to get the descriptions for.
          * @param setFeature The features to get the descriptions for.
          * @return List of {@link DescriptionElementBase}s for the specified {@link Taxon} and {@link Feature} set.
          */
         public List<DescriptionElementBase> listDescriptionElementsForTaxon(Taxon taxon, Set<Feature> setFeature){
             List<DescriptionElementBase> listDescriptionElementsForTaxon = CdmSpringContextHelper.getDescriptionService().listDescriptionElementsForTaxon(taxon, setFeature, null, null, null, DESCRIPTION_INIT_STRATEGY);
             sort(listDescriptionElementsForTaxon);
             return listDescriptionElementsForTaxon;
+        }
         /**
          * Returns the list of {@link NamedArea}s for which the distribution status can't be updated.
          * @return List of {@link NamedArea}s for which the distribution status can't be updated.
          */
         public List<NamedArea> getReadOnlyAreas(){
             List<NamedArea> readonly = new ArrayList<>();
             // TODO: HACK FOR RL 2017: Remove as soon as possible by receiving read only areas from cdm preferences
-...
             return readonly;
+        }
         /**
          * Returns the {@link NamedArea} referred to by the given {@code areaString}.
          * @param areaString An string referring to a {@link NamedArea}.
          * @return The {@link NamedArea} referred to by the given {@code areaString}.
          */
         public NamedArea getAreaFromString(String areaString){
             List<NamedArea> namedAreas = getChosenAreas();
             NamedArea area = null;
-...
             return area;
+        }
         /**
          * Returns the {@link Distribution} of the given {@link Taxon}.
          * @param taxon Taxon to get the {@link Distribution} of.
          * @return {@link Distribution} of the given {@link Taxon}.
          */
         private List<Distribution> getDistributions(Taxon taxon) {
             Set<Feature> setFeature = new HashSet<>(Arrays.asList(Feature.DISTRIBUTION()));
             List<Distribution> listTaxonDescription = CdmSpringContextHelper.getDescriptionService()
-...
+        }
         /**
          * Returns the list of chosen {@link NamedArea}s defined in the
          * related vaadin session attribute {@link DistributionEditorUtil#SATTR_SELECTED_AREAS}.
          * If this vaadin session attribute is not set, all allowed {@link NamedArea}s of the
          * chosen {@link TermVocabulary} defined by the vaadin session attribute
          * {@link DistributionEditorUtil#SATTR_SELECTED_AREA_VOCABULARY_UUID} are returned.
          * @return List of chosen {@link NamedArea}s defined in the
          * related vaadin session attribute {@link DistributionEditorUtil#SATTR_SELECTED_AREAS}.
          * If this vaadin session attribute is not set, all allowed {@link NamedArea}s of the
          * chosen {@link TermVocabulary} defined by the vaadin session attribute
          * {@link DistributionEditorUtil#SATTR_SELECTED_AREA_VOCABULARY_UUID}.
          */
     	private List<NamedArea> getChosenAreas(){
     	    List<NamedArea> namedAreas = (List<NamedArea>)VaadinSession.getCurrent().getAttribute(DistributionEditorUtil.SATTR_SELECTED_AREAS);
     	    if(namedAreas!=null && namedAreas.isEmpty()){
-...
     	    return namedAreas;
+    	}
     	/**
     	 * Returns all {@link NamedArea}s of the {@link TermVocabulary} defined
     	 * by the vaadin session attribute {@link DistributionEditorUtil#SATTR_SELECTED_AREA_VOCABULARY_UUID}
     	 * ordered by labels.
     	 * @return all {@link NamedArea}s of the {@link TermVocabulary} defined
     	 * by the vaadin session attribute {@link DistributionEditorUtil#SATTR_SELECTED_AREA_VOCABULARY_UUID}
     	 * ordered by labels..
     	 */
     	private List<NamedArea> getChosenAreasFromVoc(){
     	    VaadinSession session = VaadinSession.getCurrent();
     	    UUID vocUUID = (UUID) session.getAttribute(DistributionEditorUtil.SATTR_SELECTED_AREA_VOCABULARY_UUID);
-...
+    	}
        private List<TaxonNode> getChosenTaxonNodes() {
             VaadinSession session = VaadinSession.getCurrent();
     	/**
     	 * Returns all {@link TaxonNode}s defined by the
     	 * vaadin session attribute {@link DistributionEditorUtil#SATTR_TAXON_NODES_UUID}.
     	 * If this session attribute is not set, all {@link TaxonNode}s of the chosen
     	 * classification defined by the vaadin session attribute
     	 * {@link DistributionEditorUtil#SATTR_CLASSIFICATION} are returned.
     	 * @return All {@link TaxonNode}s defined by the
     	 * vaadin session attribute {@link DistributionEditorUtil#SATTR_TAXON_NODES_UUID}.
     	 * If this session attribute is not set, all {@link TaxonNode}s of the chosen
     	 * classification defined by the vaadin session attribute
     	 * {@link DistributionEditorUtil#SATTR_CLASSIFICATION}.
     	 */
     	private List<TaxonNode> getChosenTaxonNodes() {
     		VaadinSession session = VaadinSession.getCurrent();
             List<UUID> taxonNodeUUIDs = (List<UUID>) session.getAttribute(DistributionEditorUtil.SATTR_TAXON_NODES_UUID);
             UUID classificationUuid = (UUID)session.getAttribute(DistributionEditorUtil.SATTR_CLASSIFICATION);
             if((taxonNodeUUIDs==null || taxonNodeUUIDs.isEmpty()) && classificationUuid!=null){
-...
             return Collections.emptyList();
+        }
     	/**
     	 * Returns the list of chosen {@link TaxonNode}s returned by {@link #getChosenTaxonNodes()}
     	 * and adds their children to it.
     	 * @return List of chosen {@link TaxonNode}s returned by {@link #getChosenTaxonNodes()}
     	 * and their children.
     	 */
     	private List<TaxonNode> getAllNodes(){
     		List<TaxonNode> allNodes = new ArrayList<>();
-...
     	protected static final List<String> DESCRIPTION_INIT_STRATEGY = Arrays.asList(new String []{
                 "$", //$NON-NLS-1$
                 "elements.*", //$NON-NLS-1$
                 "elements.sources.citation.authorship.$", //$NON-NLS-1$
                 "elements.sources.nameUsedInSource.originalNameString", //$NON-NLS-1$
                 "elements.area.level", //$NON-NLS-1$
                 "elements.modifyingText", //$NON-NLS-1$
                 "elements.states.*", //$NON-NLS-1$
                 "elements.media", //$NON-NLS-1$
                 "elements.multilanguageText", //$NON-NLS-1$
                 "multilanguageText", //$NON-NLS-1$
                 "stateData.$", //$NON-NLS-1$
                 "annotations", //$NON-NLS-1$
                 "markers", //$NON-NLS-1$
                 "sources.citation.authorship", //$NON-NLS-1$
                 "sources.nameUsedInSource", //$NON-NLS-1$
                 "multilanguageText", //$NON-NLS-1$
                 "media", //$NON-NLS-1$
                 "name.$", //$NON-NLS-1$
                 "name.rank", //$NON-NLS-1$
                 "name.status.type", //$NON-NLS-1$
                 "taxon2.name", //$NON-NLS-1$
         });
     "elements.*", //$NON-NLS-1$
     "elements.sources.citation.authorship.$", //$NON-NLS-1$
     "elements.sources.nameUsedInSource.originalNameString", //$NON-NLS-1$
     "elements.area.level", //$NON-NLS-1$
     "elements.modifyingText", //$NON-NLS-1$
     "elements.states.*", //$NON-NLS-1$
     "elements.media", //$NON-NLS-1$
     "elements.multilanguageText", //$NON-NLS-1$
     "multilanguageText", //$NON-NLS-1$
     "stateData.$", //$NON-NLS-1$
     "annotations", //$NON-NLS-1$
     "markers", //$NON-NLS-1$
     "sources.citation.authorship", //$NON-NLS-1$
     "sources.nameUsedInSource", //$NON-NLS-1$
     "multilanguageText", //$NON-NLS-1$
     "media", //$NON-NLS-1$
     "name.$", //$NON-NLS-1$
     "name.rank", //$NON-NLS-1$
     "name.status.type", //$NON-NLS-1$
     "taxon2.name", //$NON-NLS-1$
     });
     	/**Helper Methods*/
     	private void sort(List<DescriptionElementBase> list){
     		Collections.sort(list, new Comparator<DescriptionElementBase>() {
     /**Helper Methods*/
     private void sort(List<DescriptionElementBase> list){
     	Collections.sort(list, new Comparator<DescriptionElementBase>() {
     			@Override
     			public int compare(DescriptionElementBase o1, DescriptionElementBase o2) {
     				String feature1 = o1.getFeature().getTitleCache();
     				String feature2 = o2.getFeature().getTitleCache();
     				if(feature1 !=null && feature2 !=null){
     					return feature1.compareTo(feature2);
     				}else{
     					return 0;
     		@Override
     		public int compare(DescriptionElementBase o1, DescriptionElementBase o2) {
     			String feature1 = o1.getFeature().getTitleCache();
     			String feature2 = o2.getFeature().getTitleCache();
     			if(feature1 !=null && feature2 !=null){
     				return feature1.compareTo(feature2);
     			}else{
     				return 0;
+    				}
+    			}
     		});
+    	}
+    		}
     	});
+    }
     	/**
+    	 *
     	 * {@inheritDoc}
     	 */
     	@Override
     	protected void onPresenterReady() {
     	    /*
              * The area and taxon settings window should only be displayed after login
              * and only when no classification and areas are chosen yet.
              */
     	    VaadinSession vaadinSession = VaadinSession.getCurrent();
     	    if(userHelper.userIsAutheticated()
     	            && !userHelper.userIsAnnonymous()
     	            && (vaadinSession.getAttribute(DistributionEditorUtil.SATTR_CLASSIFICATION) == null
     	            || vaadinSession.getAttribute(DistributionEditorUtil.SATTR_SELECTED_AREA_VOCABULARY_UUID) == null
     	            || vaadinSession.getAttribute(DistributionEditorUtil.SATTR_SELECTED_AREAS) == null)) {
                 getView().openAreaAndTaxonSettings();
+            }
     /**
+     *
      * {@inheritDoc}
      */
     @Override
     protected void onPresenterReady() {
         /*
      * The area and taxon settings window should only be displayed after login
      * and only when no classification and areas are chosen yet.
      */
         VaadinSession vaadinSession = VaadinSession.getCurrent();
         if(userHelper.userIsAutheticated()
                 && !userHelper.userIsAnnonymous()
                 && (vaadinSession.getAttribute(DistributionEditorUtil.SATTR_CLASSIFICATION) == null
                 || vaadinSession.getAttribute(DistributionEditorUtil.SATTR_SELECTED_AREA_VOCABULARY_UUID) == null
                 || vaadinSession.getAttribute(DistributionEditorUtil.SATTR_SELECTED_AREAS) == null)) {
             getView().openAreaAndTaxonSettings();
+        }
+    }
     	/**Unused Methods*/
     	// TODO: Currently unused. Remove?
         private List<String> getAbbreviatedNamedAreas() {
             List<NamedArea> terms = getChosenAreasFromVoc();
             List<String> list = new ArrayList<>();
             for(DefinedTermBase<?> dtb: terms){
                 for(Representation r : dtb.getRepresentations()){
                     list.add(r.getAbbreviatedLabel());
+                }
     /**Unused Methods*/
     // TODO: Currently unused. Remove?
     private List<String> getAbbreviatedNamedAreas() {
         List<NamedArea> terms = getChosenAreasFromVoc();
         List<String> list = new ArrayList<>();
         for(DefinedTermBase<?> dtb: terms){
             for(Representation r : dtb.getRepresentations()){
                 list.add(r.getAbbreviatedLabel());
+            }
             return list;
+        }
         return list;
+    }
         // TODO: Currently unused. Remove?
         private HashMap<DescriptionElementBase, Distribution> getDistribution(DefinedTermBase dt, Taxon taxon) {
             Set<Feature> setFeature = new HashSet<>(Arrays.asList(Feature.DISTRIBUTION()));
             List<DescriptionElementBase> listTaxonDescription = CdmSpringContextHelper.getDescriptionService().listDescriptionElementsForTaxon(taxon, setFeature, null, null, null, DESCRIPTION_INIT_STRATEGY);
             HashMap<DescriptionElementBase, Distribution> map = null;
             for(DescriptionElementBase deb : listTaxonDescription){
                 if(deb instanceof Distribution){
                     Distribution db = (Distribution)deb;
                     String titleCache = dt.getTitleCache();
                     if(db.getArea().getTitleCache().equalsIgnoreCase(titleCache)){
                         map = new HashMap<DescriptionElementBase, Distribution>();
                         map.put(deb, db);
+                    }
     // TODO: Currently unused. Remove?
     private HashMap<DescriptionElementBase, Distribution> getDistribution(DefinedTermBase dt, Taxon taxon) {
         Set<Feature> setFeature = new HashSet<>(Arrays.asList(Feature.DISTRIBUTION()));
         List<DescriptionElementBase> listTaxonDescription = CdmSpringContextHelper.getDescriptionService().listDescriptionElementsForTaxon(taxon, setFeature, null, null, null, DESCRIPTION_INIT_STRATEGY);
         HashMap<DescriptionElementBase, Distribution> map = null;
         for(DescriptionElementBase deb : listTaxonDescription){
             if(deb instanceof Distribution){
                 Distribution db = (Distribution)deb;
                 String titleCache = dt.getTitleCache();
                 if(db.getArea().getTitleCache().equalsIgnoreCase(titleCache)){
                     map = new HashMap<DescriptionElementBase, Distribution>();
                     map.put(deb, db);
+                }
+            }
             return map;
+        }
         return map;
+    }
         public LazyQueryContainer getAreaDistributionStatusContainer() {
             List<UUID> nodeUuids = getAllNodes().stream().map(n -> n.getUuid()).collect(Collectors.toCollection(ArrayList::new));
             List<NamedArea> namedAreas = getChosenAreas();
             if(namedAreas!=null){
                 QueryFactory factory = new DistributionStatusQueryFactory(this.repo, nodeUuids, namedAreas);
                 QueryDefinition defintion = new DistributionStatusQueryDefinition(namedAreas, true, 50);
                 return new LazyQueryContainer(defintion, factory);
+            }
             return null;
     public LazyQueryContainer getAreaDistributionStatusContainer() {
         List<UUID> nodeUuids = getAllNodes().stream().map(n -> n.getUuid()).collect(Collectors.toCollection(ArrayList::new));
         List<NamedArea> namedAreas = getChosenAreas();
         if(namedAreas!=null){
             QueryFactory factory = new DistributionStatusQueryFactory(this.repo, nodeUuids, namedAreas);
             QueryDefinition defintion = new DistributionStatusQueryDefinition(namedAreas, true, 50);
             return new LazyQueryContainer(defintion, factory);
+        }
         return null;
+    }
+    }

     import eu.etaxonomy.cdm.vaadin.view.AbstractPageView;
     /**
      * The main view of the distribution status editor.
+     *
      * @author freimeier
      * @since 18.10.2017
+     *
-...
     	private DistributionStatusSettingsConfigWindow distributionStatusConfigWindow;
     	private HelpWindow helpWindow;
     	/**
     	 * Creates a new distribution status editor view.
     	 */
     	public DistributionTableViewBean() {
     		super();
+    	}
     	/**
     	 * Initializes the layout of the view,
     	 * adds the {@link DistributionToolbar} and
     	 * creates the distribution status table and adds click listener for editing to it.
     	 * @return Layout of the view.
     	 */
     	private AbsoluteLayout initLayout() {
     		AbsoluteLayout mainLayout = new AbsoluteLayout();
     		mainLayout.setImmediate(false);
-...
     //        footerCell.setText(String.format(Messages.DistributionTableViewBean_TOTAL_TAXA, gridcontainer.size()));
+    	}
     	/**
     	 * Adds click listener to the buttons defined in the {@link DistributionToolbar}.
     	 */
     	private void createEditClickListener(){
     		//details
     	    Button detailButton = toolbar.getDetailButton();

     import eu.etaxonomy.vaadin.mvp.ApplicationView;
     /**
+     *
      * Interface for the distribution status editor view.
+     *
      * @author freimeier
      * @since 18.10.2017
+     *

     import com.vaadin.data.fieldgroup.FieldGroup;
     /**
      * Field group that might be used for vaadin grid
      * instantiation of the distribution status editor.
+     *
      * @author freimeier
      * @since 18.10.2017
+     *
-...
         private static final long serialVersionUID = -1666206997756640330L;
         /**
+         *
          * {@inheritDoc}
          */
         @Override
     	public boolean isReadOnly() {
     		return false;
+    	}
         /**
+         *
          * {@inheritDoc}
          */
     	@Override
     	public void commit() {}
+    }

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Revision c226920a

Added by Fabian Reimeier almost 6 years ago