ref #9816: adapt tooltip text
[taxeditor.git] / eu.etaxonomy.taxeditor.editor / src / main / java / eu / etaxonomy / taxeditor / editor / descriptiveDataSet / matrix / CharacterMatrix.java
index ef06e615db97b181db5702188862ecfa382f76c5..55950cda159450871475defb1241832064f42073 100644 (file)
@@ -11,11 +11,16 @@ package eu.etaxonomy.taxeditor.editor.descriptiveDataSet.matrix;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Properties;
 import java.util.Set;
+import java.util.TreeSet;
 import java.util.UUID;
 import java.util.stream.Collectors;
 
@@ -28,6 +33,8 @@ import org.eclipse.core.runtime.SubMonitor;
 import org.eclipse.core.runtime.jobs.IJobChangeEvent;
 import org.eclipse.core.runtime.jobs.Job;
 import org.eclipse.core.runtime.jobs.JobChangeAdapter;
+import org.eclipse.e4.core.di.annotations.Optional;
+import org.eclipse.e4.ui.di.UIEventTopic;
 import org.eclipse.e4.ui.di.UISynchronize;
 import org.eclipse.e4.ui.services.EMenuService;
 import org.eclipse.jface.layout.GridDataFactory;
@@ -42,6 +49,7 @@ import org.eclipse.nebula.widgets.nattable.coordinate.Range;
 import org.eclipse.nebula.widgets.nattable.copy.command.InternalCopyDataCommandHandler;
 import org.eclipse.nebula.widgets.nattable.copy.command.InternalPasteDataCommandHandler;
 import org.eclipse.nebula.widgets.nattable.data.IDataProvider;
+import org.eclipse.nebula.widgets.nattable.data.IRowDataProvider;
 import org.eclipse.nebula.widgets.nattable.data.ListDataProvider;
 import org.eclipse.nebula.widgets.nattable.export.command.ExportCommandHandler;
 import org.eclipse.nebula.widgets.nattable.extension.e4.selection.E4SelectionListener;
@@ -57,27 +65,28 @@ import org.eclipse.nebula.widgets.nattable.grid.command.ClientAreaResizeCommand;
 import org.eclipse.nebula.widgets.nattable.grid.data.DefaultColumnHeaderDataProvider;
 import org.eclipse.nebula.widgets.nattable.grid.data.DefaultCornerDataProvider;
 import org.eclipse.nebula.widgets.nattable.grid.data.DefaultRowHeaderDataProvider;
-import org.eclipse.nebula.widgets.nattable.grid.data.FixedSummaryRowHeaderLayer;
 import org.eclipse.nebula.widgets.nattable.grid.layer.ColumnHeaderLayer;
 import org.eclipse.nebula.widgets.nattable.grid.layer.CornerLayer;
 import org.eclipse.nebula.widgets.nattable.grid.layer.DefaultRowHeaderDataLayer;
 import org.eclipse.nebula.widgets.nattable.grid.layer.GridLayer;
+import org.eclipse.nebula.widgets.nattable.grid.layer.RowHeaderLayer;
+import org.eclipse.nebula.widgets.nattable.group.ColumnGroupGroupHeaderLayer;
+import org.eclipse.nebula.widgets.nattable.group.ColumnGroupHeaderLayer;
+import org.eclipse.nebula.widgets.nattable.group.ColumnGroupModel;
 import org.eclipse.nebula.widgets.nattable.layer.AbstractLayer;
-import org.eclipse.nebula.widgets.nattable.layer.CompositeLayer;
 import org.eclipse.nebula.widgets.nattable.layer.DataLayer;
 import org.eclipse.nebula.widgets.nattable.layer.ILayer;
-import org.eclipse.nebula.widgets.nattable.layer.cell.ColumnOverrideLabelAccumulator;
-import org.eclipse.nebula.widgets.nattable.layer.stack.DefaultBodyLayerStack;
+import org.eclipse.nebula.widgets.nattable.layer.cell.ILayerCell;
 import org.eclipse.nebula.widgets.nattable.persistence.gui.PersistenceDialog;
 import org.eclipse.nebula.widgets.nattable.selection.SelectionLayer;
+import org.eclipse.nebula.widgets.nattable.selection.command.SelectRowsCommand;
 import org.eclipse.nebula.widgets.nattable.sort.SortHeaderLayer;
 import org.eclipse.nebula.widgets.nattable.sort.config.SingleClickSortConfiguration;
-import org.eclipse.nebula.widgets.nattable.style.HorizontalAlignmentEnum;
 import org.eclipse.nebula.widgets.nattable.style.theme.ModernNatTableThemeConfiguration;
-import org.eclipse.nebula.widgets.nattable.summaryrow.FixedSummaryRowLayer;
-import org.eclipse.nebula.widgets.nattable.summaryrow.SummaryRowLayer;
+import org.eclipse.nebula.widgets.nattable.tooltip.NatTableContentTooltip;
 import org.eclipse.nebula.widgets.nattable.tree.ITreeRowModel;
 import org.eclipse.nebula.widgets.nattable.tree.TreeLayer;
+import org.eclipse.nebula.widgets.nattable.tree.command.TreeExpandToLevelCommand;
 import org.eclipse.nebula.widgets.nattable.ui.binding.UiBindingRegistry;
 import org.eclipse.nebula.widgets.nattable.ui.matcher.MouseEventMatcher;
 import org.eclipse.nebula.widgets.nattable.ui.menu.PopupMenuAction;
@@ -88,6 +97,7 @@ import org.eclipse.swt.layout.GridData;
 import org.eclipse.swt.layout.GridLayout;
 import org.eclipse.swt.widgets.Button;
 import org.eclipse.swt.widgets.Composite;
+import org.eclipse.swt.widgets.Event;
 import org.eclipse.swt.widgets.Menu;
 
 import ca.odell.glazedlists.BasicEventList;
@@ -95,23 +105,32 @@ import ca.odell.glazedlists.EventList;
 import ca.odell.glazedlists.SortedList;
 import ca.odell.glazedlists.TreeList;
 import eu.etaxonomy.cdm.api.application.CdmApplicationState;
-import eu.etaxonomy.cdm.api.service.IVocabularyService;
+import eu.etaxonomy.cdm.api.service.IDescriptiveDataSetService;
+import eu.etaxonomy.cdm.api.service.IOccurrenceService;
+import eu.etaxonomy.cdm.api.service.UpdateResult;
+import eu.etaxonomy.cdm.api.service.config.RemoveDescriptionsFromDescriptiveDataSetConfigurator;
+import eu.etaxonomy.cdm.api.service.dto.FieldUnitDTO;
 import eu.etaxonomy.cdm.api.service.dto.RowWrapperDTO;
 import eu.etaxonomy.cdm.api.service.dto.SpecimenRowWrapperDTO;
+import eu.etaxonomy.cdm.api.service.dto.TaxonRowWrapperDTO;
 import eu.etaxonomy.cdm.common.monitor.IRemotingProgressMonitor;
+import eu.etaxonomy.cdm.model.common.CdmBase;
 import eu.etaxonomy.cdm.model.description.DescriptionBase;
 import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
-import eu.etaxonomy.cdm.model.description.Feature;
-import eu.etaxonomy.cdm.model.description.MeasurementUnit;
-import eu.etaxonomy.cdm.model.description.State;
-import eu.etaxonomy.cdm.model.term.TermNode;
-import eu.etaxonomy.cdm.model.term.TermTree;
-import eu.etaxonomy.cdm.model.term.TermVocabulary;
+import eu.etaxonomy.cdm.model.description.SpecimenDescription;
+import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
+import eu.etaxonomy.cdm.persistence.dto.DescriptiveDataSetBaseDto;
+import eu.etaxonomy.cdm.persistence.dto.FeatureDto;
 import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;
 import eu.etaxonomy.cdm.persistence.dto.TermDto;
+import eu.etaxonomy.cdm.persistence.dto.TermNodeDto;
+import eu.etaxonomy.cdm.persistence.dto.TermTreeDto;
+import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
 import eu.etaxonomy.taxeditor.editor.internal.TaxeditorEditorPlugin;
 import eu.etaxonomy.taxeditor.editor.l10n.Messages;
+import eu.etaxonomy.taxeditor.event.WorkbenchEventConstants;
 import eu.etaxonomy.taxeditor.model.MessagingUtils;
+import eu.etaxonomy.taxeditor.operation.IFeedbackGenerator;
 import eu.etaxonomy.taxeditor.session.ICdmEntitySession;
 import eu.etaxonomy.taxeditor.store.CdmStore;
 import eu.etaxonomy.taxeditor.workbench.WorkbenchUtility;
@@ -120,7 +139,6 @@ import eu.etaxonomy.taxeditor.workbench.WorkbenchUtility;
  * Character matrix editor for editing specimen/taxon descriptions in a table
  * @author pplitzner
  * @since Nov 26, 2017
- *
  */
 public class CharacterMatrix extends Composite {
 
@@ -142,19 +160,20 @@ public class CharacterMatrix extends Composite {
     static final String LABEL_TAXON_DESCRIPTION = "LABEL_TAXON_DESCRIPTION"; //$NON-NLS-1$
     static final String LABEL_DESCRIPTION_HAS_SUPPLEMENTAL_DATA = "LABEL_DESCRIPTION_HAS_SUPPLEMENTAL_DATA"; //$NON-NLS-1$
 
+    boolean isFirstCall = true;
     @Inject
     private UISynchronize sync;
 
     @Inject
     private EMenuService menuService;
 
-    private DescriptiveDataSet descriptiveDataSet;
-
     private NatTable natTable;
 
-    private Map<Integer, Feature> indexToFeatureMap = new HashMap<>();
+    private HashMap<UUID, RowWrapperDTO<?>> rowsToMerge = new HashMap<>();
+
+    private Map<Integer, FeatureDto> indexToFeatureMap = new HashMap<>();
 
-    private Map<Feature, List<TermDto>> categoricalFeatureToStateMap = new HashMap<>();
+    private Map<UUID, List<TermDto>> categoricalFeatureToStateMap = new HashMap<>();
 
     private LinkedMap<String, String> propertyToLabelMap = new LinkedMap<>();
 
@@ -162,31 +181,37 @@ public class CharacterMatrix extends Composite {
 
     private Collection<SpecimenNodeWrapper> specimenCache = null;
 
-    private Map<Feature, CategoricalDataHistogram> featureToHistogramMap = new HashMap<>();
-
-    private Map<Feature, QuantitativeDataStatistics> featureToQuantDataStatisticsMap = new HashMap<>();
+    private Map<FeatureDto, CategoricalDataHistogram> featureToHistogramMap = new HashMap<>();
 
     private ListDataProvider<Object> bodyDataProvider;
 
     private FreezeLayer freezeLayer;
 
-    private List<Feature> features;
+    private List<FeatureDto> features;
 
     private CharacterMatrixPart part;
 
     private AbstractLayer topMostLayer;
 
-    private FixedSummaryRowLayer summaryRowLayer;
-
     private ConfigRegistry configRegistry;
 
-    private DefaultBodyLayerStack bodyLayer;
+    private MatrixBodyLayerStack bodyLayer;
+
+    private SelectionLayer selectionLayer;
 
     private boolean isTreeView = true;
 
     private CharacterMatrixToolbar toolbar;
 
-    private boolean isShowTooltips = true;
+    private DescriptionTreeFormat treeFormat;
+
+    private Map<RemoveDescriptionsFromDescriptiveDataSetConfigurator, List<UUID>> descriptionUuidsToDelete;
+
+    private List<SpecimenRowWrapperDTO> specimenToAdd;
+
+    private MouseEventMatcher mouseEventMatcher = null;
+
+    private Set<DescriptionBase<?>> descriptionsToSave = new HashSet<>();
 
     public CharacterMatrix(Composite parent, CharacterMatrixPart part) {
         super(parent, SWT.NONE);
@@ -196,35 +221,24 @@ public class CharacterMatrix extends Composite {
         createToolBar();
 
         natTable = new NatTable(this, false);
-
-        createBottomToolbar();
-
     }
 
     private void createToolBar(){
         toolbar = new CharacterMatrixToolbar(this, SWT.NONE);
     }
 
-    @SuppressWarnings("unused")
-    private void createBottomToolbar() {
-        new CharacterMatrixBottomToolbar(this, SWT.NONE);
-    }
-
-
     private void applyStyles(){
         ModernNatTableThemeConfiguration configuration = new ModernNatTableThemeConfiguration();
-        configuration.summaryRowHAlign = HorizontalAlignmentEnum.CENTER;
         // NOTE: Getting the colors and fonts from the GUIHelper ensures that
         // they are disposed properly (required by SWT)
         configuration.cHeaderBgColor = GUIHelper.getColor(211, 211, 211);
         configuration.rHeaderBgColor = GUIHelper.getColor(211, 211, 211);
         natTable.addConfiguration(configuration);
-
     }
 
     void toggleTreeFlat(boolean isTree, Button btnToggleFlat, Button btnToggleTree, Button btnCollapseAll, Button btnExpandAll, Button btnFreezeSuppInfo) {
         isTreeView = isTree;
-        createTable(isTree, freezeLayer.isFrozen());
+        createTable(isTree, freezeLayer.isFrozen(), true);
         btnToggleFlat.setEnabled(isTree);
         btnToggleTree.setEnabled(!isTree);
         btnCollapseAll.setEnabled(isTree);
@@ -235,7 +249,7 @@ public class CharacterMatrix extends Composite {
         return isTreeView;
     }
 
-    public void createTable(boolean treeView, boolean freezeSupplementalColumns){
+    public void createTable(boolean treeView, boolean freezeSupplementalColumns, boolean isInitialExpandToDeepestTaxonLevel){
         /**
          * layers
          */
@@ -244,7 +258,8 @@ public class CharacterMatrix extends Composite {
         /**
          * configuration
          */
-        configureNatTable(treeView, configRegistry, topMostLayer, summaryRowLayer);
+
+        configureNatTable(treeView, configRegistry, topMostLayer);
 
         /**
          * handlers and listeners
@@ -254,8 +269,8 @@ public class CharacterMatrix extends Composite {
         //grab all space
         GridDataFactory.fillDefaults().grab(true, true).applyTo(natTable);
 
-        //update label to current data set
-        toolbar.getWsLabel().setText(descriptiveDataSet.getLabel());
+        //update label to current dataset
+        toolbar.getWsLabel().setText(getDescriptiveDataSet().getTitleCache());
         toolbar.getWsLabel().setLayoutData(new GridData(SWT.FILL, SWT.CENTER, true, false));
         toolbar.getWsLabel().getParent().layout();
 
@@ -264,64 +279,107 @@ public class CharacterMatrix extends Composite {
 
 
         //add tooltip to table
-        new CategoricalChartTooltip(this);
-        new QuantitativeChartTooltip(this);
+//        new CategoricalChartTooltip(this);
+//        new QuantitativeChartTooltip(this);
 
 
         this.layout();
         natTable.doCommand(new ClientAreaResizeCommand(natTable));
 
+        // expand all taxa
+        if(isInitialExpandToDeepestTaxonLevel){
+            Integer deepestTaxonLevel = treeFormat.getDeepestTaxonLevel();
+            if(deepestTaxonLevel!=null){
+                natTable.doCommand(new TreeExpandToLevelCommand(deepestTaxonLevel-2));
+            }
+        }
+        new NatTableContentTooltip(natTable, GridRegion.BODY) {
+               protected String getText(Event event) {
+                       int col = this.natTable.getColumnPositionByX(event.x);
+               int row = this.natTable.getRowPositionByY(event.y);
+
+               ILayerCell cell = this.natTable.getCellByPosition(col, row);
+               if (cell.getConfigLabels().getLabels().contains(CharacterMatrixConfigLabelAccumulator.NOT_EDITABLE)){
+                       Object o = bodyDataProvider.getRowObject(row);
+                       String object = "";
+                       if (o instanceof TaxonRowWrapperDTO){
+                               object = "taxon";
+                       }else {
+                               object = "specimen";
+                       }
+                               
+                       return "Multiple data exist. Editing only possible in factual data view of " + object;
+               }
+                       return null;
+               }
+       };
+    
+
         // clean up table state
         getNatTableState().remove(NatTable.INITIAL_PAINT_COMPLETE_FLAG);
         getNatTableState().remove(PersistenceDialog.ACTIVE_VIEW_CONFIGURATION_KEY);
     }
 
-    private List<Feature> initFeatureList(TermNode<Feature> node){
-        List<Feature> features = new ArrayList<>();
-        node.getChildNodes().forEach(childNode->
-                {
-                    features.add(childNode.getTerm());
-                    features.addAll(initFeatureList(childNode));
-                });
+    private List<FeatureDto> initFeatureList(TermNodeDto node){
+        List<FeatureDto> features = new ArrayList<>();
+        List<TermNodeDto> childNodes = node.getChildren();
+        for (TermNodeDto childNode : childNodes) {
+            if (childNode != null){
+                features.add((FeatureDto) childNode.getTerm());
+                features.addAll(initFeatureList(childNode));
+            }
+        }
         return features;
     }
 
-    public void initDescriptiveDataSet(DescriptiveDataSet descriptiveDataSet){
-        this.descriptiveDataSet = descriptiveDataSet;
-        //get features/columns stored in descriptive data set
-        TermTree<Feature> tree = descriptiveDataSet.getDescriptiveSystem();
+    public void initDescriptiveDataSet(){
+        //get features/columns stored in descriptive dataset
+        TermTreeDto tree = getDescriptiveDataSet().getDescriptiveSystem();
         features = initFeatureList(tree.getRoot());
 
+        Set<FeatureDto> duplicateFeatures = features.stream().filter(i -> Collections.frequency(features, i) >1)
+        .collect(Collectors.toSet());
+
+        if (!duplicateFeatures.isEmpty()) {
+            throw new IllegalArgumentException("Duplicate features found: "
+                    + duplicateFeatures.stream().map(feature -> feature.getRepresentation_L10n()).collect(Collectors.joining(",")));
+        }
+
         //init state data for categorical features
-        features.forEach(feature->fetchSupportedStates(feature));
+//        features.forEach(feature->fetchSupportedStates(feature));
+        fetchSupportedStates(features);
 
         descriptions = new BasicEventList<>();
 
     }
 
-    private void fetchSupportedStates(Feature feature) {
-        if(feature.isSupportsCategoricalData()){
-            Set<TermVocabulary<State>> supportedCategoricalEnumerations = feature.getSupportedCategoricalEnumerations();
-            List<UUID> vocUuids = new ArrayList<>();
-            for (TermVocabulary<State> termVocabulary : supportedCategoricalEnumerations) {
-                vocUuids.add(termVocabulary.getUuid());
-            }
-            List<TermDto> supportedStates = new ArrayList<>(CdmStore.getService(IVocabularyService.class).getTerms(vocUuids));
-            categoricalFeatureToStateMap.put(feature, supportedStates);
-        }
+    private void fetchSupportedStates(List<FeatureDto> features) {
+        Set<UUID> featureUuids = new HashSet<>();
+        features.forEach(i->featureUuids.add(i.getUuid()));
+        categoricalFeatureToStateMap = CdmStore.getService(IDescriptiveDataSetService.class).getSupportedStatesForFeature(featureUuids);
+
     }
 
+
+
     private void createLayers(boolean treeView) {
+
         SortedList<Object> sortedList = new SortedList<>(descriptions, new MatrixRowComparator());
         // wrap the SortedList with the TreeList
-        TreeList<Object> treeList = new TreeList(sortedList, new DescriptionTreeFormat(descriptiveDataSet), TreeList.NODES_START_EXPANDED);
+        treeFormat = new DescriptionTreeFormat(getDescriptiveDataSet());
+        @SuppressWarnings("unchecked")
+        TreeList<Object> treeList = new TreeList<Object>(sortedList, treeFormat, TreeList.NODES_START_COLLAPSED);
+        // wrap the SortedList with the TreeList
+//        treeFormat = new DescriptionTreeFormat(getDescriptiveDataSet());
+
         /**
          * data provider
          */
         SpecimenColumnPropertyAccessor columnPropertyAccessor = new SpecimenColumnPropertyAccessor(this);
         bodyDataProvider = treeView?new ListDataProvider<>(treeList, columnPropertyAccessor):new ListDataProvider<>(sortedList, columnPropertyAccessor);
 
-        configRegistry = new ConfigRegistry();
+        DataLayer bodyDataLayer = new DataLayer(bodyDataProvider);
+        bodyDataLayer.registerCommandHandler(new CopyPasteUpdateDataCommandHandler(bodyDataLayer));
 
 
         /**
@@ -329,11 +387,6 @@ public class CharacterMatrix extends Composite {
          *
          *
 
-        CompositeLayer
-         - (top) SummaryRowLayer
-         - (bottom) ViewportLayer
-
-             ^
         ViewportLayer
 
              ^
@@ -354,18 +407,14 @@ public class CharacterMatrix extends Composite {
              ^
         ColumnHideShowLayer
 
-             ^
-        ColumnReorderLayer
-
              ^
         DataLayer
 
          *
 
          */
-        DataLayer bodyDataLayer = new DataLayer(bodyDataProvider);
-        bodyDataLayer.registerCommandHandler(new CopyPasteUpdateDataCommandHandler(bodyDataLayer));
 
+        configRegistry = new ConfigRegistry();
         //register labels
         CharacterMatrixConfigLabelAccumulator labelAccumulator = new CharacterMatrixConfigLabelAccumulator(this);
         bodyDataLayer.setConfigLabelAccumulator(labelAccumulator);
@@ -376,42 +425,32 @@ public class CharacterMatrix extends Composite {
         propertyToLabelMap.put(IDENTIFIER_COLUMN, Messages.CharacterMatrix_IDENTIFIER);
         propertyToLabelMap.put(COUNTRY_COLUMN, Messages.CharacterMatrix_COUNTRY);
         for(int i=0;i<features.size();i++){
-            Feature feature = features.get(i);
+            FeatureDto feature = features.get(i);
             initLabels(i, feature);
         }
 
         // layer for event handling of GlazedLists and PropertyChanges
-        GlazedListsEventLayer eventLayer = new GlazedListsEventLayer<>(bodyDataLayer, (EventList)bodyDataProvider.getList());
+        GlazedListsEventLayer<Object> eventLayer = new GlazedListsEventLayer<>(bodyDataLayer, (EventList<Object>)bodyDataProvider.getList());
+
+        GlazedListTreeData<?> treeData = new GlazedListTreeData<>(treeList);
+        ITreeRowModel<?> treeRowModel = new GlazedListTreeRowModel<>(treeData);
 
-        GlazedListTreeData treeData = new GlazedListTreeData<>(treeList);
-        ITreeRowModel treeRowModel = new GlazedListTreeRowModel<>(treeData);
+        // assemble the column groups
+        LinkedList<ColumnGroupWrapper> columnGroups = new LinkedList<>();
+        List<TermNodeDto> rootChildren = getDescriptiveDataSet().getDescriptiveSystem().getRoot().getChildren();
+        buildHeader(rootChildren, columnGroups);
 
-        bodyLayer = new DefaultBodyLayerStack(eventLayer);
-        final SelectionLayer selectionLayer = bodyLayer.getSelectionLayer();
+        bodyLayer = new MatrixBodyLayerStack(eventLayer, columnGroups);
+        selectionLayer = bodyLayer.getSelectionLayer();
         freezeLayer = new FreezeLayer(selectionLayer);
         final CompositeFreezeLayer compositeFreezeLayer = new CompositeFreezeLayer(
                 freezeLayer, bodyLayer.getViewportLayer(), selectionLayer);
-        TreeLayer treeLayer = new TreeLayer(compositeFreezeLayer, treeRowModel);
-
-        topMostLayer = treeView?treeLayer:compositeFreezeLayer;
-
-        summaryRowLayer = new FixedSummaryRowLayer(bodyDataLayer, topMostLayer, configRegistry, false);
-        //regoster labels with summary prefix for summary layer
-        ColumnOverrideLabelAccumulator summaryColumnLabelAccumulator =new ColumnOverrideLabelAccumulator(bodyDataLayer);
-        summaryRowLayer.setConfigLabelAccumulator(summaryColumnLabelAccumulator);
-        for(int i=0;i<features.size();i++){
-            Feature feature = features.get(i);
-            summaryColumnLabelAccumulator.registerColumnOverrides(
-                    i+LEADING_COLUMN_COUNT,
-                    SummaryRowLayer.DEFAULT_SUMMARY_COLUMN_CONFIG_LABEL_PREFIX+MatrixUtility.getProperty(feature));
+        TreeLayer treeLayer = null;
+        if (treeView){
+            treeLayer = new TreeLayer(compositeFreezeLayer, treeRowModel);
         }
-        // because the horizontal dependency is the ViewportLayer
-        // we need to set the composite dependency to false
-        summaryRowLayer.setHorizontalCompositeDependency(false);
 
-        CompositeLayer composite = new CompositeLayer(1, 2);
-        composite.setChildLayer("SUMMARY", summaryRowLayer, 0, 0); //$NON-NLS-1$
-        composite.setChildLayer(GridRegion.BODY, topMostLayer, 0, 1);
+        topMostLayer = treeView?treeLayer:compositeFreezeLayer;
 
 
         /**
@@ -422,50 +461,111 @@ public class CharacterMatrix extends Composite {
         DataLayer columnHeaderDataLayer = new DataLayer(columnHeaderDataProvider);
         ColumnHeaderLayer columnHeaderLayer = new ColumnHeaderLayer(columnHeaderDataLayer, topMostLayer, selectionLayer);
 
+        ILayer topHeaderLayer = columnHeaderLayer;
+
+        if(!columnGroups.isEmpty()){
+            // first group level
+            ColumnGroupWrapper groupLevel1 = columnGroups.get(0);
+            ColumnGroupHeaderLayer groupLayerLevel1 = null;
+            ColumnGroupGroupHeaderLayer groupLayerLevel2 = null;
+            groupLayerLevel1 = new ColumnGroupHeaderLayer(columnHeaderLayer, selectionLayer, groupLevel1.getModel());
+            for (Entry<TermNodeDto, TreeSet<Integer>> entry: groupLevel1.getColumnGroupToIndexMap().entrySet()) {
+                TermNodeDto group = entry.getKey();
+                TreeSet<Integer> indexList = entry.getValue();
+                int[] intArray = indexList.stream().mapToInt(Integer::intValue).toArray();
+                groupLayerLevel1.addColumnsIndexesToGroup(group.getTerm().getTitleCache(), intArray);
+                groupLayerLevel1.setGroupUnbreakable(indexList.iterator().next());
+            }
+            topHeaderLayer = groupLayerLevel1;
+
+            // second group level
+            if(columnGroups.size()>1){
+                ColumnGroupWrapper groupLevel2 = columnGroups.get(1);
+                groupLayerLevel2 = new ColumnGroupGroupHeaderLayer(groupLayerLevel1, selectionLayer, groupLevel2.getModel());
+                for (Entry<TermNodeDto, TreeSet<Integer>> entry: groupLevel2.getColumnGroupToIndexMap().entrySet()) {
+                    TermNodeDto group = entry.getKey();
+                    TreeSet<Integer> indexList = entry.getValue();
+                    int[] intArray = indexList.stream().mapToInt(Integer::intValue).toArray();
+                    groupLayerLevel2.addColumnsIndexesToGroup(group.getTerm().getTitleCache(), intArray);
+                    groupLayerLevel2.setGroupUnbreakable(indexList.iterator().next());
+                }
+                topHeaderLayer = groupLayerLevel2;
+            }
+        }
+
         // add the SortHeaderLayer to the column header layer stack
         // as we use GlazedLists, we use the GlazedListsSortModel which
         // delegates the sorting to the SortedList
-        final SortHeaderLayer<DescriptionBase> sortHeaderLayer = new SortHeaderLayer<>(
-                columnHeaderLayer,
+        final SortHeaderLayer<DescriptionBase<?>> sortHeaderLayer = new SortHeaderLayer<>(
+                topHeaderLayer,
                 new GlazedListsSortModel<>(
                         sortedList,
                         columnPropertyAccessor,
                         configRegistry,
                         columnHeaderDataLayer));
 
-
         /**
          * row header layer
          */
         IDataProvider rowHeaderDataProvider = new DefaultRowHeaderDataProvider(bodyDataProvider);
         DefaultRowHeaderDataLayer rowHeaderDataLayer = new DefaultRowHeaderDataLayer(rowHeaderDataProvider);
-        FixedSummaryRowHeaderLayer fixedSummaryRowHeaderLayer = new FixedSummaryRowHeaderLayer(rowHeaderDataLayer,
-                composite, selectionLayer);
-        fixedSummaryRowHeaderLayer.setSummaryRowLabel("\u2211"); //$NON-NLS-1$
-
+        RowHeaderLayer rowHeaderLayer = new RowHeaderLayer(rowHeaderDataLayer,
+                topMostLayer, selectionLayer);
 
         /**
          * corner layer
          */
         ILayer cornerLayer = new CornerLayer(
                 new DataLayer(new DefaultCornerDataProvider(columnHeaderDataProvider, rowHeaderDataProvider)),
-                fixedSummaryRowHeaderLayer, sortHeaderLayer);
-
+                rowHeaderLayer, sortHeaderLayer);
 
         /**
          * GRID layer (composition of all other layers)
          */
-        GridLayer gridLayer = new GridLayer(composite, sortHeaderLayer, fixedSummaryRowHeaderLayer, cornerLayer);
-
+        GridLayer gridLayer = new GridLayer(topMostLayer, sortHeaderLayer, rowHeaderLayer, cornerLayer);
         natTable.setLayer(gridLayer);
+    }
+
+    private TreeSet<Integer> recurseChildIndexes(TermNodeDto node){
+        TreeSet<Integer> childIndexes = new TreeSet<>();
+        if(node.getChildren().size() >0){
+            List<TermNodeDto> childNodes = node.getChildren();
+            for (TermNodeDto childNode: childNodes) {
+                if (childNode != null){
+                    childIndexes.addAll(recurseChildIndexes(childNode));
+                }
+            }
+        }
+        childIndexes.add(features.indexOf(node.getTerm())+LEADING_COLUMN_COUNT);
+        return childIndexes;
+    }
 
+    private void buildHeader(List<TermNodeDto> nodes, LinkedList<ColumnGroupWrapper> columnGroups){
+        Map<TermNodeDto, TreeSet<Integer>> columnGroupToIndexMap = new HashMap<>();
+        List<TermNodeDto> childNodes = new ArrayList<>();
+        for (TermNodeDto node : nodes) {
+            if (node != null){
+                TreeSet<Integer> childIndexes = recurseChildIndexes(node);
+                if(childIndexes.size()>1){
+                    // filter out groups that only have one member
+                    columnGroupToIndexMap.put(node, childIndexes);
+                }
+                childNodes.addAll(node.getChildren());
+            }
+        }
+        if(!columnGroupToIndexMap.isEmpty()){
+            columnGroups.addFirst(new ColumnGroupWrapper(new ColumnGroupModel(), columnGroupToIndexMap));
+        }
+        if(!childNodes.isEmpty()){
+            buildHeader(childNodes, columnGroups);
+        }
     }
 
     private void registerHandlersAndListeners() {
         natTable.registerCommandHandler(new ExportCommandHandler(natTable));
 
         //selection listener
-        E4SelectionListener selectionListener = new CellSelectionListener(part.getSelectionService(),
+        E4SelectionListener<Object> selectionListener = new CellSelectionListener(part.getSelectionService(),
                 bodyLayer.getSelectionLayer(), bodyDataProvider, part);
         bodyLayer.getSelectionLayer().addLayerListener(selectionListener);
         selectionListener.setFullySelectedRowsOnly(false);
@@ -482,11 +582,15 @@ public class CharacterMatrix extends Composite {
 
     private void configureNatTable(boolean treeView,
             ConfigRegistry configRegistry,
-            AbstractLayer topMostLayer,
-            FixedSummaryRowLayer summaryRowLayer) {
+            AbstractLayer topMostLayer) {
         /**
          * CONFIGURATION
          */
+      //+++CONTEXT MENU+++
+        menuService.registerContextMenu(natTable, "eu.etaxonomy.taxeditor.editor.popupmenu.charactermatrix"); //$NON-NLS-1$
+        // get the menu registered by EMenuService
+        final Menu e4Menu = natTable.getMenu();
+
         natTable.setConfigRegistry(configRegistry);
 
         applyStyles();
@@ -495,7 +599,7 @@ public class CharacterMatrix extends Composite {
         natTable.addConfiguration(new DefaultNatTableStyleConfiguration());
 
         // this is for DEBUG ONLY
-        //        natTable.addConfiguration(new DebugMenuConfiguration(natTable));
+//                natTable.addConfiguration(new DebugMenuConfiguration(natTable));
 
         // override the default sort configuration and change the mouse bindings
         // to sort on a single click
@@ -507,80 +611,97 @@ public class CharacterMatrix extends Composite {
 
         // add the header menu configuration for adding the column header menu
         // with hide/show actions
-        natTable.addConfiguration(new CharacterMatrixHeaderMenuConfiguration(natTable));
+//        natTable.addConfiguration(new CharacterMatrixHeaderMenuConfiguration(natTable));
 
         // add custom configuration for data conversion and add column labels to viewport layer
         topMostLayer.addConfiguration(new CellEditorDataConversionConfiguration(this));
 
-        //register aggregation configuration
-        summaryRowLayer.addConfiguration(new AggregationConfiguration(this));
-
         //copy&paste configuration
         natTable.addConfiguration(new CopyPasteEditBindings(bodyLayer.getSelectionLayer(), natTable.getInternalCellClipboard()));
 
-      //+++CONTEXT MENU+++
-        menuService.registerContextMenu(natTable, "eu.etaxonomy.taxeditor.editor.popupmenu.charactermatrix"); //$NON-NLS-1$
-        // get the menu registered by EMenuService
-        final Menu e4Menu = natTable.getMenu();
+
         // remove the menu reference from NatTable instance
         natTable.setMenu(null);
-        natTable.addConfiguration(
-                new AbstractUiBindingConfiguration() {
-            @Override
-            public void configureUiBindings(
-                    UiBindingRegistry uiBindingRegistry) {
-                // add e4 menu to NatTable
-                new PopupMenuBuilder(natTable, e4Menu)
-                    .build();
-
-                // register the UI binding for header, corner and body region
-                uiBindingRegistry.registerMouseDownBinding(
-                        new MouseEventMatcher(
-                                SWT.NONE,
-                                null,
-                                MouseEventMatcher.RIGHT_BUTTON),
-                        new PopupMenuAction(e4Menu));
-            }
-        });
+
+
+//        natTable.addConfiguration(new CharacterMatrixHeaderMenuConfiguration(natTable));
+
 
         natTable.configure();
+
+
+        natTable.addConfiguration(
+                    new AbstractUiBindingConfiguration() {
+                @Override
+                public void configureUiBindings(
+                        UiBindingRegistry uiBindingRegistry) {
+                    // add e4 menu to NatTable
+                    uiBindingRegistry.unregisterMouseDownBinding(mouseEventMatcher);
+                    if (isFirstCall){
+                           new PopupMenuBuilder(natTable, e4Menu)
+                           .withHideColumnMenuItem()
+                           .withShowAllColumnsMenuItem()
+                           .build();
+                           isFirstCall = false;
+                    }else{
+                       new PopupMenuBuilder(natTable, e4Menu)
+                           .build();
+                    }
+                    // register the UI binding for header, corner and body region
+                    mouseEventMatcher = new MouseEventMatcher(
+                            SWT.NONE,
+                            null,
+                            MouseEventMatcher.RIGHT_BUTTON);
+                    uiBindingRegistry.registerMouseDownBinding(mouseEventMatcher,
+                            new PopupMenuAction(e4Menu));
+                }
+            });
+
     }
 
     void freezeSupplementalColumns(boolean freeze){
+        int rightMostFreezeColumIndex = LEADING_COLUMN_COUNT-1;
+        Collection<Integer> hiddenColumnIndexes = bodyLayer.getColumnHideShowLayer().getHiddenColumnIndexes();
+        for (Integer integer : hiddenColumnIndexes) {
+            if(integer<LEADING_COLUMN_COUNT){
+                rightMostFreezeColumIndex--;
+            }
+        }
         if(freeze){
             FreezeHelper.freeze(freezeLayer, bodyLayer.getViewportLayer(),
                     new PositionCoordinate(bodyLayer.getViewportLayer(), 0, 0),
-                    new PositionCoordinate(bodyLayer.getViewportLayer(), LEADING_COLUMN_COUNT-1, -1));
+                    new PositionCoordinate(bodyLayer.getViewportLayer(), rightMostFreezeColumIndex, -1));
         }
         else{
             FreezeHelper.unfreeze(freezeLayer, bodyLayer.getViewportLayer());
         }
     }
 
-    private void initLabels(int index, Feature feature) {
+    private void initLabels(int index, FeatureDto feature) {
         indexToFeatureMap.put(index+LEADING_COLUMN_COUNT, feature);
 
-        String label = feature.getLabel();
+        String label = feature.getTitleCache();
         String property = feature.getUuid().toString();
         //show unit for quantitative data
         if(feature.isSupportsQuantitativeData()){
-            Set<MeasurementUnit> recommendedMeasurementUnits = feature.getRecommendedMeasurementUnits();
-            if(recommendedMeasurementUnits.size()>1){
-                MessagingUtils.warningDialog(Messages.CharacterMatrix_INIT_PROBLEM, CharacterMatrix.class,
-                        String.format(Messages.CharacterMatrix_INIT_PROBLEM_MESSAGE, feature.getLabel()));
-            }
+            Set<TermDto> recommendedMeasurementUnits = feature.getRecommendedMeasurementUnits();
+//            if(recommendedMeasurementUnits.size()>1){
+//                MessagingUtils.warningDialog(Messages.CharacterMatrix_INIT_PROBLEM, CharacterMatrix.class,
+//                        String.format(Messages.CharacterMatrix_INIT_PROBLEM_MESSAGE, feature.getLabel()));
+//            }
             if(recommendedMeasurementUnits.size()==1){
-                MeasurementUnit unit = recommendedMeasurementUnits.iterator().next();
+                TermDto unit = recommendedMeasurementUnits.iterator().next();
                 label += " ["+unit.getIdInVocabulary()+"]"; //$NON-NLS-1$ //$NON-NLS-2$
             }
         }
         propertyToLabelMap.put(property, label);
     }
 
-    public void loadDescriptions(DescriptiveDataSet descriptiveDataSet) {
-        UUID monitorUuid =  CdmApplicationState.getLongRunningTasksService().monitGetRowWrapper(descriptiveDataSet);
+    public void loadDescriptions(boolean isInitialExpandToDeepestTaxonLevel, boolean initialLoading) {
+       
+        UUID monitorUuid =  CdmApplicationState.getLongRunningTasksService().monitGetRowWrapper(this.getDescriptiveDataSet().getUuid());
 
-        final Collection<RowWrapperDTO> wrappers = new ArrayList<>();
+        final Collection<RowWrapperDTO<?>> wrappers = new ArrayList<>();
         String jobLabel = Messages.CharacterMatrix_LOAD_CHARACTER_DATA;
         Job job = Job.create(jobLabel, (ICoreRunnable) monitor -> {
             SubMonitor subMonitor = SubMonitor.convert(monitor);
@@ -592,7 +713,7 @@ public class CharacterMatrix extends Composite {
                         monitorUuid,
                         50,
                         null,
-                        (List)null,
+                        (List<IFeedbackGenerator>)null,
                         subMonitor);
             } catch (InterruptedException e) {
                 MessagingUtils.informationDialog(Messages.CharacterMatrix_LOADING_FAILED_TITLE,
@@ -601,7 +722,7 @@ public class CharacterMatrix extends Composite {
             }
             Object result = remotingMonitor.getResult();
             if(result instanceof Collection){
-                wrappers.addAll((Collection<RowWrapperDTO>) result);
+                wrappers.addAll((Collection<RowWrapperDTO<?>>) result);
             }
             if(result instanceof Exception){
                 MessagingUtils.errorDialog("Exception during description loading", this.getClass(), "An exception occured during loading", TaxeditorEditorPlugin.PLUGIN_ID, (Throwable) result, true);
@@ -627,8 +748,12 @@ public class CharacterMatrix extends Composite {
                                 String.format(Messages.CharacterMatrix_NO_NODE_FOUND_MESSAGE, collect)
                                 );
                     }
+                    descriptions.clear();
+//                    part.setDescriptiveDataSet(CdmStore.getService(IDescriptiveDataSetService.class).getDescriptiveDataSetDtoByUuid(part.getDescriptiveDataSet().getUuid()));
                     wrappers.stream().filter(row->row.getTaxonNode()!=null).forEach(wrapper->CharacterMatrix.this.descriptions.add(wrapper));
-                    loadingDone();
+                    if(initialLoading){
+                        loadingDone(isInitialExpandToDeepestTaxonLevel);
+                    }
                 });
             }
         });
@@ -646,16 +771,25 @@ public class CharacterMatrix extends Composite {
         return new StructuredSelection(selectedObjects);
     }
 
-    private void loadingDone() {
+    private void loadingDone(boolean isInitialExpandToDeepestTaxonLevel) {
         this.part.loadingDone();
-        createTable(isTreeView, freezeLayer.isFrozen());
+        createTable(isTreeView, freezeLayer.isFrozen(), isInitialExpandToDeepestTaxonLevel);
+
     }
 
-    public List<TermDto> getSupportedStatesForCategoricalFeature(Feature feature){
-        return categoricalFeatureToStateMap.get(feature);
+    public List<TermDto> getSupportedStatesForCategoricalFeature(UUID featureUuid){
+        return categoricalFeatureToStateMap.get(featureUuid);
     }
 
-    public Map<Integer, Feature> getIndexToFeatureMap() {
+    public Set<DescriptionBase<?>> getDescriptionsToSave() {
+        return descriptionsToSave;
+    }
+
+    public void addDescriptionToSave(DescriptionBase<?> descriptionToSave) {
+        this.descriptionsToSave.add(descriptionToSave);
+    }
+
+    public Map<Integer, FeatureDto> getIndexToFeatureMap() {
         return indexToFeatureMap;
     }
 
@@ -667,6 +801,46 @@ public class CharacterMatrix extends Composite {
         part.setDirty();
     }
 
+    public Map<RemoveDescriptionsFromDescriptiveDataSetConfigurator, List<UUID>> getDescriptionsToDelete() {
+        return descriptionUuidsToDelete;
+    }
+
+    public void addDescriptionToDelete(UUID descriptionToDelete, RemoveDescriptionsFromDescriptiveDataSetConfigurator config) {
+        if (descriptionUuidsToDelete == null){
+            descriptionUuidsToDelete = new HashMap<>();
+        }
+        if (descriptionUuidsToDelete.get(config) != null){
+            descriptionUuidsToDelete.get(config).add(descriptionToDelete);
+        }else{
+            List<UUID> uuidList = new ArrayList<>();
+            uuidList.add(descriptionToDelete);
+            this.descriptionUuidsToDelete.put(config, uuidList);
+        }
+
+
+    }
+
+    public List<SpecimenRowWrapperDTO> getSpecimenToAdd() {
+        return specimenToAdd;
+    }
+
+    public void addSpecimenToAdd(Collection<SpecimenRowWrapperDTO> specimenToAdd) {
+        if (this.specimenToAdd == null){
+            this.specimenToAdd = new ArrayList<>();
+        }
+
+        this.specimenToAdd.addAll(specimenToAdd);
+        this.specimenCache.removeAll(specimenToAdd);
+    }
+    public void addSpecimenToAdd(SpecimenRowWrapperDTO specimenToAdd) {
+        if (this.specimenToAdd == null){
+            this.specimenToAdd = new ArrayList<>();
+        }
+
+        this.specimenToAdd.add(specimenToAdd);
+        this.specimenCache.remove(specimenToAdd);
+    }
+
     public CharacterMatrixPart getPart() {
         return part;
     }
@@ -679,12 +853,16 @@ public class CharacterMatrix extends Composite {
         return descriptions;
     }
 
-    public DescriptiveDataSet getDescriptiveDataSet() {
-        return descriptiveDataSet;
+    public DescriptiveDataSetBaseDto getDescriptiveDataSet() {
+        return part.getDescriptiveDataSet();
+    }
+
+    public void setDescriptiveDataSet(DescriptiveDataSetBaseDto dataSet) {
+        part.setDescriptiveDataSet(dataSet);
     }
 
     public Collection<SpecimenNodeWrapper> getSpecimenCache() {
-        return specimenCache;
+             return specimenCache;
     }
 
     public void setSpecimenCache(Collection<SpecimenNodeWrapper> specimenCache) {
@@ -693,14 +871,33 @@ public class CharacterMatrix extends Composite {
         //map descriptions on a list of uuids of the described specimen
         !this.descriptions.stream()
         .filter(rowWrapper->rowWrapper instanceof SpecimenRowWrapperDTO)
-        .map(specimenRowWrapper->((SpecimenRowWrapperDTO) specimenRowWrapper).getSpecimen().getUuid())
+        .map(specimenRowWrapper->((SpecimenRowWrapperDTO) specimenRowWrapper).getSpecimenDto().getUuid())
         .collect(Collectors.toList())
-        //an check if the specimen to add is already contained
+        //and check if the specimen to add is already contained
         .contains(wrapper.getUuidAndTitleCache().getUuid())
         )
         .collect(Collectors.toList());
     }
 
+//    public void addRowToSave(RowWrapperDTO<?> row){
+//        rowsToMerge.put(row.getDescription().getDescription().getUuid(), row);
+//    }
+//
+//    public HashMap<UUID,RowWrapperDTO<?>> getRowsToSave() {
+//        return rowsToMerge;
+//    }
+
+    public HashMap<UUID, RowWrapperDTO<?>> getRowsToMerge() {
+        return rowsToMerge;
+    }
+
+    public void putRowToMerge(RowWrapperDTO<?> rowToMerge) {
+        if (this.rowsToMerge == null){
+            this.rowsToMerge = new HashMap<>();
+        }
+        this.rowsToMerge.put(rowToMerge.getDescription().getDescriptionUuid(), rowToMerge);
+    }
+
     public Properties getNatTableState() {
         return toolbar.getNatTableState();
     }
@@ -709,7 +906,7 @@ public class CharacterMatrix extends Composite {
         return bodyDataProvider;
     }
 
-    DefaultBodyLayerStack getBodyLayer() {
+    MatrixBodyLayerStack getBodyLayer() {
         return bodyLayer;
     }
 
@@ -717,28 +914,158 @@ public class CharacterMatrix extends Composite {
         return new File(WorkbenchUtility.getBaseLocation(), CHARACTER_MATRIX_STATE_PROPERTIES);
     }
 
-    public List<Feature> getFeatures() {
+    public List<FeatureDto> getFeatures() {
         return features;
     }
 
-    public Map<Feature, CategoricalDataHistogram> getFeatureToHistogramMap() {
+    public Map<FeatureDto, CategoricalDataHistogram> getFeatureToHistogramMap() {
         return featureToHistogramMap;
     }
 
-    public Map<Feature, QuantitativeDataStatistics> getFeatureToQuantDataStatisticsMap() {
-        return featureToQuantDataStatisticsMap;
+
+
+    public ICdmEntitySession getCdmEntitySession(){
+        return part.getCdmEntitySession();
     }
 
-    public void toogleIsShowTooltips() {
-        this.isShowTooltips = !this.isShowTooltips;
+    @Inject
+    @Optional
+    private void updateSpecimenList(@UIEventTopic(WorkbenchEventConstants.REFRESH_DESCRIPTIVE_DATASET)UUID uuid){
+        if(uuid!= null && uuid.equals(part.getDescriptiveDataSet().getUuid())){
+           this.specimenCache = null;
+
+        }
     }
 
-    public boolean isShowTooltips() {
-        return isShowTooltips;
+    public void addRowsToMatrix(Collection<SpecimenNodeWrapper> wrappers){
+
+        List<UUID> specimenUuids = new ArrayList<>();
+        wrappers.forEach(wrapper -> specimenUuids.add(wrapper.getUuidAndTitleCache().getUuid()));
+//        List<SpecimenOrObservationBase> specimens = CdmStore.getService(IOccurrenceService.class).load(specimenUuids, null);
+        Map<UUID, UuidAndTitleCache<FieldUnit>> specimenMap = new HashMap<>();
+
+        for (UUID specimenUuid: specimenUuids ){
+            try{
+                FieldUnitDTO fieldUnitDto = CdmStore.getService(IOccurrenceService.class).loadFieldUnitDTO(specimenUuid);
+                if (fieldUnitDto != null){
+                    UuidAndTitleCache<FieldUnit> fieldUnit = new UuidAndTitleCache<>(FieldUnit.class, fieldUnitDto.getUuid(), null, fieldUnitDto.getLabel());
+                    specimenMap.put(specimenUuid, fieldUnit);
+                }
+            }catch(Exception e){
+                e.printStackTrace();
+            }
+
+        }
+        for (SpecimenNodeWrapper wrapper: wrappers){
+            SpecimenRowWrapperDTO rowWrapper = CdmStore.getService(IDescriptiveDataSetService.class).createSpecimenRowWrapper(wrapper.getUuidAndTitleCache().getUuid(), wrapper.getTaxonNode().getUuid(), getDescriptiveDataSet().getUuid());
+            addSpecimenToAdd(rowWrapper);
+//            SpecimenRowWrapperDTO rowWrapper = new SpecimenRowWrapperDTO(wrapper.getUuidAndTitleCache(), wrapper.getType(), wrapper.getTaxonNode(), specimenMap.get(wrapper.getUuidAndTitleCache().getUuid()), null, null);
+            descriptions.add(rowWrapper);
+        }
+
+
+        setDirty();
     }
 
-    public ICdmEntitySession getCdmEntitiySession(){
-        return part.getCdmEntitySession();
+    public HashMap<UUID, DescriptionBase<?>> addSpecimensToDescriptiveDataSet(){
+        if (specimenToAdd == null || specimenToAdd.isEmpty()){
+            return new HashMap<>();
+        }
+        UpdateResult result = CdmStore.getService(IDescriptiveDataSetService.class).addRowWrapperToDataset(specimenToAdd, getDescriptiveDataSet().getUuid());
+        if(!result.getExceptions().isEmpty()){
+            MessagingUtils.warningDialog(Messages.CharacterMatrixBottomToolbar_ERROR_ROW_CREATION_TITLE, this,
+                    String.format(Messages.CharacterMatrixBottomToolbar_ERROR_ROW_CREATION_MESSAGE, result.getExceptions()
+                            .stream().map(ex->ex.toString())
+                            .collect(Collectors.joining("\n"))));
+        }
+        DescriptiveDataSet dataSet = (DescriptiveDataSet) result.getCdmEntity();
+        HashMap<UUID, DescriptionBase<?>> resultMap = new HashMap<>();
+        for (CdmBase updated: result.getUpdatedObjects()){
+            if (updated instanceof SpecimenDescription){
+                resultMap.put(updated.getUuid(), (DescriptionBase<?>)updated);
+            }
+
+
+        }
+        dataSet = this.getCdmEntitySession().load(dataSet, true);
+        // update local dataset
+        DescriptiveDataSetBaseDto dto = DescriptiveDataSetBaseDto.fromDescriptiveDataSet(dataSet);
+        this.setDescriptiveDataSet(dto);
+
+        //these descriptions are already updated
+        for (SpecimenRowWrapperDTO row: specimenToAdd){
+            this.rowsToMerge.remove(row.getDescription().getDescriptionUuid());
+        }
+        specimenToAdd.clear();
+        return resultMap;
+
+    }
+    public void setSelectedObject(Object selectedObject){
+
+        int rowIndex = ((IRowDataProvider<Object>)bodyDataProvider).indexOfRowObject(selectedObject);
+       int rowPosition = selectionLayer.getRowPositionByIndex(rowIndex);
+       natTable.doCommand( new SelectRowsCommand(natTable, 1, rowPosition, false, false));
+    }
+
+    public TreeList<Object> updateDescriptions(boolean treeView){
+       SortedList<Object> sortedList = new SortedList<>(descriptions, new MatrixRowComparator());
+        // wrap the SortedList with the TreeList
+        treeFormat = new DescriptionTreeFormat(getDescriptiveDataSet());
+        TreeList<Object> treeList = new TreeList<Object>(sortedList, treeFormat, TreeList.NODES_START_COLLAPSED);
+        // wrap the SortedList with the TreeList
+//        treeFormat = new DescriptionTreeFormat(getDescriptiveDataSet());
+
+        /**
+         * data provider
+         */
+        SpecimenColumnPropertyAccessor columnPropertyAccessor = new SpecimenColumnPropertyAccessor(this);
+        bodyDataProvider = treeView?new ListDataProvider<>(treeList, columnPropertyAccessor):new ListDataProvider<>(sortedList, columnPropertyAccessor);
+        return treeList;
+
+    }
+
+
+    @Inject
+    @Optional
+    private void updateView(@UIEventTopic(WorkbenchEventConstants.ADD_TO_MERGE_ROWS) UUID uuid) {
+
+    }
+
+    @Override
+    public void dispose () {
+        super.dispose();
+        if (descriptions != null){
+               descriptions.dispose();
+        }
+        descriptions = null;
+        this.natTable.dispose();
+        this.natTable = null;
+        categoricalFeatureToStateMap = null;
+        rowsToMerge.clear();
+        rowsToMerge = null;
+        indexToFeatureMap = null;
+        propertyToLabelMap = null;
+        specimenCache = null;
+        featureToHistogramMap = null;
+        bodyDataProvider = null;
+        freezeLayer = null;
+        features = null;
+        topMostLayer.dispose();
+        topMostLayer = null;
+        configRegistry = null;
+        bodyLayer.dispose();
+        bodyLayer = null;
+        toolbar.dispose();
+        toolbar = null;
+        treeFormat = null;
+        descriptionUuidsToDelete = null;
+        specimenToAdd = null;
+        mouseEventMatcher = null;
+        descriptionsToSave = null;
+        menuService = null;
+        sync = null;
+        part = null;
+
     }
 
 }