EDIT

package eu.etaxonomy.taxeditor.editor.view.derivate;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.Collection;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.eclipse.core.runtime.IProgressMonitor;

import org.eclipse.jface.action.MenuManager;

import org.eclipse.jface.util.LocalSelectionTransfer;

import org.eclipse.jface.viewers.AbstractTreeViewer;

import org.eclipse.jface.viewers.ISelection;

import org.eclipse.jface.viewers.IStructuredSelection;

import org.eclipse.jface.viewers.StructuredSelection;

import org.eclipse.jface.viewers.TreeNode;

import org.eclipse.jface.viewers.TreeSelection;

import org.eclipse.jface.viewers.TreeViewer;

import org.eclipse.swt.SWT;

import org.eclipse.swt.dnd.DND;

import org.eclipse.swt.dnd.Transfer;

import org.eclipse.swt.layout.GridData;

import org.eclipse.swt.layout.GridLayout;

import org.eclipse.swt.widgets.Composite;

import org.eclipse.swt.widgets.Control;

import org.eclipse.swt.widgets.Display;

import org.eclipse.swt.widgets.Menu;

import org.eclipse.swt.widgets.Tree;

import org.eclipse.ui.IEditorInput;

import org.eclipse.ui.IEditorPart;

import org.eclipse.ui.IEditorSite;

import org.eclipse.ui.IMemento;

import org.eclipse.ui.ISelectionListener;

import org.eclipse.ui.ISelectionService;

import org.eclipse.ui.IWorkbenchPart;

import org.eclipse.ui.PartInitException;

import org.eclipse.ui.part.EditorPart;

import eu.etaxonomy.cdm.api.conversation.ConversationHolder;

import eu.etaxonomy.cdm.api.conversation.IConversationEnabled;

import eu.etaxonomy.cdm.api.service.IOccurrenceService;

import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;

import eu.etaxonomy.cdm.model.common.CdmBase;

import eu.etaxonomy.cdm.model.molecular.SingleRead;

import eu.etaxonomy.cdm.model.occurrence.FieldUnit;

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonNode;

import eu.etaxonomy.cdm.persistence.hibernate.CdmDataChangeMap;

import eu.etaxonomy.taxeditor.editor.EditorUtil;

import eu.etaxonomy.taxeditor.editor.Messages;

import eu.etaxonomy.taxeditor.editor.MultiPageTaxonEditor;

import eu.etaxonomy.taxeditor.editor.view.derivate.searchFilter.DerivateSearchCompositeController;

import eu.etaxonomy.taxeditor.model.IContextListener;

import eu.etaxonomy.taxeditor.model.IDirtyMarkable;

import eu.etaxonomy.taxeditor.model.IPartContentHasDetails;

import eu.etaxonomy.taxeditor.model.IPartContentHasFactualData;

import eu.etaxonomy.taxeditor.model.IPartContentHasMedia;

import eu.etaxonomy.taxeditor.model.IPartContentHasSupplementalData;

import eu.etaxonomy.taxeditor.model.MessagingUtils;

import eu.etaxonomy.taxeditor.operation.IPostOperationEnabled;

import eu.etaxonomy.taxeditor.session.ICdmEntitySession;

import eu.etaxonomy.taxeditor.session.ICdmEntitySessionEnabled;

import eu.etaxonomy.taxeditor.store.CdmStore;

import eu.etaxonomy.taxeditor.view.derivateSearch.DerivateContentProvider;

import eu.etaxonomy.taxeditor.view.derivateSearch.DerivateLabelProvider;

/**

 * Displays the derivate hierarchy of the specimen specified in the editor input.

 *

 */

public class DerivateView extends EditorPart implements IPartContentHasFactualData, IConversationEnabled,

        ICdmEntitySessionEnabled, IDirtyMarkable, IPostOperationEnabled, IPartContentHasDetails, IPartContentHasSupplementalData, IPartContentHasMedia,

        IContextListener, ISelectionListener {

    public static final String ID = "eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView"; //$NON-NLS-1$

    public static final String YOU_NEED_TO_SAVE_BEFORE_PERFORMING_THIS_ACTION = Messages.DerivateView_YOU_NEED_TO_SAVE;

    public static final String VIEW_HAS_UNSAVED_CHANGES = Messages.DerivateView_UNSAVED_CHANGES;

    private static final List<String> SPECIMEN_INIT_STRATEGY = Arrays.asList(new String[] {

            "descriptions",

            "annotations",

            "markers",

            "credits",

            "extensions",

            "rights",

            "sources",

            "derivationEvents.derivatives.annotations",

            "derivationEvents.derivatives.markers",

            "derivationEvents.derivatives.credits",

            "derivationEvents.derivatives.extensions",

            "derivationEvents.derivatives.rights",

            "derivationEvents.derivatives.sources"

    });

	private static final int WARN_THRESHOLD = 200;

    private DelaySelection delaySelection = null;

    /**

     * This is the monitor for the DelaySelection runnable.

     * If it is <code>true</code> then it is currently delaying a selection.

     */

    private boolean isInDelay;

    /**

     * This class invokes internal_selectionChanged() in a separate thread.

     * This allows an asynchronous and/or delayed handling of selection changes

     */

    private class DelaySelection implements Runnable{

        private IWorkbenchPart part;

        private ISelection selection;

        public DelaySelection(IWorkbenchPart part, ISelection selection) {

            super();

            this.part = part;

            this.selection = selection;

        }

        @Override

        public void run() {

            try{

                selectionChanged_internal(part, selection);

            }

            finally{

                isInDelay = false;

            }

        }

        public synchronized void setSelection(ISelection selection) {

            this.selection = selection;

        }

        public synchronized void setPart(IWorkbenchPart part) {

            this.part = part;

        }

    }

	private ConversationHolder conversation;

	private TreeViewer viewer;

    private boolean isDirty;

    private final int dndOperations = DND.DROP_MOVE;

    private DerivateLabelProvider labelProvider;

    private DerivateContentProvider contentProvider;

    private DerivateSearchCompositeController derivateSearchCompositeController;

    /**

     * A map with keys being the derivative entities belonging to the {@link UUID}s passed to the constructor

     * and values being the root elements of the hierarchy (may be the same objects as the derivative entities)

     */

    private Map<SpecimenOrObservationBase<?>, SpecimenOrObservationBase<?>> derivateToRootEntityMap;

    /**

     * The set of root elements

     */

    private Set<SpecimenOrObservationBase<?>> rootElements;

    private ICdmEntitySession cdmEntitySession;

    /**

     * <code>true</code> if this view is listening to selection  changes

     */

    private boolean listenToSelectionChange;

    private Taxon selectedTaxon;

    private ISelectionService selectionService;

    /**

     * Default constructor

     */

    public DerivateView() {

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public void init(IEditorSite site, IEditorInput input) throws PartInitException {

        this.setSite(site);

        this.setInput(input);

        this.derivateToRootEntityMap = new HashMap<SpecimenOrObservationBase<?>, SpecimenOrObservationBase<?>>();

        this.rootElements = new HashSet<SpecimenOrObservationBase<?>>();

        if (CdmStore.isActive() && conversation == null) {

            conversation = CdmStore.createConversation();

        }

        if (CdmStore.isActive()) {

            cdmEntitySession = CdmStore.getCurrentSessionManager().newSession(this, true);

        }

        //listen to context changes

        CdmStore.getContextManager().addContextListener(this);

    }

    @Override

    public void createPartControl(Composite parent) {

        parent.setLayout(new GridLayout());

        //---search and filter---

        derivateSearchCompositeController = new DerivateSearchCompositeController(parent, this);

        GridData gridDataSearchBar = new GridData();

        gridDataSearchBar.horizontalAlignment = GridData.FILL;

        gridDataSearchBar.grabExcessHorizontalSpace = true;

        derivateSearchCompositeController.setLayoutData(gridDataSearchBar);

        derivateSearchCompositeController.setEnabled(CdmStore.isActive());

        //---tree viewer---

        viewer = new TreeViewer(new Tree(parent, SWT.MULTI | SWT.H_SCROLL | SWT.V_SCROLL | SWT.FULL_SELECTION));

        GridData gridDataTree = new GridData();

        gridDataTree.horizontalAlignment = GridData.FILL;

        gridDataTree.verticalAlignment = GridData.FILL;

        gridDataTree.grabExcessVerticalSpace = true;

        gridDataTree.grabExcessHorizontalSpace = true;

        viewer.getTree().setLayoutData(gridDataTree);

        contentProvider = new DerivateContentProvider();

        viewer.setContentProvider(contentProvider);

        labelProvider = new DerivateLabelProvider();

        labelProvider.setConversation(conversation);

        viewer.setLabelProvider(labelProvider);

        viewer.setAutoExpandLevel(AbstractTreeViewer.ALL_LEVELS);

        viewer.getTree().setEnabled(CdmStore.isActive());

        // Propagate selection from viewer

        getSite().setSelectionProvider(viewer);

        //listen to selection changes

        selectionService = getSite().getWorkbenchWindow().getSelectionService();

        selectionService.addSelectionListener(this);

        //create context menu

        MenuManager menuManager = new MenuManager();

        menuManager.setRemoveAllWhenShown(true);

        getSite().registerContextMenu(menuManager, viewer);

        Control control = viewer.getControl();

        Menu menu = menuManager.createContextMenu(control);

        control.setMenu(menu);

        //init tree

        Collection<UUID> derivativeUuids = ((DerivateViewEditorInput)getEditorInput()).getDerivativeUuids();

        checkWarnThreshold(derivativeUuids);

		updateRootEntities(derivativeUuids);

        //set taxon filter

        derivateSearchCompositeController.setTaxonFilter(((DerivateViewEditorInput) getEditorInput()).getTaxonUuid());

        //reset status bar

        getEditorSite().getActionBars().getStatusLineManager().setMessage("");

        //add drag'n'drop support

        Transfer[] transfers = new Transfer[] {LocalSelectionTransfer.getTransfer(),};

        viewer.addDragSupport(dndOperations, transfers, new DerivateDragListener(this));

        viewer.addDropSupport(dndOperations, transfers, new DerivateDropListener(this));

    }

    public void updateRootEntities() {

        updateRootEntities((Collection)null);

    }

    public void updateRootEntities(Collection<UUID> derivativeUuids) {

        if(conversation!=null){

            if (!conversation.isBound()) {

                conversation.bind();

            }

            /*

             * If the active session is not the session of the Derivative Editor

             * then we will save the active session for later, bind temporarily

             * to our session and rebind to the original session when we are

             * done. This happens e.g. if a selection change happens in the

             * taxon editor and "Link with editor" is enabled. The selection

             * change event and thus the loading in updateRootEntities() happens

             * in the session of the taxon editor.

             */

            ICdmEntitySession previousCdmEntitySession = CdmStore.getCurrentSessionManager().getActiveSession();

            if(cdmEntitySession != null) {

                cdmEntitySession.bind();

            }

            List<SpecimenOrObservationBase> derivates = null;

            if(derivativeUuids!=null){

                this.derivateToRootEntityMap = new HashMap<SpecimenOrObservationBase<?>, SpecimenOrObservationBase<?>>();

                this.rootElements = new HashSet<SpecimenOrObservationBase<?>>();

                derivates = CdmStore.getService(IOccurrenceService.class).load(new ArrayList(derivativeUuids), SPECIMEN_INIT_STRATEGY);

            }

            updateRootEntities(derivates);

            previousCdmEntitySession.bind();

        }

    }

    public void updateRootEntities(List<SpecimenOrObservationBase> derivates) {

            if(derivates!=null){

                this.derivateToRootEntityMap = new HashMap<SpecimenOrObservationBase<?>, SpecimenOrObservationBase<?>>();

                this.rootElements = new HashSet<SpecimenOrObservationBase<?>>();

                for (SpecimenOrObservationBase derivate : derivates) {

                    if(derivate instanceof FieldUnit){

                        derivateToRootEntityMap.put(derivate, derivate);

                    }

                    else {

                        SpecimenOrObservationBase<?> topMostDerivate = EditorUtil.getTopMostDerivate(derivate);

                        if(topMostDerivate!=null){

                            derivateToRootEntityMap.put(derivate, topMostDerivate);

                        }

                        else{

                            derivateToRootEntityMap.put(derivate, derivate);

                        }

                    }

                }

                for (SpecimenOrObservationBase<?> specimen : derivateToRootEntityMap.values()) {

                    rootElements.add(specimen);

                }

            }

            labelProvider.updateLabelCache(rootElements);

            viewer.setInput(rootElements);

            getEditorSite().getActionBars().getStatusLineManager().setMessage(rootElements.size() +" derivative hierarchies found");

            //set selection to derivatives if the filter criteria

            //taxon assignment or derivative type are set

            if(derivates!=null && !derivateSearchCompositeController.isDefaultSearch()){

                List<TreeNode> nodesToSelect = new ArrayList<TreeNode>();

                for (SpecimenOrObservationBase specimenOrObservationBase : derivates) {

                    nodesToSelect.add(new TreeNode(specimenOrObservationBase));

                }

                viewer.setSelection(new StructuredSelection(nodesToSelect));

            }

            else{

                viewer.setSelection(null);

            }

    }

    public void updateLabelCache(){

        labelProvider.updateLabelCache(rootElements);

    }

    @Override

    public void doSave(IProgressMonitor monitor) {

        String taskName = Messages.DerivateView_SAVING_HIERARCHY;

        monitor.beginTask(taskName, 3);

        if (!conversation.isBound()) {

            conversation.bind();

        }

        monitor.worked(1);

        // commit the conversation and start a new transaction immediately

        conversation.commit(true);

        if(CdmStore.getCurrentSessionManager().isRemoting()) {

            CdmStore.getService(IOccurrenceService.class).merge(new ArrayList<SpecimenOrObservationBase>(rootElements), true);

        }

        monitor.worked(1);

        this.setDirty(false);

        monitor.worked(1);

        monitor.done();

        firePropertyChange(PROP_DIRTY);

        refreshTree();

    }

    @Override

    public void doSaveAs() {

    }

    @Override

    public String getTitleToolTip() {

        return Messages.DerivateView_DERIVATIVE_EDITOR;

    }

    @Override

    public boolean isDirty() {

        return isDirty;

    }

    /**

     * @param isDirty the isDirty to set

     */

    public void setDirty(boolean isDirty) {

        this.isDirty = isDirty;

    }

    @Override

    public boolean isSaveAsAllowed() {

        return false;

    }

    @Override

    public void setFocus() {

        viewer.getControl().setFocus();

        //make sure to bind again if maybe in another view the conversation was unbound

        if(conversation!=null && !conversation.isBound()){

            conversation.bind();

        }

        if(cdmEntitySession != null) {

            cdmEntitySession.bind();

        }

    }

    @Override

    public void update(CdmDataChangeMap changeEvents) {

    }

    @Override

    public ConversationHolder getConversationHolder() {

        return conversation;

    }

    @Override

    public void changed(Object element) {

        setDirty(true);

        firePropertyChange(IEditorPart.PROP_DIRTY);

        viewer.update(new TreeNode(element), null);

    }

    @Override

    public void forceDirty() {

        changed(null);

    }

    @Override

    public Map<Object, List<String>> getPropertyPathsMap() {

        List<String> specimenPropertyPaths = Arrays.asList(new String[] {

                "descriptions",

                "derivationEvents.derivates",

                "annotations",

                "markers",

                "credits",

                "extensions",

                "rights",

                "sources"

        });

        Map<Object, List<String>> specimenPropertyPathMap =

                new HashMap<Object, List<String>>();

        specimenPropertyPathMap.put(SpecimenOrObservationBase.class,specimenPropertyPaths);

        return specimenPropertyPathMap;

    }

    /**

     * Refreshes the derivate hierarchy tree and expands the tree

     * to show and select the given object.

     *

     * @param expandTo the object to which the tree should be expanded

     */

    public void refreshTree(Object expandTo){

        refreshTree();

        TreeSelection selection = (TreeSelection) viewer.getSelection();

        viewer.expandToLevel(selection.getFirstElement(), 1);

        viewer.setSelection(new StructuredSelection(new TreeNode(expandTo)));

    }

    /**

     * Refreshes the derivate hierarchy tree

     */

    public void refreshTree(){

        viewer.refresh();

    }

    //FIXME:Remoting hack to make this work for remoting

    //This should actually be resolved using remoting post operations

    public void remove(Object obj) {

        rootElements.remove(obj);

        viewer.setInput(rootElements);

    }

    /**

     * @return a set of {@link SingleRead}s that have multiple parents

     */

    public Set<SingleRead> getMultiLinkSingleReads() {

        return DerivateLabelProvider.getMultiLinkSingleReads();

    }

    public Object getSelectionInput() {

        return selectedTaxon;

    }

    public DerivateLabelProvider getLabelProvider() {

        return labelProvider;

    }

    @Override

    public boolean postOperation(CdmBase objectAffectedByOperation) {

        refreshTree();

        if(objectAffectedByOperation!=null){

            changed(objectAffectedByOperation);

        }

        return true;

    }

    @Override

    public boolean onComplete() {

        return true;

    }

    @Override

    public boolean canAttachMedia() {

        return true;

    }

    public void addFieldUnit(FieldUnit fieldUnit) {

        rootElements.add(fieldUnit);

        derivateToRootEntityMap.put(fieldUnit, fieldUnit);

    }

    @Override

    public ICdmEntitySession getCdmEntitySession() {

        return cdmEntitySession;

    }

    @Override

    public void dispose() {

        super.dispose();

        if(conversation!=null){

            conversation.close();

        }

        if(cdmEntitySession != null) {

            cdmEntitySession.dispose();

        }

    }

    public void selectionChanged_internal(IWorkbenchPart part, ISelection selection) {

    	if(part == this){

            return;

        }

        if(viewer.getTree().isDisposed()){

            return;

        }

        if(listenToSelectionChange){

            if(part instanceof MultiPageTaxonEditor){

                selectedTaxon = ((MultiPageTaxonEditor) part).getTaxon();

            }

            else if(selection instanceof IStructuredSelection){

                Object selectedElement = ((IStructuredSelection) selection).getFirstElement();

                if(selectedElement instanceof CdmBase){

                    if(((CdmBase) selectedElement).isInstanceOf(TaxonNode.class)){

                        selectedTaxon = HibernateProxyHelper.deproxy(selectedElement, TaxonNode.class).getTaxon();

                    }

                    else if(((CdmBase) selectedElement).isInstanceOf(Taxon.class)){

                        selectedTaxon = HibernateProxyHelper.deproxy(selectedElement, Taxon.class);

                    }

                }

            }

            if(selectedTaxon!=null){

                Collection<SpecimenOrObservationBase> fieldUnits = CdmStore.getService(IOccurrenceService.class).listFieldUnitsByAssociatedTaxon(selectedTaxon, null, null);

                Collection<UUID> uuids = new HashSet<UUID>();

                for (SpecimenOrObservationBase specimenOrObservationBase : fieldUnits) {

                    uuids.add(specimenOrObservationBase.getUuid());

                }

                checkWarnThreshold(uuids);

                updateRootEntities(uuids);

                setPartName("Derivative Editor: " + selectedTaxon.getName());

            }

        }

    }

    @Override

    public void selectionChanged(IWorkbenchPart part, ISelection selection) {

    	if(delaySelection==null){

            delaySelection = new DelaySelection(part, selection);

        }

        delaySelection.setPart(part);

        delaySelection.setSelection(selection);

        if(!isInDelay){

            isInDelay = true;

            Display.getCurrent().asyncExec(delaySelection);

        }

    }

	private void checkWarnThreshold(Collection<UUID> uuids) {

		if(uuids!=null && uuids.size()>WARN_THRESHOLD){

			MessagingUtils.warningDialog("Performance warning", this.getClass(), String.format("Specimens will not be loaded!\n"

					+ "There are %d specimens associated with the current "

					+ "selection. If you really want to show all of them in the specimen editor please "

					+ "use the taxon filter in the search bar.", uuids.size()));

			uuids.clear();

		}

	}

    public TreeViewer getViewer() {

        return viewer;

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public List<SpecimenOrObservationBase<?>> getRootEntities() {

        return new ArrayList<SpecimenOrObservationBase<?>>(rootElements);

    }

    public void toggleListenToSelectionChange() {

        listenToSelectionChange = !listenToSelectionChange;

        derivateSearchCompositeController.setEnabled(!listenToSelectionChange);

        if(!listenToSelectionChange){

            selectedTaxon = null;

            setPartName("Derivative Editor");

        }

        else if(selectedTaxon==null){

            setPartName("Derivative Editor [no taxon selected]");

        }

    }

    public boolean isListenToSelectionChange(){

        return listenToSelectionChange;

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public void contextAboutToStop(IMemento memento, IProgressMonitor monitor) {

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public void contextStop(IMemento memento, IProgressMonitor monitor) {

        derivateSearchCompositeController.setEnabled(false);

        if(!viewer.getTree().isDisposed()) {

            viewer.getTree().setEnabled(false);

            viewer.setInput(null);

        }

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public void contextStart(IMemento memento, IProgressMonitor monitor) {

        derivateSearchCompositeController.setEnabled(!listenToSelectionChange);

        if(!viewer.getTree().isDisposed()){

            viewer.getTree().setEnabled(true);

        }

        refreshTree();

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public void contextRefresh(IProgressMonitor monitor) {

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public void workbenchShutdown(IMemento memento, IProgressMonitor monitor) {

    }

}