private void updateFromDB() {
   InstanceListPane touchedList = null;
   // Find out which instances have been selected in all relevant lists
   // Update the attribute values for changed list.
   try {
     if (changedList != null) {
       java.util.List list = new ArrayList(changedList.getSelection()); // To support it.remove()
       // Use a new ArrayList.
       if (list != null && list.size() > 0) {
         for (Iterator it = list.iterator(); it.hasNext(); ) {
           GKInstance instance = (GKInstance) it.next();
           // Fetch GKInstance based on its DB_ID since SchemaClass might be changed.
           GKInstance localCopy = fileAdaptor.fetchInstance(instance.getDBID());
           dbAdaptor.setUseCache(false);
           GKInstance dbCopy = dbAdaptor.fetchInstance(instance.getDBID());
           dbAdaptor.setUseCache(true);
           if (SynchronizationManager.getManager().updateFromDB(localCopy, dbCopy, this)) {
             AttributeEditManager.getManager().attributeEdit(localCopy);
             fileAdaptor.removeDirtyFlag(localCopy);
           } else it.remove(); // Remove from the list
         }
         // Remove all selected instances
         changedList.deleteInstances(list);
         touchedList = changedList;
       }
     }
     if (localHasMoreIEList != null && localHasMoreIEList.getSelection().size() > 0) {
       List list = new ArrayList(localHasMoreIEList.getSelection());
       for (Iterator it = list.iterator(); it.hasNext(); ) {
         GKInstance localCopy = (GKInstance) it.next();
         dbAdaptor.setUseCache(false);
         GKInstance dbCopy = dbAdaptor.fetchInstance(localCopy.getDBID());
         dbAdaptor.setUseCache(true);
         if (SynchronizationManager.getManager().updateFromDB(localCopy, dbCopy, this)) {
           AttributeEditManager.getManager().attributeEdit(localCopy);
           fileAdaptor.removeDirtyFlag(localCopy);
         } else it.remove(); // Remove from the list, if it it cancelled by the user.
       }
       localHasMoreIEList.deleteInstances(list);
       touchedList = localHasMoreIEList;
     }
     // Delete the local copy for deleteInDBList.
     if (deleteInDBList != null) {
       java.util.List list = deleteInDBList.getSelection();
       if (list != null && list.size() > 0) {
         for (Iterator it = list.iterator(); it.hasNext(); ) {
           GKInstance instance = (GKInstance) it.next();
           fileAdaptor.deleteInstance(instance);
         }
       }
       deleteInDBList.deleteInstances(list);
       touchedList = deleteInDBList;
     }
     // Get another copy for the local repository
     if (deleteList != null) {
       java.util.List<?> list = deleteList.getSelection();
       if (list != null && list.size() > 0) {
         Map<SchemaClass, Set<GKInstance>> checkOutMap =
             new HashMap<SchemaClass, Set<GKInstance>>(); // All checked out Instances
         for (Iterator<?> it = list.iterator(); it.hasNext(); ) {
           GKInstance instance = (GKInstance) it.next();
           Map<SchemaClass, List<GKInstance>> schemaMap =
               InstanceUtilities.listDownloadableInstances(instance);
           // Have to merge schemaMap to checkOutMap
           for (SchemaClass key : schemaMap.keySet()) {
             List<GKInstance> list1 = schemaMap.get(key);
             if (list1 != null && list1.size() > 0) {
               Set<GKInstance> list2 = checkOutMap.get(key);
               if (list2 == null) {
                 list2 = new HashSet<GKInstance>();
                 checkOutMap.put(key, list2);
               }
               // Remove first to avoid any duplication
               list2.addAll(list1);
             }
           }
         }
         fileAdaptor.store(checkOutMap);
         InstanceUtilities.clearShellFlags(checkOutMap);
         // There are maybe more than selected instances after checking out
         List<GKInstance> checkedOut = new ArrayList<GKInstance>();
         for (Set<GKInstance> set : checkOutMap.values()) {
           checkedOut.addAll(set);
         }
         deleteList.deleteInstances(checkedOut);
         // deleteList.deleteInstances(list);
         // Need to clear out these deletion records
         List<Long> dbIds = new ArrayList<Long>();
         for (GKInstance inst : checkedOut) dbIds.add(inst.getDBID());
         fileAdaptor.clearDeleteRecord(dbIds);
         touchedList = deleteList;
       }
     }
   } catch (Exception e) {
     System.err.println("SynchronizationDialog.updateFromDB(): " + e);
     e.printStackTrace();
   }
   updateInstanceList(touchedList);
 }
  private void showComparison() {
    // Find the instance that can be used for comparision. This instance
    // should be chosen from changedList or localHasUnexpInstance
    GKInstance instance = null;
    if (changedList != null) { // Check changedList first
      List selection = changedList.getSelection();
      if (selection.size() > 0) instance = (GKInstance) selection.get(0);
    }
    if (instance == null && localHasMoreIEList != null) {
      List selection = localHasMoreIEList.getSelection();
      if (selection.size() > 0) instance = (GKInstance) selection.get(0);
    }
    if (instance == null) return;
    final InstanceComparisonPane comparisonPane = new InstanceComparisonPane();
    // Fine tune comparison pane for making comparisons with
    // database
    comparisonPane.setSaveDialogHideUnusedButtons(true);
    comparisonPane.setSaveDialogSaveAsNewBtnFirst(false);
    comparisonPane.setSaveDialogSaveAsNewBtnTitle(
        "Create new local instance and put merge into that");
    comparisonPane.setSaveDialogReplaceFirstBtnTitle(
        "Overwrite existing instance with merge (recommended)");
    comparisonPane.setCloseAfterSaving(true);
    try {
      String clsName = instance.getSchemClass().getName();
      Long instanceId = instance.getDBID();
      final GKInstance localCopy = fileAdaptor.fetchInstance(clsName, instanceId);
      dbAdaptor.setUseCache(false);
      // final GKInstance dbCopy = dbAdaptor.fetchInstance(clsName, instanceId);
      // The class type might be changed locally or remotely. So not clsName should be used
      // to fetch database instance. Otherwise, null exception will be thrown. The same thing
      // is done also in creating synchronization result.
      final GKInstance dbCopy = dbAdaptor.fetchInstance(instanceId);
      dbAdaptor.setUseCache(true);
      comparisonPane.setInstances(localCopy, dbCopy);
      String title =
          "Comparing Instances \""
              + instance.getDisplayName()
              + "\" in the local and DB repositories";
      JDialog parentDialog = (JDialog) SwingUtilities.getAncestorOfClass(JDialog.class, centerPane);
      final JDialog dialog = new JDialog(parentDialog, title);
      // Try to update the list automatically
      dialog.addWindowListener(
          new WindowAdapter() {
            public void windowClosed(WindowEvent e) {
              handleMergeResult(localCopy, dbCopy, comparisonPane);
              // To prevent double calling. It is called again when parentDialog is closed.
              dialog.removeWindowListener(this);
            }
          });
      dialog.getContentPane().add(comparisonPane, BorderLayout.CENTER);
      dialog.setModal(true);
      dialog.setSize(800, 600);
      GKApplicationUtilities.center(dialog);
      dialog.setVisible(true);

      // Update synchronization dialog panels depending on user
      // choice.
      if (comparisonPane.getSaveMergeOption() == InstanceComparisonPane.SAVE_AS_NEW) {
        GKInstance merged = comparisonPane.getMerged();

        if (newList == null) {
          List list = new ArrayList();
          list.add(merged);
          newList = initInstanceListPane(list, "Instances created locally: " + list.size());
        } else newList.addInstance(merged);
      } else if (comparisonPane.getSaveMergeOption() == InstanceComparisonPane.OVERWRITE_FIRST) {
        dbAdaptor.setUseCache(false);
        GKInstance remoteCopy = dbAdaptor.fetchInstance(instance.getDBID());
        dbAdaptor.setUseCache(true);
        if (remoteCopy != null) {
          InstanceComparer comparer = new InstanceComparer();
          int reply = comparer.compare(instance, remoteCopy);
          if (reply == InstanceComparer.LOCAL_HAS_MORE_IE) {
            if (localHasMoreIEList == null) {
              List list = new ArrayList();
              list.add(instance);
              localHasMoreIEList =
                  initInstanceListPane(
                      list, "Local instances having unexpected InstanceEdits: " + list.size());
            } else localHasMoreIEList.addInstance(instance);
          } else if (reply == InstanceComparer.IS_IDENTICAL) {
            // Merge has made local and database copies
            // identical - don't need to check in anymore
            changedList.deleteInstance(instance);
          } else if (reply != InstanceComparer.NEW_CHANGE_IN_LOCAL) {
            // Merge has produced a conflict
            typeMap.put(mapCompareResultToString(reply), instance);
          } else
            // The user should now be allowed to commit this
            // instance, because it will now have changed.
            commitToDBAction.setEnabled(true);

          JOptionPane.showMessageDialog(
              parentDialog,
              "Merge successful, you will need to check the merged instance into the database.\n\n",
              "Merge OK",
              JOptionPane.INFORMATION_MESSAGE);
        }
      }

    } catch (Exception e1) {
      System.err.println("Synchronization.createDisplayMapPane(): " + e1);
      e1.printStackTrace();
      JOptionPane.showMessageDialog(
          this,
          "Error in comparing: " + instance.toString(),
          "Error in Comparing",
          JOptionPane.ERROR_MESSAGE);
    }
  }
Пример #3
0
 private void convertReactomeToGPML(Long dbID, String outputFileName) throws Exception {
   GKInstance pathway = adaptor.fetchInstance(dbID);
   convertReactomeToGPML(pathway, outputFileName);
 }