fixed PY-14121 IPython Notebook: missing Undo action

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/IpnbEditorState.java

@@ -20,7 +20,7 @@ import com.intellij.openapi.fileEditor.FileEditorStateLevel;
 
 final class IpnbEditorState implements FileEditorState{
   private final transient long myDocumentModificationStamp; // should not be serialized
-  private int mySelectedIndex;
+  private int mySelectedIndex = 0;
   private int mySelectedTop;
 
   public IpnbEditorState(final long modificationStamp, int selectedComponentIndex, int top) {
@@ -34,9 +34,8 @@ final class IpnbEditorState implements FileEditorState{
     if (!(o instanceof IpnbEditorState)) return false;
 
     final IpnbEditorState state = (IpnbEditorState)o;
-
-    return myDocumentModificationStamp == state.myDocumentModificationStamp && mySelectedIndex == state.mySelectedIndex &&
-      mySelectedTop == state.mySelectedTop;
+    if (mySelectedIndex == -1) return true;
+    return myDocumentModificationStamp == state.myDocumentModificationStamp;
   }
 
   public int getSelectedTop() {

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/IpnbFileEditor.java

@@ -1,11 +1,11 @@
 package org.jetbrains.plugins.ipnb.editor;
 
 import com.google.common.collect.Lists;
-import com.intellij.AppTopics;
 import com.intellij.codeHighlighting.BackgroundEditorHighlighter;
 import com.intellij.icons.AllIcons;
 import com.intellij.ide.structureView.StructureViewBuilder;
 import com.intellij.openapi.actionSystem.CustomShortcutSet;
+import com.intellij.openapi.editor.Document;
 import com.intellij.openapi.editor.Editor;
 import com.intellij.openapi.fileEditor.*;
 import com.intellij.openapi.fileEditor.ex.FileEditorProviderManager;
@@ -63,27 +63,15 @@ public class IpnbFileEditor extends UserDataHolderBase implements FileEditor, Te
 
 
   public IpnbFileEditor(Project project, final VirtualFile vFile) {
-    project.getMessageBus().connect(this).subscribe(AppTopics.FILE_DOCUMENT_SYNC, new FileDocumentManagerAdapter() {
-      @Override
-      public void beforeAllDocumentsSaving() {
-        if (!new File(vFile.getPath()).exists()) return;
-        final IpnbFilePanel filePanel = myIpnbFilePanel;
-        if (filePanel != null) {
-          IpnbParser.saveIpnbFile(filePanel);
-          vFile.refresh(false, false);
-        }
-
-      }
-    });
-
     project.getMessageBus().connect(this).subscribe(FileEditorManagerListener.Before.FILE_EDITOR_MANAGER, new FileEditorManagerListener.Before.Adapter() {
       @Override
       public void beforeFileClosed(@NotNull FileEditorManager source, @NotNull VirtualFile file) {
         if (!new File(file.getPath()).exists()) return;
         IpnbParser.saveIpnbFile(myIpnbFilePanel);
-          file.refresh(false, false);
+        file.refresh(false, false);
       }
     });
+
     myFile = vFile;
 
     myName = vFile.getName();
@@ -94,7 +82,7 @@ public class IpnbFileEditor extends UserDataHolderBase implements FileEditor, Te
     myEditorPanel.setBackground(IpnbEditorUtil.getBackground());
 
     myIpnbFilePanel = createIpnbEditorPanel(project, vFile);
-
+    Disposer.register(this, myIpnbFilePanel);
     final JPanel controlPanel = createControlPanel();
     myEditorPanel.add(controlPanel, BorderLayout.NORTH);
     myScrollPane = ScrollPaneFactory.createScrollPane(myIpnbFilePanel);
@@ -156,7 +144,9 @@ public class IpnbFileEditor extends UserDataHolderBase implements FileEditor, Te
       }
     });
     final IpnbPanel selectedCell = myIpnbFilePanel.getSelectedCell();
-    updateCellTypeCombo(selectedCell);
+    if (selectedCell != null) {
+      updateCellTypeCombo(selectedCell);
+    }
     controlPanel.add(myCellTypeCombo);
     final MatteBorder border = BorderFactory.createMatteBorder(0, 0, 1, 0, JBColor.GRAY);
     controlPanel.setBorder(border);
@@ -329,7 +319,7 @@ public class IpnbFileEditor extends UserDataHolderBase implements FileEditor, Te
                              });
   }
 
-  private void updateCellTypeCombo(IpnbPanel ipnbPanel) {
+  private void updateCellTypeCombo(@NotNull final IpnbPanel ipnbPanel) {
     if (ipnbPanel instanceof IpnbHeadingPanel) {
       final IpnbHeadingCell cell = ((IpnbHeadingPanel)ipnbPanel).getCell();
       final int level = cell.getLevel();
@@ -370,7 +360,9 @@ public class IpnbFileEditor extends UserDataHolderBase implements FileEditor, Te
     final int index = getIpnbFilePanel().getSelectedIndex();
     final IpnbEditablePanel cell = getIpnbFilePanel().getSelectedCell();
     final int top = cell != null ? cell.getTop() : 0;
-    return new IpnbEditorState(-1, index, top);
+    final Document document = FileDocumentManager.getInstance().getCachedDocument(myFile);
+    long modificationStamp = document != null ? document.getModificationStamp() : myFile.getModificationStamp();
+    return new IpnbEditorState(modificationStamp, index, top);
   }
 
   @Override

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/actions/IpnbAddCellAboveAction.java

@@ -4,6 +4,8 @@ import com.intellij.openapi.actionSystem.AnAction;
 import com.intellij.openapi.actionSystem.AnActionEvent;
 import com.intellij.openapi.actionSystem.DataContext;
 import com.intellij.openapi.actionSystem.PlatformDataKeys;
+import com.intellij.openapi.application.ApplicationManager;
+import com.intellij.openapi.command.CommandProcessor;
 import com.intellij.openapi.fileEditor.FileEditor;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.plugins.ipnb.editor.IpnbFileEditor;
@@ -22,6 +24,16 @@ public class IpnbAddCellAboveAction extends AnAction {
   }
 
   public void addCell(@NotNull final IpnbFilePanel ipnbFilePanel) {
-    ipnbFilePanel.createAndAddCell(false);
+    CommandProcessor.getInstance().executeCommand(ipnbFilePanel.getProject(), new Runnable() {
+      public void run() {
+        ApplicationManager.getApplication().runWriteAction(new Runnable() {
+          public void run() {
+            ipnbFilePanel.createAndAddCell(false);
+            ipnbFilePanel.saveToFile();
+          }
+        });
+      }
+    }, "Ipnb.createAndAddCell", new Object());
+
   }
 }

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/actions/IpnbAddCellBelowAction.java

@@ -4,6 +4,8 @@ import com.intellij.openapi.actionSystem.AnAction;
 import com.intellij.openapi.actionSystem.AnActionEvent;
 import com.intellij.openapi.actionSystem.DataContext;
 import com.intellij.openapi.actionSystem.PlatformDataKeys;
+import com.intellij.openapi.application.ApplicationManager;
+import com.intellij.openapi.command.CommandProcessor;
 import com.intellij.openapi.fileEditor.FileEditor;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.plugins.ipnb.editor.IpnbFileEditor;
@@ -22,6 +24,15 @@ public class IpnbAddCellBelowAction extends AnAction {
   }
 
   public static void addCell(@NotNull final IpnbFilePanel ipnbFilePanel) {
-    ipnbFilePanel.createAndAddCell(true);
+    CommandProcessor.getInstance().executeCommand(ipnbFilePanel.getProject(), new Runnable() {
+      public void run() {
+        ApplicationManager.getApplication().runWriteAction(new Runnable() {
+          public void run() {
+            ipnbFilePanel.createAndAddCell(true);
+            ipnbFilePanel.saveToFile();
+          }
+        });
+      }
+    }, "Ipnb.createAndAddCell", new Object());
   }
 }

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/actions/IpnbCodeCellAction.java

@@ -31,6 +31,7 @@ public class IpnbCodeCellAction extends AnAction {
   public void changeTypeToCode(@NotNull final IpnbFileEditor editor) {
     final IpnbFilePanel filePanel = editor.getIpnbFilePanel();
     final IpnbEditablePanel selectedCell = filePanel.getSelectedCell();
+    if (selectedCell == null) return;
     final IpnbEditableCell cell = selectedCell.getCell();
 
     final List<IpnbCell> cells = filePanel.getIpnbFile().getCells();

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/actions/IpnbCutCellAction.java

@@ -5,6 +5,8 @@ import com.intellij.openapi.actionSystem.AnAction;
 import com.intellij.openapi.actionSystem.AnActionEvent;
 import com.intellij.openapi.actionSystem.DataContext;
 import com.intellij.openapi.actionSystem.PlatformDataKeys;
+import com.intellij.openapi.application.ApplicationManager;
+import com.intellij.openapi.command.CommandProcessor;
 import com.intellij.openapi.fileEditor.FileEditor;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.plugins.ipnb.editor.IpnbFileEditor;
@@ -26,8 +28,15 @@ public class IpnbCutCellAction extends AnAction {
   }
 
   public static void cutCell(@NotNull final IpnbFilePanel ipnbFilePanel) {
-    ipnbFilePanel.cutCell();
-    ipnbFilePanel.revalidate();
-    ipnbFilePanel.repaint();
+    CommandProcessor.getInstance().executeCommand(ipnbFilePanel.getProject(), new Runnable() {
+      public void run() {
+        ApplicationManager.getApplication().runWriteAction(new Runnable() {
+          public void run() {
+            ipnbFilePanel.cutCell();
+            ipnbFilePanel.saveToFile();
+          }
+        });
+      }
+    }, "Ipnb.cutCell", new Object());
   }
 }

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/actions/IpnbDeleteCellAction.java

@@ -5,6 +5,8 @@ import com.intellij.openapi.actionSystem.AnAction;
 import com.intellij.openapi.actionSystem.AnActionEvent;
 import com.intellij.openapi.actionSystem.DataContext;
 import com.intellij.openapi.actionSystem.PlatformDataKeys;
+import com.intellij.openapi.application.ApplicationManager;
+import com.intellij.openapi.command.CommandProcessor;
 import com.intellij.openapi.fileEditor.FileEditor;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.plugins.ipnb.editor.IpnbFileEditor;
@@ -21,13 +23,20 @@ public class IpnbDeleteCellAction extends AnAction {
     final FileEditor editor = PlatformDataKeys.FILE_EDITOR.getData(context);
     if (editor instanceof IpnbFileEditor) {
       final IpnbFilePanel component = ((IpnbFileEditor)editor).getIpnbFilePanel();
-      cutCell(component);
+      deleteCell(component);
     }
   }
 
-  public void cutCell(@NotNull final IpnbFilePanel ipnbFilePanel) {
-    ipnbFilePanel.deleteSelectedCell();
-    ipnbFilePanel.revalidate();
-    ipnbFilePanel.repaint();
+  public static void deleteCell(@NotNull final IpnbFilePanel ipnbFilePanel) {
+    CommandProcessor.getInstance().executeCommand(ipnbFilePanel.getProject(), new Runnable() {
+      public void run() {
+        ApplicationManager.getApplication().runWriteAction(new Runnable() {
+          public void run() {
+            ipnbFilePanel.deleteSelectedCell();
+            ipnbFilePanel.saveToFile();
+          }
+        });
+      }
+    }, "Ipnb.deleteCell", new Object());
   }
 }

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/actions/IpnbHeadingCellActionBase.java

@@ -34,6 +34,7 @@ public class IpnbHeadingCellActionBase extends AnAction {
   public void changeTypeToHeading(@NotNull final IpnbFileEditor editor) {
     final IpnbFilePanel filePanel = editor.getIpnbFilePanel();
     final IpnbEditablePanel selectedCell = filePanel.getSelectedCell();
+    if (selectedCell == null) return;
     final IpnbEditableCell cell = selectedCell.getCell();
 
     final List<IpnbCell> cells = filePanel.getIpnbFile().getCells();

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/actions/IpnbMarkdownCellAction.java

@@ -29,6 +29,7 @@ public class IpnbMarkdownCellAction extends AnAction {
   public void changeTypeToMarkdown(@NotNull final IpnbFileEditor editor) {
     final IpnbFilePanel filePanel = editor.getIpnbFilePanel();
     final IpnbEditablePanel selectedCell = filePanel.getSelectedCell();
+    if (selectedCell == null) return;
     final IpnbEditableCell cell = selectedCell.getCell();
 
     final List<IpnbCell> cells = filePanel.getIpnbFile().getCells();

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/actions/IpnbMoveCellDownAction.java

@@ -4,6 +4,8 @@ import com.intellij.openapi.actionSystem.AnAction;
 import com.intellij.openapi.actionSystem.AnActionEvent;
 import com.intellij.openapi.actionSystem.DataContext;
 import com.intellij.openapi.actionSystem.PlatformDataKeys;
+import com.intellij.openapi.application.ApplicationManager;
+import com.intellij.openapi.command.CommandProcessor;
 import com.intellij.openapi.fileEditor.FileEditor;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.plugins.ipnb.editor.IpnbFileEditor;
@@ -17,7 +19,17 @@ public class IpnbMoveCellDownAction extends AnAction {
     final FileEditor editor = PlatformDataKeys.FILE_EDITOR.getData(context);
     if (editor instanceof IpnbFileEditor) {
       final IpnbFilePanel ipnbFilePanel = ((IpnbFileEditor)editor).getIpnbFilePanel();
-      ipnbFilePanel.moveCell(true);
+      CommandProcessor.getInstance().executeCommand(ipnbFilePanel.getProject(), new Runnable() {
+        public void run() {
+          ApplicationManager.getApplication().runWriteAction(new Runnable() {
+            public void run() {
+              ipnbFilePanel.moveCell(true);
+              ipnbFilePanel.saveToFile();
+            }
+          });
+        }
+      }, "Ipnb.moveCell", new Object());
+
     }
   }
 }

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/actions/IpnbMoveCellUpAction.java

@@ -4,6 +4,8 @@ import com.intellij.openapi.actionSystem.AnAction;
 import com.intellij.openapi.actionSystem.AnActionEvent;
 import com.intellij.openapi.actionSystem.DataContext;
 import com.intellij.openapi.actionSystem.PlatformDataKeys;
+import com.intellij.openapi.application.ApplicationManager;
+import com.intellij.openapi.command.CommandProcessor;
 import com.intellij.openapi.fileEditor.FileEditor;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.plugins.ipnb.editor.IpnbFileEditor;
@@ -16,8 +18,18 @@ public class IpnbMoveCellUpAction extends AnAction {
     final DataContext context = event.getDataContext();
     final FileEditor editor = PlatformDataKeys.FILE_EDITOR.getData(context);
     if (editor instanceof IpnbFileEditor) {
-      final IpnbFilePanel filePanel = ((IpnbFileEditor)editor).getIpnbFilePanel();
-      filePanel.moveCell(false);
+      final IpnbFilePanel ipnbFilePanel = ((IpnbFileEditor)editor).getIpnbFilePanel();
+      CommandProcessor.getInstance().executeCommand(ipnbFilePanel.getProject(), new Runnable() {
+        public void run() {
+          ApplicationManager.getApplication().runWriteAction(new Runnable() {
+            public void run() {
+              ipnbFilePanel.moveCell(false);
+              ipnbFilePanel.saveToFile();
+            }
+          });
+        }
+      }, "Ipnb.moveCell", new Object());
+
     }
   }
 

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/actions/IpnbPasteCellAction.java

@@ -5,6 +5,8 @@ import com.intellij.openapi.actionSystem.AnAction;
 import com.intellij.openapi.actionSystem.AnActionEvent;
 import com.intellij.openapi.actionSystem.DataContext;
 import com.intellij.openapi.actionSystem.PlatformDataKeys;
+import com.intellij.openapi.application.ApplicationManager;
+import com.intellij.openapi.command.CommandProcessor;
 import com.intellij.openapi.fileEditor.FileEditor;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.plugins.ipnb.editor.IpnbFileEditor;
@@ -26,6 +28,16 @@ public class IpnbPasteCellAction extends AnAction {
   }
 
   public static void pasteCell(@NotNull final IpnbFilePanel ipnbFilePanel) {
-    ipnbFilePanel.pasteCell();
+    CommandProcessor.getInstance().executeCommand(ipnbFilePanel.getProject(), new Runnable() {
+      public void run() {
+        ApplicationManager.getApplication().runWriteAction(new Runnable() {
+          public void run() {
+            ipnbFilePanel.pasteCell();
+            ipnbFilePanel.saveToFile();
+          }
+        });
+      }
+    }, "Ipnb.pasteCell", new Object());
+
   }
 }

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/actions/IpnbRunCellBaseAction.java

@@ -19,6 +19,7 @@ public abstract class IpnbRunCellBaseAction extends AnAction {
       final int index = ipnbFilePanel.getSelectedIndex();
       if (ipnbFilePanel.getIpnbPanels().size()-1 == index) {
         ipnbFilePanel.createAndAddCell(true);
+        ipnbFilePanel.saveToFile();
       }
       ipnbFilePanel.selectNext(cell);
     }

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/panels/IpnbFilePanel.java

@@ -1,19 +1,31 @@
 package org.jetbrains.plugins.ipnb.editor.panels;
 
 import com.google.common.collect.Lists;
+import com.intellij.openapi.Disposable;
 import com.intellij.openapi.actionSystem.DataProvider;
 import com.intellij.openapi.application.ApplicationManager;
+import com.intellij.openapi.application.ModalityState;
+import com.intellij.openapi.command.CommandProcessor;
+import com.intellij.openapi.diagnostic.Logger;
+import com.intellij.openapi.editor.Document;
+import com.intellij.openapi.editor.event.DocumentAdapter;
+import com.intellij.openapi.editor.event.DocumentEvent;
 import com.intellij.openapi.fileEditor.OpenFileDescriptor;
 import com.intellij.openapi.project.Project;
 import com.intellij.openapi.ui.Messages;
 import com.intellij.openapi.ui.VerticalFlowLayout;
 import com.intellij.openapi.vfs.VirtualFile;
+import com.intellij.psi.PsiDocumentManager;
 import com.intellij.ui.JBColor;
+import com.intellij.util.Alarm;
 import com.intellij.util.ui.UIUtil;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.jetbrains.plugins.ipnb.editor.IpnbEditorUtil;
 import org.jetbrains.plugins.ipnb.editor.IpnbFileEditor;
+import org.jetbrains.plugins.ipnb.editor.actions.IpnbCutCellAction;
+import org.jetbrains.plugins.ipnb.editor.actions.IpnbDeleteCellAction;
+import org.jetbrains.plugins.ipnb.editor.actions.IpnbPasteCellAction;
 import org.jetbrains.plugins.ipnb.editor.panels.code.IpnbCodePanel;
 import org.jetbrains.plugins.ipnb.format.IpnbFile;
 import org.jetbrains.plugins.ipnb.format.IpnbParser;
@@ -30,16 +42,19 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
-public class IpnbFilePanel extends JPanel implements Scrollable, DataProvider {
+public class IpnbFilePanel extends JPanel implements Scrollable, DataProvider, Disposable {
+  private static final Logger LOG = Logger.getInstance(IpnbFilePanel.class);
+  private final DocumentAdapter myDocumentListener;
+  private Document myDocument;
   private IpnbFile myIpnbFile;
-
   private Project myProject;
   @NotNull private IpnbFileEditor myParent;
+  @NotNull private final VirtualFile myVirtualFile;
   @NotNull private final IpnbFileEditor.CellSelectionListener myListener;
 
   private final List<IpnbEditablePanel> myIpnbPanels = Lists.newArrayList();
 
-  private IpnbEditablePanel mySelectedCell;
+  @Nullable private IpnbEditablePanel mySelectedCell;
   private IpnbEditablePanel myBufferPanel;
   private int myIncrement = 10;
   private int myInitialSelection = 0;
@@ -50,37 +65,61 @@ public class IpnbFilePanel extends JPanel implements Scrollable, DataProvider {
     super(new VerticalFlowLayout(VerticalFlowLayout.TOP, 100, 5, true, false));
     myProject = project;
     myParent = parent;
+    myVirtualFile = vFile;
     myListener = listener;
     setBackground(IpnbEditorUtil.getBackground());
 
-    ApplicationManager.getApplication().invokeLater(new Runnable() {
+    final Alarm alarm = new Alarm();
+    myDocumentListener = new DocumentAdapter() {
+      public void documentChanged(final DocumentEvent e) {
+        alarm.cancelAllRequests();
+        alarm.addRequest(new MySynchronizeRequest(), 10, ModalityState.stateForComponent(IpnbFilePanel.this));
+      }
+    };
+    myDocument = myParent.getEditor().getDocument();
+    myDocument.addDocumentListener(myDocumentListener);
+
+    alarm.addRequest(new Runnable() {
       @Override
       public void run() {
-        try {
-          myIpnbFile = IpnbParser.parseIpnbFile(vFile);
-          if (myIpnbFile.getCells().isEmpty()) {
-            final IpnbCodeCell cell = new IpnbCodeCell("python", new String[]{""}, null, new ArrayList<IpnbOutputCell>());
-            myIpnbFile.addCell(cell, 0);
+        readFromFile(true);
+        addMouseListener(new MouseAdapter() {
+          @Override
+          public void mouseClicked(MouseEvent e) {
+            updateCellSelection(e);
           }
-          layoutFile();
-          addMouseListener(new MouseAdapter() {
-            @Override
-            public void mouseClicked(MouseEvent e) {
-              updateCellSelection(e);
-            }
-          });
-          setFocusable(true);
-
-        }
-        catch (IOException e) {
-          Messages.showErrorDialog(project, e.getMessage(), "Can't open " + vFile.getPath());
-        }
+        });
+        setFocusable(true);
       }
-    });
+    }, 10, ModalityState.stateForComponent(this));
 
     UIUtil.requestFocus(this);
   }
 
+  public void dispose() {
+    myDocument.removeDocumentListener(myDocumentListener);
+  }
+
+  private void readFromFile(boolean showError) {
+    try {
+      myIpnbPanels.clear();
+      mySelectedCell = null;
+      myIpnbFile = IpnbParser.parseIpnbFile(myDocument, myVirtualFile.getPath());
+      if (myIpnbFile.getCells().isEmpty()) {
+        final IpnbCodeCell cell = new IpnbCodeCell("python", new String[]{""}, null, new ArrayList<IpnbOutputCell>());
+        myIpnbFile.addCell(cell, 0);
+        saveToFile();
+      }
+    } catch (IOException e) {
+      if (showError)
+        Messages.showErrorDialog(getProject(), e.getMessage(), "Can't open " + myVirtualFile.getPath());
+      else
+        LOG.error(e.getMessage(), "Can't open " + myVirtualFile.getPath());
+
+    }
+    layoutFile();
+  }
+
   public List<IpnbEditablePanel> getIpnbPanels() {
     return myIpnbPanels;
   }
@@ -119,8 +158,7 @@ public class IpnbFilePanel extends JPanel implements Scrollable, DataProvider {
     }
   }
 
-  public void createAndAddCell(boolean below) {
-    removeAll();
+  public void createAndAddCell(final boolean below) {
     final IpnbCodeCell cell = new IpnbCodeCell("python", new String[]{""}, null, new ArrayList<IpnbOutputCell>());
     final IpnbCodePanel codePanel = new IpnbCodePanel(myProject, myParent, cell);
 
@@ -128,7 +166,6 @@ public class IpnbFilePanel extends JPanel implements Scrollable, DataProvider {
   }
 
   private void addCell(@NotNull final IpnbEditablePanel panel, boolean below) {
-    removeAll();
     final IpnbEditablePanel selectedCell = getSelectedCell();
     int index = myIpnbPanels.indexOf(selectedCell);
     if (below) {
@@ -137,16 +174,7 @@ public class IpnbFilePanel extends JPanel implements Scrollable, DataProvider {
     final IpnbEditableCell cell = panel.getCell();
     myIpnbFile.addCell(cell, index);
     myIpnbPanels.add(index, panel);
-
-    for (IpnbPanel comp : myIpnbPanels) {
-      add(comp);
-    }
-    add(createEmptyPanel());
-
     setSelectedCell(panel);
-    requestFocus();
-    revalidate();
-    repaint();
   }
 
   public void cutCell() {
@@ -171,7 +199,10 @@ public class IpnbFilePanel extends JPanel implements Scrollable, DataProvider {
 
     if (down) {
       deleteSelectedCell();
-      addCell(selectedCell, true);
+      final IpnbEditableCell cell = selectedCell.getCell();
+      myIpnbFile.addCell(cell, index + 1);
+      myIpnbPanels.add(index + 1, selectedCell);
+      setSelectedCell(selectedCell);
     }
     else {
       final IpnbEditablePanel siblingPanel = myIpnbPanels.get(siblingIndex);
@@ -183,65 +214,161 @@ public class IpnbFilePanel extends JPanel implements Scrollable, DataProvider {
 
   public void deleteSelectedCell() {
     final IpnbEditablePanel cell = getSelectedCell();
-    deleteCell(cell);
+    if (cell != null)
+      deleteCell(cell);
   }
 
-  private void deleteCell(@NotNull final IpnbEditablePanel cell) {
-    selectNextOrPrev(cell);
+  private boolean deleteCell(@NotNull final IpnbEditablePanel cell) {
     final int index = myIpnbPanels.indexOf(cell);
-    if (index < 0) return;
+    if (index < 0) return true;
     myIpnbPanels.remove(index);
     myIpnbFile.removeCell(index);
+    if (myIpnbFile.getCells().isEmpty()) {
+      final IpnbCodeCell newCell = new IpnbCodeCell("python", new String[]{""}, null, new ArrayList<IpnbOutputCell>());
+      final IpnbCodePanel codePanel = new IpnbCodePanel(myProject, myParent, newCell);
+      addCell(codePanel, false);
+    }
+    return false;
+  }
 
-    remove(cell);
-    if (myIpnbPanels.isEmpty()) {
-      createAndAddCell(true);
+  public void saveToFile() {
+    final String oldText = myDocument.getText();
+    final String newText = IpnbParser.newDocumentText(this);
+    try {
+      final ReplaceInfo replaceInfo = findFragmentToChange(oldText, newText);
+      if (replaceInfo.getStartOffset() != -1) {
+        myDocument.replaceString(replaceInfo.getStartOffset(), replaceInfo.getEndOffset(), replaceInfo.getReplacement());
+      }
+    }
+    catch (Exception e) {
+      myDocument.replaceString(0, oldText.length(), newText);
     }
   }
 
+  public static final class ReplaceInfo {
+    private final int myStartOffset;
+    private final int myEndOffset;
+    private final String myReplacement;
+
+    public ReplaceInfo(final int startOffset, final int endOffset, final String replacement) {
+      myStartOffset = startOffset;
+      myEndOffset = endOffset;
+      myReplacement = replacement;
+    }
+
+    public int getStartOffset() {
+      return myStartOffset;
+    }
+
+    public int getEndOffset() {
+      return myEndOffset;
+    }
+
+    public String getReplacement() {
+      return myReplacement;
+    }
+  }
+
+  public static ReplaceInfo findFragmentToChange(final String oldText, final String newText) {
+    if (oldText.equals(newText)) {
+      return new ReplaceInfo(-1, -1, null);
+    }
+
+    final int oldLength = oldText.length();
+    final int newLength = newText.length();
+
+    int startOffset = 0;
+    while (
+      startOffset < oldLength && startOffset < newLength &&
+      oldText.charAt(startOffset) == newText.charAt(startOffset)
+      ) {
+      startOffset++;
+    }
+
+    int endOffset = oldLength;
+    while (true) {
+      if (endOffset <= startOffset) {
+        break;
+      }
+      final int idxInNew = newLength - (oldLength - endOffset) - 1;
+      if (idxInNew < startOffset) {
+        break;
+      }
+
+      final char c1 = oldText.charAt(endOffset - 1);
+      final char c2 = newText.charAt(idxInNew);
+      if (c1 != c2) {
+        break;
+      }
+      endOffset--;
+    }
+
+    return new ReplaceInfo(startOffset, endOffset, newText.substring(startOffset, newLength - (oldLength - endOffset)));
+  }
+
+  private class MySynchronizeRequest implements Runnable {
+
+    public void run() {
+      final Project project = getProject();
+      if (project.isDisposed()) {
+        return;
+      }
+      PsiDocumentManager.getInstance(project).commitDocument(myDocument);
+      final IpnbEditablePanel selectedCell = getSelectedCell();
+      final int index = myIpnbPanels.indexOf(selectedCell);
+      myInitialSelection = index >= 0 && index < myIpnbPanels.size() ? index : myIpnbPanels.size() - 1;
+      removeAll();
+      readFromFile(false);
+    }
+  }
+
+
   public void copyCell() {
     myBufferPanel = getSelectedCell();
   }
 
   public void pasteCell() {
     if (myBufferPanel == null) return;
-    removeAll();
     final IpnbEditablePanel editablePanel = (IpnbEditablePanel)myBufferPanel.clone();
     addCell(editablePanel, true);
   }
 
   public void replaceComponent(@NotNull final IpnbEditablePanel from, @NotNull final IpnbCell cell) {
-    removeAll();
-    final int index = myIpnbPanels.indexOf(from);
-    IpnbEditablePanel panel;
-    if (cell instanceof IpnbCodeCell) {
-      panel = new IpnbCodePanel(myProject, myParent, (IpnbCodeCell)cell);
-    }
-    else if (cell instanceof IpnbMarkdownCell) {
-      panel = new IpnbMarkdownPanel((IpnbMarkdownCell)cell);
-    }
-    else if (cell instanceof IpnbHeadingCell) {
-      panel = new IpnbHeadingPanel((IpnbHeadingCell)cell);
-    }
-    else {
-      throw new UnsupportedOperationException(cell.getClass().toString());
-    }
-    if (index >= 0) {
-      myIpnbPanels.remove(index);
-      myIpnbPanels.add(index, panel);
-    }
-    for (IpnbPanel comp : myIpnbPanels) {
-      add(comp);
-    }
-    add(createEmptyPanel());
+    CommandProcessor.getInstance().executeCommand(getProject(), new Runnable() {
+      public void run() {
+        ApplicationManager.getApplication().runWriteAction(new Runnable() {
+          public void run() {
+            final int index = myIpnbPanels.indexOf(from);
+            IpnbEditablePanel panel;
+            if (cell instanceof IpnbCodeCell) {
+              panel = new IpnbCodePanel(myProject, myParent, (IpnbCodeCell)cell);
+            }
+            else if (cell instanceof IpnbMarkdownCell) {
+              panel = new IpnbMarkdownPanel((IpnbMarkdownCell)cell);
+            }
+            else if (cell instanceof IpnbHeadingCell) {
+              panel = new IpnbHeadingPanel((IpnbHeadingCell)cell);
+            }
+            else {
+              throw new UnsupportedOperationException(cell.getClass().toString());
+            }
+            if (index >= 0) {
+              myIpnbFile.removeCell(index);
+              myIpnbFile.addCell(cell, index);
+              myIpnbPanels.remove(index);
+              myIpnbPanels.add(index, panel);
+            }
+
+            if (from instanceof IpnbCodePanel) {
+              panel.switchToEditing();
+            }
+            setSelectedCell(panel);
+            saveToFile();
+          }
+        });
+      }
+    }, "Ipnb.changeCellType", new Object());
 
-    if (from instanceof IpnbCodePanel) {
-      panel.switchToEditing();
-    }
-    setSelectedCell(panel);
-    remove(from);
-    revalidate();
-    repaint();
   }
 
   private void addComponent(@NotNull final IpnbEditablePanel comp) {
@@ -287,20 +414,26 @@ public class IpnbFilePanel extends JPanel implements Scrollable, DataProvider {
         }
       }
       else if (e.getKeyCode() == KeyEvent.VK_DELETE) {
-        if (!mySelectedCell.isEditing())
-          deleteCell(mySelectedCell);
+        if (!mySelectedCell.isEditing()) {
+          IpnbDeleteCellAction.deleteCell(this);
+        }
       }
-      else if (e.getKeyCode() == KeyEvent.VK_X && e.getModifiers() == InputEvent.CTRL_MASK) {
-        if (!mySelectedCell.isEditing())
-          cutCell();
-      }
-      else if (e.getKeyCode() == KeyEvent.VK_C && e.getModifiers() == InputEvent.CTRL_MASK) {
-        if (!mySelectedCell.isEditing())
-          copyCell();
-      }
-      else if (e.getKeyCode() == KeyEvent.VK_V && e.getModifiers() == InputEvent.CTRL_MASK) {
-        if (!mySelectedCell.isEditing())
-          pasteCell();
+      else if (e.getModifiers() == InputEvent.CTRL_MASK) {
+        if (e.getKeyCode() == KeyEvent.VK_X) {
+          if (!mySelectedCell.isEditing()) {
+            IpnbCutCellAction.cutCell(this);
+          }
+        }
+        else if (e.getKeyCode() == KeyEvent.VK_C) {
+          if (!mySelectedCell.isEditing()) {
+            copyCell();
+          }
+        }
+        else if (e.getKeyCode() == KeyEvent.VK_V) {
+          if (!mySelectedCell.isEditing()) {
+            IpnbPasteCellAction.pasteCell(this);
+          }
+        }
       }
       else {
         getParent().dispatchEvent(e);
@@ -435,4 +568,8 @@ public class IpnbFilePanel extends JPanel implements Scrollable, DataProvider {
     }
     return null;
   }
+
+  public Project getProject() {
+    return myProject;
+  }
 }

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/panels/code/IpnbCodePanel.java

@@ -1,13 +1,10 @@
 package org.jetbrains.plugins.ipnb.editor.panels.code;
 
 import com.google.common.collect.Lists;
-import com.intellij.openapi.Disposable;
 import com.intellij.openapi.application.ApplicationManager;
 import com.intellij.openapi.editor.Document;
 import com.intellij.openapi.editor.Editor;
-import com.intellij.openapi.editor.EditorFactory;
 import com.intellij.openapi.project.Project;
-import com.intellij.openapi.util.Disposer;
 import com.intellij.openapi.util.text.StringUtil;
 import com.intellij.util.ui.UIUtil;
 import org.jetbrains.annotations.NotNull;
@@ -30,7 +27,7 @@ public class IpnbCodePanel extends IpnbEditablePanel<JComponent, IpnbCodeCell> {
   private IpnbCodeSourcePanel myCodeSourcePanel;
   private final List<IpnbPanel> myOutputPanels = Lists.newArrayList();
 
-  public IpnbCodePanel(@NotNull final Project project, final IpnbFileEditor parent, @NotNull final IpnbCodeCell cell) {
+  public IpnbCodePanel(@NotNull final Project project, @NotNull final IpnbFileEditor parent, @NotNull final IpnbCodeCell cell) {
     super(cell, new BorderLayout());
     myProject = project;
     myParent = parent;
@@ -40,7 +37,6 @@ public class IpnbCodePanel extends IpnbEditablePanel<JComponent, IpnbCodeCell> {
   }
 
   public IpnbFileEditor getFileEditor() {
-    assert myParent != null;
     return myParent;
   }
 
@@ -68,13 +64,6 @@ public class IpnbCodePanel extends IpnbEditablePanel<JComponent, IpnbCodeCell> {
     c.gridwidth = 1;
 
     myCodeSourcePanel = new IpnbCodeSourcePanel(myProject, this, myCell);
-    if (myParent != null)
-      Disposer.register(myParent, new Disposable() {
-      @Override
-      public void dispose() {
-        EditorFactory.getInstance().releaseEditor(myCodeSourcePanel.getEditor());
-      }
-    });
     addPromptPanel(panel, myCell.getPromptNumber(), IpnbEditorUtil.PromptType.In, myCodeSourcePanel, c);
 
     c.gridx = 1;

python/ipnb/src/org/jetbrains/plugins/ipnb/editor/panels/code/IpnbCodeSourcePanel.java

@@ -15,15 +15,16 @@
  */
 package org.jetbrains.plugins.ipnb.editor.panels.code;
 
-import com.intellij.openapi.actionSystem.ActionManager;
+import com.intellij.openapi.Disposable;
 import com.intellij.openapi.editor.Editor;
+import com.intellij.openapi.editor.EditorFactory;
 import com.intellij.openapi.project.Project;
+import com.intellij.openapi.util.Disposer;
 import com.intellij.ui.Gray;
 import com.intellij.util.ui.UIUtil;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.plugins.ipnb.editor.IpnbEditorUtil;
-import org.jetbrains.plugins.ipnb.editor.actions.IpnbRunCellAction;
-import org.jetbrains.plugins.ipnb.editor.actions.IpnbRunCellInplaceAction;
+import org.jetbrains.plugins.ipnb.editor.actions.IpnbRunCellBaseAction;
 import org.jetbrains.plugins.ipnb.editor.panels.IpnbEditorPanel;
 import org.jetbrains.plugins.ipnb.editor.panels.IpnbFilePanel;
 import org.jetbrains.plugins.ipnb.editor.panels.IpnbPanel;
@@ -73,7 +74,12 @@ public class IpnbCodeSourcePanel extends IpnbPanel<JComponent, IpnbCodeCell> imp
     else {
       myEditor = IpnbEditorUtil.createPythonCodeEditor(myProject, this);
     }
-
+    Disposer.register(myParent.getFileEditor(), new Disposable() {
+      @Override
+      public void dispose() {
+        EditorFactory.getInstance().releaseEditor(myEditor);
+      }
+    });
     final JComponent component = myEditor.getComponent();
     final JComponent contentComponent = myEditor.getContentComponent();
 
@@ -100,12 +106,10 @@ public class IpnbCodeSourcePanel extends IpnbPanel<JComponent, IpnbCodeCell> imp
             UIUtil.requestFocus(getIpnbCodePanel().getFileEditor().getIpnbFilePanel());
           }
           else if (keyCode == KeyEvent.VK_ENTER && InputEvent.CTRL_DOWN_MASK == e.getModifiersEx()) {
-            final IpnbRunCellInplaceAction action = (IpnbRunCellInplaceAction)ActionManager.getInstance().getAction("IpnbRunCellInplaceAction");
-            action.runCell(ipnbFilePanel, false);
+            IpnbRunCellBaseAction.runCell(ipnbFilePanel, false);
           }
           else if (keyCode == KeyEvent.VK_ENTER && InputEvent.SHIFT_DOWN_MASK == e.getModifiersEx()) {
-            final IpnbRunCellAction action = (IpnbRunCellAction)ActionManager.getInstance().getAction("IpnbRunCellAction");
-            action.runCell(ipnbFilePanel, true);
+            IpnbRunCellBaseAction.runCell(ipnbFilePanel, true);
           }
         }
 

python/ipnb/src/org/jetbrains/plugins/ipnb/format/IpnbParser.java

@@ -4,8 +4,7 @@ import com.google.common.collect.Lists;
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
 import com.intellij.openapi.diagnostic.Logger;
-import com.intellij.openapi.vfs.CharsetToolkit;
-import com.intellij.openapi.vfs.VirtualFile;
+import com.intellij.openapi.editor.Document;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.plugins.ipnb.editor.panels.IpnbEditablePanel;
 import org.jetbrains.plugins.ipnb.editor.panels.IpnbFilePanel;
@@ -31,13 +30,13 @@ public class IpnbParser {
   }
 
   @NotNull
-  public static IpnbFile parseIpnbFile(@NotNull String fileText, String path) throws IOException {
-    IpnbFileRaw rawFile = gson.fromJson(fileText, IpnbFileRaw.class);
+  public static IpnbFile parseIpnbFile(@NotNull final CharSequence fileText, String path) throws IOException {
+    IpnbFileRaw rawFile = gson.fromJson(fileText.toString(), IpnbFileRaw.class);
     if (rawFile == null) return new IpnbFile(new IpnbFileRaw(), Lists.<IpnbCell>newArrayList(), path);
     List<IpnbCell> cells = new ArrayList<IpnbCell>();
     final IpnbWorksheet[] worksheets = rawFile.worksheets;
     for (IpnbWorksheet worksheet : worksheets) {
-      final IpnbCellRaw[] rawCells = worksheet.cells;
+      final List<IpnbCellRaw> rawCells = worksheet.cells;
       for (IpnbCellRaw rawCell : rawCells) {
         cells.add(rawCell.createCell());
       }
@@ -46,14 +45,19 @@ public class IpnbParser {
   }
 
   @NotNull
-  public static IpnbFile parseIpnbFile(@NotNull VirtualFile virtualFile) throws IOException {
-    final String fileText = new String(virtualFile.contentsToByteArray(), CharsetToolkit.UTF8);
-    return parseIpnbFile(fileText, virtualFile.getPath());
+  public static IpnbFile parseIpnbFile(@NotNull Document document, @NotNull final String path) throws IOException {
+    return parseIpnbFile(document.getImmutableCharSequence(), path);
   }
 
   public static void saveIpnbFile(@NotNull final IpnbFilePanel ipnbPanel) {
+    final String json = newDocumentText(ipnbPanel);
+    if (json == null) return;
+    writeToFile(ipnbPanel.getIpnbFile().getPath(), json);
+  }
+
+  public static String newDocumentText(@NotNull final IpnbFilePanel ipnbPanel) {
     final IpnbFile ipnbFile = ipnbPanel.getIpnbFile();
-    if (ipnbFile == null) return;
+    if (ipnbFile == null) return null;
     for (IpnbEditablePanel panel : ipnbPanel.getIpnbPanels()) {
       if (panel.isModified()) {
         panel.updateCellSource();
@@ -62,14 +66,14 @@ public class IpnbParser {
 
     final IpnbFileRaw fileRaw = ipnbFile.getRawFile();
     final IpnbWorksheet worksheet = new IpnbWorksheet();
-    final ArrayList<IpnbCellRaw> cellRaws = new ArrayList<IpnbCellRaw>();
     for (IpnbCell cell: ipnbFile.getCells()) {
-      cellRaws.add(IpnbCellRaw.fromCell(cell));
+      worksheet.cells.add(IpnbCellRaw.fromCell(cell));
     }
-    worksheet.cells = cellRaws.toArray(new IpnbCellRaw[cellRaws.size()]);
     fileRaw.worksheets = new IpnbWorksheet[]{worksheet};
-    final String json = gson.toJson(fileRaw);
-    final String path = ipnbFile.getPath();
+    return gson.toJson(fileRaw);
+  }
+
+  private static void writeToFile(@NotNull final String path, @NotNull final String json) {
     final File file = new File(path);
     FileWriter writer = null;
     try {
@@ -96,8 +100,9 @@ public class IpnbParser {
   }
 
   private static class IpnbWorksheet {
-    IpnbCellRaw[] cells;
+    List<IpnbCellRaw> cells = new ArrayList<IpnbCellRaw>();
   }
+
   private static class IpnbCellRaw {
     String cell_type;
     Integer level;