eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/contextMenu/CreateDerivateContextMenu.java

   1 package eu.etaxonomy.taxeditor.editor.view.derivate.contextMenu;
   2
   3 import org.eclipse.jface.action.ContributionItem;
   4 import org.eclipse.jface.action.IContributionItem;
   5 import org.eclipse.jface.viewers.ISelection;
   6 import org.eclipse.jface.viewers.TreeNode;
   7 import org.eclipse.swt.SWT;
   8 import org.eclipse.swt.events.SelectionAdapter;
   9 import org.eclipse.swt.events.SelectionEvent;
  10 import org.eclipse.swt.widgets.Menu;
  11 import org.eclipse.swt.widgets.MenuItem;
  12 import org.eclipse.ui.IWorkbenchWindow;
  13 import org.eclipse.ui.PlatformUI;
  14 import org.eclipse.ui.actions.CompoundContributionItem;
  15
  16 import eu.etaxonomy.cdm.api.application.CdmApplicationState;
  17 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeCacheStrategy;
  18 import eu.etaxonomy.cdm.api.service.IOccurrenceService;
  19 import eu.etaxonomy.cdm.model.media.Media;
  20 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  21 import eu.etaxonomy.cdm.model.molecular.Sequence;
  22 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  23 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  24 import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
  25 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  26 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  27 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  28 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  29 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  30 import eu.etaxonomy.taxeditor.editor.EditorUtil;
  31 import eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView;
  32 import eu.etaxonomy.taxeditor.model.AbstractUtility;
  33 import eu.etaxonomy.taxeditor.model.MessagingUtils;
  34 import eu.etaxonomy.taxeditor.store.CdmStore;
  35 import eu.etaxonomy.taxeditor.ui.dialog.selection.MediaSelectionDialog;
  36
  37 /**
  38  * Context menu for the creation of derivates in the derivate hierarchy.
  39  *
  40  */
  41 public class CreateDerivateContextMenu extends CompoundContributionItem {
  42
  43     @Override
  44     protected IContributionItem[] getContributionItems() {
  45         IContributionItem[] contributionItems = new IContributionItem[] {
  46                 new ContributionItem() {
  47                     @Override
  48                     public void fill(Menu menu, int index) {
  49                         MenuItem addItem = new MenuItem(menu, SWT.CASCADE);
  50                         addItem.setText("Add...");
  51                         Menu addMenu = new Menu(menu);
  52                         addItem.setMenu(addMenu);
  53                         final IWorkbenchWindow window = PlatformUI.getWorkbench().getActiveWorkbenchWindow();
  54                         final ISelection selection = window.getActivePage().getSelection();
  55                         TreeNode selectedTreeNode = EditorUtil.getTreeNodeOfSelection(selection);
  56                         if(selectedTreeNode!=null){
  57                             //context menu for FieldUnit
  58                             if(selectedTreeNode.getValue() instanceof FieldUnit){
  59                                 createMenuItem(addMenu, "Specimen", selectedTreeNode, DerivedUnit.class, SpecimenOrObservationType.PreservedSpecimen, DerivationEventType.GATHERING_IN_SITU());
  60                                 new MenuItem(addMenu, SWT.SEPARATOR);
  61                                 createMenuItem(addMenu, "Tissue Sample", selectedTreeNode, DnaSample.class, SpecimenOrObservationType.TissueSample, DerivationEventType.PREPARATION());
  62                                 createMenuItem(addMenu, "DNA Sample", selectedTreeNode, DnaSample.class, SpecimenOrObservationType.DnaSample, DerivationEventType.DNA_EXTRACTION());
  63                                 createMenuItem(addMenu, "Media Specimen", selectedTreeNode, MediaSpecimen.class, SpecimenOrObservationType.Media, DerivationEventType.ACCESSIONING());
  64                             }
  65                             //context menu for Specimen
  66                             else if(selectedTreeNode.getValue() instanceof DerivedUnit && ((DerivedUnit)selectedTreeNode.getValue()).getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
  67
  68                                 createMenuItem(addMenu, "Tissue Sample", selectedTreeNode, DnaSample.class, SpecimenOrObservationType.TissueSample, DerivationEventType.PREPARATION());
  69                                 createMenuItem(addMenu, "DNA Sample", selectedTreeNode, DnaSample.class, SpecimenOrObservationType.DnaSample, DerivationEventType.DNA_EXTRACTION());
  70                                 createMenuItem(addMenu, "Media Specimen", selectedTreeNode, MediaSpecimen.class, SpecimenOrObservationType.Media, DerivationEventType.ACCESSIONING());
  71                             }
  72                             //context menu for TissueSample
  73                             else if(selectedTreeNode.getValue() instanceof DnaSample && ((DnaSample)selectedTreeNode.getValue()).getRecordBasis()==SpecimenOrObservationType.TissueSample){
  74                                 createMenuItem(addMenu, "DnaSample", selectedTreeNode, DnaSample.class, SpecimenOrObservationType.DnaSample, DerivationEventType.DNA_EXTRACTION());
  75                                 createMenuItem(addMenu, "Media Specimen", selectedTreeNode, MediaSpecimen.class, SpecimenOrObservationType.Media, DerivationEventType.ACCESSIONING());
  76                             }
  77                             //context menu for DnaSample
  78                             else if(selectedTreeNode.getValue() instanceof DnaSample && ((DnaSample)selectedTreeNode.getValue()).getRecordBasis()==SpecimenOrObservationType.DnaSample){
  79                                 createMenuItem(addMenu, "Consensus Sequence", selectedTreeNode, Sequence.class, null, null);
  80                                 createMenuItem(addMenu, "Media Specimen", selectedTreeNode, MediaSpecimen.class, SpecimenOrObservationType.Media, DerivationEventType.ACCESSIONING());
  81                             }
  82                             //context menu for Sequence
  83                             else if(selectedTreeNode.getValue() instanceof Sequence){
  84                                 createMenuItem(addMenu, "Single Read", selectedTreeNode, SingleRead.class, null, null);
  85                             }
  86                             //default
  87                             else{
  88                                 MenuItem menuItem = new MenuItem(addMenu, SWT.NONE);
  89                                 menuItem.setText("No child derivates");
  90                                 menuItem.setEnabled(false);
  91                             }
  92                         }
  93                     }
  94
  95
  96                 }
  97         };
  98         return contributionItems;
  99     }
 100
 101     private void createMenuItem(Menu menu, String menuLabel, final TreeNode selectedNode, Class<?> childClass, final SpecimenOrObservationType specimenType, final DerivationEventType derivationEventType) {
 102         if(specimenType!=null && specimenType.equals(SpecimenOrObservationType.Media)){
 103             //media submenu
 104             MenuItem mediaItem = new MenuItem(menu, SWT.CASCADE);
 105             mediaItem.setText("Media...");
 106             Menu mediaMenu = new Menu(menu);
 107             mediaItem.setMenu(mediaMenu);
 108
 109             //media specimen menu
 110             MenuItem menuItem = new MenuItem(mediaMenu, SWT.NONE);
 111             menuItem.setText(menuLabel);
 112             menuItem.addSelectionListener(new WidgetSelectionListener(selectedNode, childClass, specimenType, derivationEventType));
 113
 114             //existing media menu
 115             MenuItem existingMediaItem = new MenuItem(mediaMenu, SWT.NONE);
 116             existingMediaItem.setText("Media Specimen with existing media");
 117             existingMediaItem.addSelectionListener(new SelectionAdapter() {
 118                 @Override
 119                 public void widgetSelected(SelectionEvent e) {
 120                     //select media
 121                     Media media = MediaSelectionDialog.select(AbstractUtility.getShell(), null, null);
 122                     //create MediaSpecimen
 123                     MediaSpecimen mediaSpecimen = MediaSpecimen.NewInstance(specimenType);
 124                     mediaSpecimen.setMediaSpecimen(media);
 125
 126                     //attach to parent
 127                     if(selectedNode.getValue() instanceof SpecimenOrObservationBase){
 128                         SpecimenOrObservationBase<?> specimenOrObservationBase = (SpecimenOrObservationBase<?>)selectedNode.getValue();
 129
 130                         specimenOrObservationBase.addDerivationEvent(DerivationEvent.NewSimpleInstance(specimenOrObservationBase, mediaSpecimen, derivationEventType));
 131                         mediaSpecimen.setCacheStrategy(new DerivedUnitFacadeCacheStrategy());
 132                         mediaSpecimen.getTitleCache(); //update title cache
 133                         CdmStore.getService(IOccurrenceService.class).merge(specimenOrObservationBase);
 134                     }
 135
 136                     //refresh view
 137                     DerivateView derivateView = null;
 138                     if(AbstractUtility.getActivePart() instanceof DerivateView){
 139                         derivateView = (DerivateView) AbstractUtility.getActivePart();
 140                     }
 141                     if(derivateView!=null){
 142
 143                         derivateView.getConversationHolder().commit();
 144                         derivateView.refreshTree(mediaSpecimen);
 145                     }
 146                 }
 147             });
 148         }
 149         else{
 150             MenuItem menuItem = new MenuItem(menu, SWT.NONE);
 151             menuItem.setText(menuLabel);
 152             menuItem.addSelectionListener(new WidgetSelectionListener(selectedNode, childClass, specimenType, derivationEventType));
 153         }
 154     }
 155
 156     private class WidgetSelectionListener extends SelectionAdapter{
 157
 158         private final TreeNode selectedNode;
 159         //TODO: we need a common interface for the generic like e.g. "IDerivateHierarchyNode"
 160         private final Class<?> childClass;
 161         private final SpecimenOrObservationType specimenType;
 162         private final DerivationEventType derivationEventType;
 163
 164         /**
 165          * @param selectedNode
 166          * @param specimenType
 167          */
 168         public WidgetSelectionListener(TreeNode selectedNode, Class<?> childClass, SpecimenOrObservationType specimenType, DerivationEventType derivationEventType) {
 169             this.selectedNode = selectedNode;
 170             this.childClass = childClass;
 171             this.specimenType = specimenType;
 172             this.derivationEventType = derivationEventType;
 173         }
 174
 175         @Override
 176         public void widgetSelected(SelectionEvent e) {
 177             DerivateView derivateView = null;
 178             if(AbstractUtility.getActivePart() instanceof DerivateView){
 179                 derivateView = (DerivateView) AbstractUtility.getActivePart();
 180             }
 181             if(derivateView!=null){
 182                 if(derivateView.isDirty()){
 183                     e.doit = false;
 184                     MessagingUtils.warningDialog("View has unsaved changes", this, "You need to save before performing this action");
 185                     return;
 186                 }
 187             }
 188
 189             Object createdElement = null;
 190             Object selectedDerivate = selectedNode.getValue();
 191             if(selectedDerivate instanceof DnaSample && ((DnaSample) selectedDerivate).getRecordBasis()==SpecimenOrObservationType.DnaSample){
 192                 DnaSample dnaSample = (DnaSample)selectedDerivate;
 193                 if(childClass.equals(Sequence.class)){
 194                     Sequence newInstance = Sequence.NewInstance(dnaSample, "", 0);
 195                     createdElement = newInstance;
 196                 }
 197                 CdmStore.getService(IOccurrenceService.class).merge((SpecimenOrObservationBase) selectedDerivate);
 198             }
 199             else if(selectedDerivate instanceof Sequence){
 200                 SingleRead newInstance = SingleRead.NewInstance();
 201                 ((Sequence) selectedDerivate).addSingleRead(newInstance);
 202                 createdElement = newInstance;
 203                 CdmApplicationState.getCurrentAppConfig().getSequenceService().merge((Sequence)selectedDerivate);
 204             }
 205             else if(selectedDerivate instanceof SpecimenOrObservationBase && DerivedUnit.class.isAssignableFrom(childClass)){
 206                 SpecimenOrObservationBase<?> specimenOrObservationBase = (SpecimenOrObservationBase<?>)selectedDerivate;
 207                 DerivedUnit derivedUnit;
 208                 if(childClass.equals(DnaSample.class)){
 209                     derivedUnit = DnaSample.NewInstance();
 210                     if(specimenType==SpecimenOrObservationType.DnaSample){
 211                         derivedUnit.setRecordBasis(SpecimenOrObservationType.DnaSample);
 212                     }
 213                     else if(specimenType==SpecimenOrObservationType.TissueSample){
 214                         derivedUnit.setRecordBasis(SpecimenOrObservationType.TissueSample);
 215                     }
 216                 }
 217                 else if(childClass.equals(MediaSpecimen.class)){
 218                     derivedUnit = MediaSpecimen.NewInstance(specimenType);
 219                     //a MediaSpecimen with no media attached does not make sense. Hence we add one
 220                     ((MediaSpecimen)derivedUnit).setMediaSpecimen(Media.NewInstance());
 221                 }
 222                 else{
 223                     derivedUnit = DerivedUnit.NewInstance(specimenType);
 224                 }
 225                 specimenOrObservationBase.addDerivationEvent(DerivationEvent.NewSimpleInstance(specimenOrObservationBase, derivedUnit, derivationEventType));
 226                 derivedUnit.setCacheStrategy(new DerivedUnitFacadeCacheStrategy());
 227                 derivedUnit.getTitleCache(); //update title cache
 228                 createdElement = derivedUnit;
 229                 CdmStore.getService(IOccurrenceService.class).merge((SpecimenOrObservationBase) selectedDerivate);
 230             }
 231
 232             //refresh view
 233             if(derivateView!=null){
 234                 //CdmStore.getService(IOccurrenceService.class).merge((SpecimenOrObservationBase) selectedDerivate);
 235                 derivateView.getConversationHolder().commit();
 236                 derivateView.refreshTree(createdElement);
 237             }
 238         }
 239     }
 240
 241 }