Merge branch 'master' of https://github.com/sleuthkit/autopsy

Core/manifest.mf

@@ -1,8 +1,8 @@
 Manifest-Version: 1.0
-OpenIDE-Module: org.sleuthkit.autopsy.core/5
+OpenIDE-Module: org.sleuthkit.autopsy.core/6
 OpenIDE-Module-Localizing-Bundle: org/sleuthkit/autopsy/core/Bundle.properties
 OpenIDE-Module-Layer: org/sleuthkit/autopsy/core/layer.xml
-OpenIDE-Module-Implementation-Version: 3
+OpenIDE-Module-Implementation-Version: 4
 OpenIDE-Module-Requires: org.openide.windows.WindowManager, org.netbeans.api.javahelp.Help
 AutoUpdate-Show-In-Client: true
 AutoUpdate-Essential-Module: true

Core/nbproject/project.properties

@@ -5,5 +5,5 @@ license.file=../LICENSE-2.0.txt
 nbm.homepage=http://www.sleuthkit.org/
 nbm.module.author=Brian Carrier
 nbm.needs.restart=true
-spec.version.base=3.0
+spec.version.base=4.0
 

Core/src/org/sleuthkit/autopsy/corecomponentinterfaces/DataResultViewer.java

@@ -80,4 +80,11 @@ public interface DataResultViewer {
      * @return True if supported, else false
      */
     public boolean isSupported(Node selectedNode);
+    
+    /**
+     * Set a custom content viewer to respond to selection events from this result viewer.
+     * If not set, the default content viewer is user
+     * @param contentViewer content viewer to respond to selection events from this viewer
+     */
+    public void setContentViewer(DataContent contentViewer);
 }

Core/src/org/sleuthkit/autopsy/corecomponents/AbstractDataResultViewer.java

@@ -43,9 +43,19 @@ public abstract class AbstractDataResultViewer extends JPanel implements
     private static final Logger logger = Logger.getLogger(AbstractDataResultViewer.class.getName());
     protected transient ExplorerManager em = new ExplorerManager();
     private PropertyChangeListener nodeSelListener;
+    
+    /**
+     * Content viewer to respond to selection events
+     * Either the main one, or custom one if set
+     */
+    protected DataContent contentViewer;
 
     public AbstractDataResultViewer() {
 
+        //DataContent is designed to return only the default viewer from lookup
+        //use the default one unless set otherwise
+       contentViewer = Lookup.getDefault().lookup(DataContent.class);
+        
         //property listener to send nodes to content viewer    
         nodeSelListener = new PropertyChangeListener() {
                         
@@ -70,17 +80,16 @@ public abstract class AbstractDataResultViewer extends JPanel implements
                         
                         nodeSelected(selectedNode);
 
-                        // DataContent is designed to return only the default viewer
-                        DataContent dataContent = Lookup.getDefault().lookup(DataContent.class);
+                        
 
                         if (selectedNode != null) {
                             // there's a new/changed node to display
                             Node newSelectedNode = selectedNode; // get the selected Node on the table
                             // push the node to default "DataContent"
-                            dataContent.setNode(newSelectedNode);
+                            contentViewer.setNode(newSelectedNode);
                         } else {
                             // clear the node viewer
-                            dataContent.setNode(null);
+                            contentViewer.setNode(null);
                         }
                     } finally {
                         setCursor(null);
@@ -155,4 +164,9 @@ public abstract class AbstractDataResultViewer extends JPanel implements
             logger.log(Level.WARNING, "Couldn't set selected nodes.", ex);
         }
     }
+    
+    @Override
+    public void setContentViewer(DataContent contentViewer) {
+        this.contentViewer = contentViewer;
+    }
 }

Core/src/org/sleuthkit/autopsy/corecomponents/DataResultTopComponent.java

@@ -18,7 +18,6 @@
  */
 package org.sleuthkit.autopsy.corecomponents;
 
-import java.awt.Component;
 import java.awt.Cursor;
 import java.beans.PropertyChangeListener;
 import org.sleuthkit.autopsy.corecomponentinterfaces.DataResult;
@@ -33,6 +32,7 @@ import org.openide.windows.TopComponent;
 import org.openide.nodes.Node;
 import org.openide.util.Lookup;
 import org.sleuthkit.autopsy.casemodule.Case;
+import org.sleuthkit.autopsy.corecomponentinterfaces.DataContent;
 import org.sleuthkit.autopsy.corecomponentinterfaces.DataResultViewer;
 
 /**
@@ -52,7 +52,15 @@ public final class DataResultTopComponent extends TopComponent implements DataRe
     public static String REMOVE_FILESEARCH = "RemoveFileSearchTopComponent";
     // Different DataResultsViewers
     private List<UpdateWrapper> viewers = new ArrayList<UpdateWrapper>();
+    
+    //custom content viewer to send selections to, or null if the main one
+    private DataContent customContentViewer;
 
+    /**
+     * Create a new data result top component
+     * @param isMain whether it is the main, application default result viewer, there can be only 1 main result viewer
+     * @param title title of the data result window
+     */
     public DataResultTopComponent(boolean isMain, String title) {
         initComponents();
         setToolTipText(NbBundle.getMessage(DataResultTopComponent.class, "HINT_NodeTableTopComponent"));
@@ -65,6 +73,19 @@ public final class DataResultTopComponent extends TopComponent implements DataRe
 
         this.dataResultTabbedPanel.addChangeListener(this);
     }
+    
+    /**
+     * Create a new, custom data result top component, in addition to the application main one
+     * @param title title of the data result window
+     * @param customContentViewer custom content viewer to send selection events to
+     */
+    public DataResultTopComponent(String title, DataContentTopComponent customContentViewer) {
+        this(false, title);
+        
+        //custom content viewer tc to setup for every result viewer
+        this.customContentViewer = customContentViewer;
+    }
+    
 
     private static class UpdateWrapper {
 
@@ -102,8 +123,23 @@ public final class DataResultTopComponent extends TopComponent implements DataRe
         boolean isSupported(Node selectedNode) {
             return this.wrapped.isSupported(selectedNode);
         }
+        
+        void setContentViewer(DataContent contentViewer) {
+            this.wrapped.setContentViewer(contentViewer);
+        }
     }
 
+    
+    private static void createInstanceCommon(String pathText, Node givenNode, int totalMatches, DataResultTopComponent newDataResult) {
+        newDataResult.numberMatchLabel.setText(Integer.toString(totalMatches));
+
+        newDataResult.open(); // open it first so the component can be initialized
+
+        // set the tree table view
+        newDataResult.setNode(givenNode);
+        newDataResult.setPath(pathText);
+    }
+    
     /**
      * Creates a new non-default DataResult component
      *
@@ -116,13 +152,25 @@ public final class DataResultTopComponent extends TopComponent implements DataRe
     public static DataResultTopComponent createInstance(String title, String pathText, Node givenNode, int totalMatches) {
         DataResultTopComponent newDataResult = new DataResultTopComponent(false, title);
 
-        newDataResult.numberMatchLabel.setText(Integer.toString(totalMatches));
+        createInstanceCommon(pathText, givenNode, totalMatches, newDataResult);
 
-        newDataResult.open(); // open it first so the component can be initialized
+        return newDataResult;
+    }
+    
+        /**
+     * Creates a new non-default DataResult component
+     *
+     * @param title Title of the component window
+     * @param pathText Descriptive text about the source of the nodes displayed
+     * @param givenNode The new root node
+     * @param totalMatches Cardinality of root node's children
+     * @param dataContentWindow a handle to data content top component window to send events to from the new result viewer
+     * @return
+     */
+    public static DataResultTopComponent createInstance(String title, String pathText, Node givenNode, int totalMatches, DataContentTopComponent dataContentWindow) {
+        DataResultTopComponent newDataResult = new DataResultTopComponent(title, dataContentWindow);
 
-        // set the tree table view
-        newDataResult.setNode(givenNode);
-        newDataResult.setPath(pathText);
+        createInstanceCommon(pathText, givenNode, totalMatches, newDataResult);
 
         return newDataResult;
     }
@@ -191,8 +239,14 @@ public final class DataResultTopComponent extends TopComponent implements DataRe
             // find all dataContentViewer and add them to the tabbed pane
             for (DataResultViewer factory : Lookup.getDefault().lookupAll(DataResultViewer.class)) {
                 DataResultViewer drv = factory.getInstance();
-                this.viewers.add(new UpdateWrapper(drv));
+                UpdateWrapper resultViewer = new UpdateWrapper(drv);
+                if (customContentViewer != null) {
+                    //set custom content viewer to respond to events from this result viewer
+                    resultViewer.setContentViewer(customContentViewer);
+                }
+                this.viewers.add(resultViewer);
                 this.dataResultTabbedPanel.addTab(drv.getTitle(), drv.getComponent());
+                
             }
         }
 

Core/src/org/sleuthkit/autopsy/coreutils/FileUtil.java

@@ -21,6 +21,7 @@ package org.sleuthkit.autopsy.coreutils;
 import java.io.File;
 import java.io.IOException;
 import java.util.logging.Level;
+import java.util.regex.Matcher;
 import org.openide.filesystems.FileObject;
 
 /**
@@ -149,4 +150,15 @@ public class FileUtil {
         
         return created.getPath();
     }
+    
+    /**
+     * Escape special characters in a file name or a file name component
+     * @param fileName to escape
+     * @return escaped string
+     */
+    public static String escapeFileName(String fileName) {        
+        //for now escaping / (not valid in file name, at least on Windows)
+        //with underscores.  Windows/Java seem to ignore \\/ and \\\\/ escapings 
+        return fileName.replaceAll("/", "_"); 
+    }
 }

Core/src/org/sleuthkit/autopsy/coreutils/MessageNotifyUtil.java

@@ -0,0 +1,203 @@
+/*
+ * Autopsy Forensic Browser
+ *
+ * Copyright 2013 Basis Technology Corp.
+ * Contact: carrier <at> sleuthkit <dot> org
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.sleuthkit.autopsy.coreutils;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.net.URL;
+import java.util.logging.Level;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import org.openide.DialogDisplayer;
+import org.openide.NotifyDescriptor;
+import org.openide.awt.NotificationDisplayer;
+import org.openide.util.ImageUtilities;
+
+/**
+ * Utility for displaying messages and notifications in status area. Wraps
+ * around NB RCP NotificationDisplayer.
+ *
+ * Messages can optionally contain click-able Actions.
+ *
+ * Based on:
+ * http://qbeukes.blogspot.com/2009/11/netbeans-platform-notifications.html
+ *
+ * @license Apache License 2.0
+ */
+public class MessageNotifyUtil {
+
+    private MessageNotifyUtil() {
+    }
+
+    public enum MessageType {
+
+        INFO(NotifyDescriptor.INFORMATION_MESSAGE, "info-icon-16.png"),
+        ERROR(NotifyDescriptor.ERROR_MESSAGE, "error-icon-16.png"),
+        WARNING(NotifyDescriptor.WARNING_MESSAGE, "warning-icon-16.png");
+        private int notifyDescriptorType;
+        private Icon icon;
+
+        private MessageType(int notifyDescriptorType, String resourceName) {
+            this.notifyDescriptorType = notifyDescriptorType;
+            if (resourceName == null) {
+                icon = new ImageIcon();
+            } else {
+                icon = loadIcon(resourceName);
+            }
+        }
+
+        private static Icon loadIcon(String resourceName) {
+            Icon icon = ImageUtilities.loadImageIcon("org/sleuthkit/autopsy/images/" + resourceName, false);
+            if (icon == null) {
+                Logger logger = Logger.getLogger(org.sleuthkit.autopsy.coreutils.MessageNotifyUtil.MessageType.class.getName());
+                logger.log(Level.SEVERE, "Failed to load icon resource: " + resourceName + ". Using blank image.");
+                icon = new ImageIcon();
+            }
+            return icon;
+        }
+
+        int getNotifyDescriptorType() {
+            return notifyDescriptorType;
+        }
+
+        Icon getIcon() {
+            return icon;
+        }
+    }
+
+    /**
+     * Utility to display messages
+     */
+    public static class Message {
+
+        private Message() {
+        }
+
+        /**
+         * @return The dialog displayer used to show message boxes
+         */
+        public static DialogDisplayer getDialogDisplayer() {
+            return DialogDisplayer.getDefault();
+        }
+
+        /**
+         * Show a message of the specified type
+         *
+         * @param message message to show
+         * @param messageType message type to show
+         */
+        public static void show(String message, MessageType messageType) {
+            getDialogDisplayer().notify(new NotifyDescriptor.Message(message,
+                    messageType.getNotifyDescriptorType()));
+        }
+
+        /**
+         * Show an information dialog
+         *
+         * @param message message to show
+         */
+        public static void info(String message) {
+            show(message, MessageType.INFO);
+        }
+
+        /**
+         * Show an error dialog
+         *
+         * @param message message to shpw
+         */
+        public static void error(String message) {
+            show(message, MessageType.ERROR);
+        }
+
+        /**
+         * Show an warning dialog
+         *
+         * @param message message to show
+         */
+        public static void warn(String message) {
+            show(message, MessageType.WARNING);
+        }
+    }
+
+    /**
+     * Utility to display notifications with baloons
+     */
+    public static class Notify {
+
+        private Notify() {
+        }
+
+        /**
+         * Show message with the specified type and action listener
+         */
+        public static void show(String title, String message, MessageType type, ActionListener actionListener) {
+            NotificationDisplayer.getDefault().notify(title, type.getIcon(), message, actionListener);
+        }
+
+        /**
+         * Show message with the specified type and a default action which
+         * displays the message using MessageNotifyUtil.Message with the same
+         * message type
+         *
+         * @param title message title
+         * @param message message text
+         * @param type type of the message
+         */
+        public static void show(String title, final String message, final MessageType type) {
+            ActionListener actionListener = new ActionListener() {
+                @Override
+                public void actionPerformed(ActionEvent e) {
+                    MessageNotifyUtil.Message.show(message, type);
+                }
+            };
+
+            show(title, message, type, actionListener);
+        }
+
+        /**
+         * Show an information notification
+         *
+         * @param title message title
+         * @param message message text
+         */
+        public static void info(String title, String message) {
+            show(title, message, MessageType.INFO);
+        }
+
+        /**
+         * Show an error notification
+         *
+         * @param title message title
+         * @param message message text
+         */
+        public static void error(String title, String message) {
+            show(title, message, MessageType.ERROR);
+        }
+
+        /**
+         * Show an warning notification
+         *
+         * @param title message title
+         * @param message message text
+         */
+        public static void warn(String title, String message) {
+            show(title, message, MessageType.WARNING);
+        }
+    }
+}

Core/src/org/sleuthkit/autopsy/datamodel/AbstractContentChildren.java

@@ -26,12 +26,12 @@ import org.sleuthkit.autopsy.datamodel.KeywordHits.KeywordHitsRootNode;
 import org.sleuthkit.datamodel.Directory;
 import org.sleuthkit.datamodel.File;
 import org.sleuthkit.datamodel.Image;
-import org.sleuthkit.datamodel.VirtualDirectory;
-import org.sleuthkit.datamodel.SleuthkitVisitableItem;
-import org.sleuthkit.datamodel.SleuthkitItemVisitor;
-import org.sleuthkit.datamodel.TskException;
-import org.sleuthkit.datamodel.Volume;
 import org.sleuthkit.datamodel.LayoutFile;
+import org.sleuthkit.datamodel.SleuthkitItemVisitor;
+import org.sleuthkit.datamodel.SleuthkitVisitableItem;
+import org.sleuthkit.datamodel.TskException;
+import org.sleuthkit.datamodel.VirtualDirectory;
+import org.sleuthkit.datamodel.Volume;
 
 /**
  * Abstract subclass for ContentChildren and RootContentChildren implementations
@@ -137,11 +137,16 @@ abstract class AbstractContentChildren<T> extends Keys<T> {
             return ee.new EmailExtractedRootNode();
         }
         
-         @Override
+        @Override
         public AbstractNode visit(Bookmarks bks) {
             return bks.new BookmarksRootNode();
         }
         
+        @Override
+        public AbstractNode visit(Tags t) {
+            return t.new TagsRootNode();
+        }
+        
         @Override
         public AbstractNode visit(Images i) {
             try {

Core/src/org/sleuthkit/autopsy/datamodel/ArtifactStringContent.java

@@ -104,6 +104,22 @@ public class ArtifactStringContent implements StringContent {
                 buffer.append("</td>");
                 buffer.append("</tr>");
             }
+            
+            //add file path
+            buffer.append("<tr>");
+            buffer.append("<td>Source File</td>");
+            buffer.append("<td>");
+            final Content content = getAssociatedContent(wrapped);
+            buffer.append(content.getName());
+            buffer.append("</td>");
+            buffer.append("</tr>");
+            buffer.append("<tr>");
+            buffer.append("<td>Source File Path</td>");
+            buffer.append("<td>");
+            buffer.append(DataConversion.getformattedPath(ContentUtils.getDisplayPath(content), 0, 1));
+            buffer.append("</td>");
+            buffer.append("</tr>");
+            
             buffer.append("</table>");
             buffer.append("</html>");
             return buffer.toString();

Core/src/org/sleuthkit/autopsy/datamodel/AutopsyItemVisitor.java

@@ -34,6 +34,7 @@ public interface AutopsyItemVisitor<T> {
     T visit(HashsetHits hh);
     T visit(EmailExtracted ee);
     T visit(Bookmarks bks);
+    T visit(Tags t);
     T visit(Images i);
     T visit(Views v);
     T visit(Results r);
@@ -92,6 +93,11 @@ public interface AutopsyItemVisitor<T> {
             return defaultVisit(bks);
         }
         
+        @Override
+        public T visit(Tags t) {
+            return defaultVisit(t);
+        }
+        
         @Override
         public T visit(Images i) {
             return defaultVisit(i);

Core/src/org/sleuthkit/autopsy/datamodel/ContentChildren.java

@@ -28,7 +28,7 @@ import org.sleuthkit.datamodel.Content;
  * Class for Children of all ContentNodes. Handles creating child ContentNodes.
  * TODO consider a ContentChildren child factory
  */
-class ContentChildren extends AbstractContentChildren {
+class ContentChildren extends AbstractContentChildren<Content> {
     
     private static final Logger logger = Logger.getLogger(ContentChildren.class.getName());
     //private static final int MAX_CHILD_COUNT = 1000000;
@@ -72,7 +72,7 @@ class ContentChildren extends AbstractContentChildren {
     @Override
     protected void removeNotify() {
         super.removeNotify();
-        setKeys(Collections.EMPTY_SET);
+        setKeys(new ArrayList<Content>());
     }
     
 }

Core/src/org/sleuthkit/autopsy/datamodel/DisplayableItemNodeVisitor.java

@@ -28,6 +28,8 @@ import org.sleuthkit.autopsy.datamodel.HashsetHits.HashsetHitsSetNode;
 import org.sleuthkit.autopsy.datamodel.KeywordHits.KeywordHitsKeywordNode;
 import org.sleuthkit.autopsy.datamodel.KeywordHits.KeywordHitsListNode;
 import org.sleuthkit.autopsy.datamodel.KeywordHits.KeywordHitsRootNode;
+import org.sleuthkit.autopsy.datamodel.Tags.TagsNodeRoot;
+import org.sleuthkit.autopsy.datamodel.Tags.TagsRootNode;
 
 /**
  * Visitor pattern for DisplayableItemNodes
@@ -55,6 +57,8 @@ public interface DisplayableItemNodeVisitor<T> {
     T visit(EmailExtractedFolderNode eefn);
     T visit(BookmarksRootNode bksrn);
     T visit(BookmarksNodeRoot bksrn);
+    T visit(TagsRootNode bksrn);
+    T visit(TagsNodeRoot bksrn);
     T visit(ViewsNode vn);
     T visit(ResultsNode rn);
     T visit(ImagesNode in);
@@ -204,5 +208,15 @@ public interface DisplayableItemNodeVisitor<T> {
         public T visit(BookmarksNodeRoot bksnr) {
             return defaultVisit(bksnr);
         }
+        
+        @Override
+        public T visit(TagsRootNode bksrn) {
+            return defaultVisit(bksrn);
+        }
+        
+        @Override
+        public T visit(TagsNodeRoot bksnr) {
+            return defaultVisit(bksnr);
+        }
     }
 }

Core/src/org/sleuthkit/autopsy/datamodel/EmailExtracted.java

@@ -60,6 +60,7 @@ public class EmailExtracted implements AutopsyVisitableItem {
         accounts = new LinkedHashMap<String, Map<String, List<Long>>>();
     }
 
+    @SuppressWarnings("deprecation")
     private void initArtifacts() {
         accounts.clear();
         try {

Core/src/org/sleuthkit/autopsy/datamodel/FileSearchFilterChildren.java

@@ -28,6 +28,7 @@ import org.sleuthkit.autopsy.coreutils.Logger;
 import org.openide.nodes.AbstractNode;
 import org.openide.nodes.ChildFactory;
 import org.openide.nodes.Node;
+import org.openide.util.Exceptions;
 import org.openide.util.lookup.Lookups;
 import org.sleuthkit.autopsy.datamodel.SearchFilters.FileSearchFilter;
 import org.sleuthkit.datamodel.Content;
@@ -69,22 +70,29 @@ class FileSearchFilterChildren extends ChildFactory<Content> {
         return query;
     }
     
+    @SuppressWarnings("deprecation")
     private List<FsContent> runQuery(){
+        ResultSet rs = null;
         List<FsContent> list = new ArrayList<FsContent>();
         try {
-            ResultSet rs = skCase.runQuery(createQuery());
+            rs = skCase.runQuery(createQuery());
             for(FsContent c : skCase.resultSetToFsContents(rs)){
                 if(c.isFile()){
                     list.add(c);
                 }
             }
-            Statement s = rs.getStatement();
-            rs.close();
-            if (s != null)
-                s.close();
         } catch (SQLException ex) {
             logger.log(Level.WARNING, "Couldn't get search results", ex);
         }
+        finally {
+            if (rs != null) {
+                try {
+                    skCase.closeRunQuery(rs);
+                } catch (SQLException ex) {
+                    logger.log(Level.SEVERE, "Error closing result set after executing fscontents query for file search results", ex);
+                }
+            }
+        }
         return list;
         
     }

Core/src/org/sleuthkit/autopsy/datamodel/HashsetHits.java

@@ -34,6 +34,7 @@ import org.openide.nodes.ChildFactory;
 import org.openide.nodes.Children;
 import org.openide.nodes.Node;
 import org.openide.nodes.Sheet;
+import org.openide.util.Exceptions;
 import org.openide.util.lookup.Lookups;
 import org.sleuthkit.datamodel.BlackboardArtifact;
 import org.sleuthkit.datamodel.BlackboardAttribute;
@@ -56,8 +57,10 @@ public class HashsetHits implements AutopsyVisitableItem {
         hashSetHitsMap = new LinkedHashMap<String, Set<Long>>();
     }
 
+    @SuppressWarnings("deprecation")
     private void initArtifacts() {
         hashSetHitsMap.clear();
+        ResultSet rs = null;
         try {
             int setNameId = BlackboardAttribute.ATTRIBUTE_TYPE.TSK_SET_NAME.getTypeID();
             int artId = BlackboardArtifact.ARTIFACT_TYPE.TSK_HASHSET_HIT.getTypeID();
@@ -66,7 +69,7 @@ public class HashsetHits implements AutopsyVisitableItem {
                     + "attribute_type_id=" + setNameId
                     + " AND blackboard_attributes.artifact_id=blackboard_artifacts.artifact_id"
                     + " AND blackboard_artifacts.artifact_type_id=" + artId;
-            ResultSet rs = skCase.runQuery(query);
+            rs = skCase.runQuery(query);
             while (rs.next()) {
                 String value = rs.getString("value_text");
                 long artifactId = rs.getLong("artifact_id");
@@ -76,14 +79,19 @@ public class HashsetHits implements AutopsyVisitableItem {
                 hashSetHitsMap.get(value).add(artifactId);
 
             }
-            Statement s = rs.getStatement();
-            rs.close();
-            if (s != null) {
-                s.close();
-            }
+           
         } catch (SQLException ex) {
             logger.log(Level.WARNING, "SQL Exception occurred: ", ex);
         }
+        finally {
+            if (rs != null) {
+                try {
+                    skCase.closeRunQuery(rs);
+                } catch (SQLException ex) {
+                   logger.log(Level.WARNING, "Error closing result set after getting hashset hits", ex);
+                }
+            }
+        }
     }
 
     @Override

Core/src/org/sleuthkit/autopsy/datamodel/KeywordHits.java

@@ -106,8 +106,10 @@ public class KeywordHits implements AutopsyVisitableItem {
         }
     }
 
+    @SuppressWarnings("deprecation")
     private void initArtifacts() {
         artifacts.clear();
+        ResultSet rs = null;
         try {
             int setId = BlackboardAttribute.ATTRIBUTE_TYPE.TSK_SET_NAME.getTypeID();
             int wordId = BlackboardAttribute.ATTRIBUTE_TYPE.TSK_KEYWORD.getTypeID();
@@ -120,7 +122,7 @@ public class KeywordHits implements AutopsyVisitableItem {
                     + ") AND (attribute_type_id=" + setId + " OR "
                     + "attribute_type_id=" + wordId + " OR "
                     + "attribute_type_id=" + regexId + ")";
-            ResultSet rs = skCase.runQuery(query);
+            rs = skCase.runQuery(query);
             while (rs.next()) {
                 String value = rs.getString("value_text");
                 long artifactId = rs.getLong("artifact_id");
@@ -133,14 +135,19 @@ public class KeywordHits implements AutopsyVisitableItem {
                 }
 
             }
-            Statement s = rs.getStatement();
-            rs.close();
-            if (s != null) {
-                s.close();
-            }
+      
         } catch (SQLException ex) {
             logger.log(Level.WARNING, "SQL Exception occurred: ", ex);
         }
+        finally {
+              if (rs != null) {
+                try {
+                    skCase.closeRunQuery(rs);
+                } catch (SQLException ex) {
+                   logger.log(Level.WARNING, "Error closing result set after getting keyword hits", ex);
+                }
+            }
+        }
     }
 
     @Override

Core/src/org/sleuthkit/autopsy/datamodel/RecentFilesChildren.java

@@ -34,12 +34,12 @@ import org.sleuthkit.datamodel.SleuthkitCase;
  *
  * @author dfickling
  */
-public class RecentFilesChildren extends ChildFactory<RecentFiles.RecentFilesFilter>{
-    
+public class RecentFilesChildren extends ChildFactory<RecentFiles.RecentFilesFilter> {
+
     SleuthkitCase skCase;
     Calendar lastDay;
     private final static Logger logger = Logger.getLogger(RecentFilesChildren.class.getName());
-    
+
     public RecentFilesChildren(SleuthkitCase skCase) {
         this.skCase = skCase;
     }
@@ -48,7 +48,7 @@ public class RecentFilesChildren extends ChildFactory<RecentFiles.RecentFilesFil
     protected boolean createKeys(List<RecentFiles.RecentFilesFilter> list) {
         list.addAll(Arrays.asList(RecentFiles.RecentFilesFilter.values()));
         lastDay = Calendar.getInstance();
-        lastDay.setTimeInMillis(getLastTime()*1000);
+        lastDay.setTimeInMillis(getLastTime() * 1000);
         lastDay.set(Calendar.HOUR_OF_DAY, 0);
         lastDay.set(Calendar.MINUTE, 0);
         lastDay.set(Calendar.SECOND, 0);
@@ -57,10 +57,10 @@ public class RecentFilesChildren extends ChildFactory<RecentFiles.RecentFilesFil
     }
 
     @Override
-    protected Node createNodeForKey(RecentFiles.RecentFilesFilter key){
+    protected Node createNodeForKey(RecentFiles.RecentFilesFilter key) {
         return new RecentFilesFilterNode(skCase, key, lastDay);
     }
-    
+
     private long getLastTime() {
         String query = createMaxQuery("crtime");
         long maxcr = runTimeQuery(query);
@@ -73,25 +73,29 @@ public class RecentFilesChildren extends ChildFactory<RecentFiles.RecentFilesFil
         //return Math.max(maxcr, Math.max(maxc, Math.max(maxm, maxa)));
         return Math.max(maxcr, Math.max(maxc, maxm));
     }
-    
-    private String createMaxQuery(String attr){
-        return "select max(" + attr + ") from tsk_files where " + attr + " < " + System.currentTimeMillis()/1000;
+
+    private String createMaxQuery(String attr) {
+        return "select max(" + attr + ") from tsk_files where " + attr + " < " + System.currentTimeMillis() / 1000;
     }
-    
+
+    @SuppressWarnings("deprecation")
     private long runTimeQuery(String query) {
         long result = 0;
+        ResultSet rs = null;
         try {
-            ResultSet rs = skCase.runQuery(query);
+            rs = skCase.runQuery(query);
             result = rs.getLong(1);
-            Statement s = rs.getStatement();
-            rs.close();
-            if (s != null)
-                s.close();
         } catch (SQLException ex) {
-            Logger.getLogger(RecentFilesFilterChildren.class.getName())
-                    .log(Level.WARNING, "Couldn't get search results", ex);
+            logger.log(Level.WARNING, "Couldn't get recent files results", ex);
+        } finally {
+            if (rs != null) {
+                try {
+                    skCase.closeRunQuery(rs);
+                } catch (SQLException ex) {
+                    logger.log(Level.WARNING, "Error closing result set after getting recent files results", ex);
+                }
+            }
         }
         return result;
     }
-    
 }

Core/src/org/sleuthkit/autopsy/datamodel/RecentFilesFilterChildren.java

@@ -41,8 +41,8 @@ import org.sleuthkit.datamodel.SleuthkitCase;
  *
  * @author dfickling
  */
-public class RecentFilesFilterChildren extends ChildFactory<Content>{
-    
+public class RecentFilesFilterChildren extends ChildFactory<Content> {
+
     SleuthkitCase skCase;
     RecentFilesFilter filter;
     Calendar prevDay;
@@ -61,13 +61,13 @@ public class RecentFilesFilterChildren extends ChildFactory<Content>{
         list.addAll(runFsQuery());
         return true;
     }
-    
-    private String createQuery(){
+
+    private String createQuery() {
         String query = "select * from tsk_files where known <> 1 and (";
-        long lowerLimit = prevDay.getTimeInMillis()/1000;
+        long lowerLimit = prevDay.getTimeInMillis() / 1000;
         prevDay.add(Calendar.DATE, 1);
         prevDay.add(Calendar.MILLISECOND, -1);
-        long upperLimit = prevDay.getTimeInMillis()/1000;
+        long upperLimit = prevDay.getTimeInMillis() / 1000;
         query += "(crtime between " + lowerLimit + " and " + upperLimit + ") or ";
         query += "(ctime between " + lowerLimit + " and " + upperLimit + ") or ";
         //query += "(atime between " + lowerLimit + " and " + upperLimit + ") or ";
@@ -75,33 +75,39 @@ public class RecentFilesFilterChildren extends ChildFactory<Content>{
         //query += " limit " + MAX_OBJECTS;
         return query;
     }
-    
-    private List<FsContent> runFsQuery(){
+
+    @SuppressWarnings("deprecation")
+    private List<FsContent> runFsQuery() {
         List<FsContent> list = new ArrayList<FsContent>();
+        ResultSet rs = null;
         try {
-            ResultSet rs = skCase.runQuery(createQuery());
-            for(FsContent c : skCase.resultSetToFsContents(rs)){
-                if(c.isFile()){
+            rs = skCase.runQuery(createQuery());
+            for (FsContent c : skCase.resultSetToFsContents(rs)) {
+                if (c.isFile()) {
                     list.add(c);
                 }
             }
-            Statement s = rs.getStatement();
-            rs.close();
-            if (s != null)
-                s.close();
+
         } catch (SQLException ex) {
             logger.log(Level.WARNING, "Couldn't get search results", ex);
+        } finally {
+            if (rs != null) {
+                try {
+                    skCase.closeRunQuery(rs);
+                } catch (SQLException ex) {
+                    logger.log(Level.WARNING, "Error closing result set after getting recent files results", ex);
+                }
+            }
         }
         return list;
-        
+
     }
-    
+
     @Override
-    protected Node createNodeForKey(Content key){
-        return key.accept(new ContentVisitor.Default<AbstractNode>(){
-            
+    protected Node createNodeForKey(Content key) {
+        return key.accept(new ContentVisitor.Default<AbstractNode>() {
             @Override
-            public FileNode visit(File f){
+            public FileNode visit(File f) {
                 return new FileNode(f, false);
             }
 
@@ -109,7 +115,6 @@ public class RecentFilesFilterChildren extends ChildFactory<Content>{
             protected AbstractNode defaultVisit(Content di) {
                 throw new UnsupportedOperationException("Not supported for this type of Displayable Item: " + di.toString());
             }
-            
         });
     }
 }

Core/src/org/sleuthkit/autopsy/datamodel/ResultsNode.java

@@ -36,7 +36,8 @@ public class ResultsNode extends DisplayableItemNode {
                 new KeywordHits(sleuthkitCase),
                 new HashsetHits(sleuthkitCase),
                 new EmailExtracted(sleuthkitCase),
-                new Bookmarks(sleuthkitCase) //TODO move to the top of the tree 
+                new Bookmarks(sleuthkitCase), //TODO move to the top of the tree 
+                new Tags(sleuthkitCase) //TODO move to the top of the tree 
                 )), Lookups.singleton(NAME));
         setName(NAME);
         setDisplayName(NAME);

Core/src/org/sleuthkit/autopsy/datamodel/RootContentChildren.java

@@ -21,7 +21,6 @@ package org.sleuthkit.autopsy.datamodel;
 
 import java.util.Collection;
 import java.util.Collections;
-import org.sleuthkit.autopsy.coreutils.Logger;
 import org.sleuthkit.datamodel.BlackboardArtifact;
 
 /**
@@ -73,12 +72,16 @@ public class RootContentChildren extends AbstractContentChildren<Object> {
                     case TSK_TAG_FILE:
                         if (o instanceof Bookmarks)
                             this.refreshKey(o);
+                        if (o instanceof Tags)
+                            this.refreshKey(o);
                         break;
                         
                         //TODO check
                      case TSK_TAG_ARTIFACT:
                         if (o instanceof Bookmarks)
                             this.refreshKey(o);
+                        if (o instanceof Tags)
+                            this.refreshKey(o);
                         break;
                     default:
                         if (o instanceof ExtractedContent)
@@ -95,6 +98,8 @@ public class RootContentChildren extends AbstractContentChildren<Object> {
                     this.refreshKey(o);
                 else if (o instanceof Bookmarks)
                     this.refreshKey(o);
+                else if (o instanceof Tags)
+                    this.refreshKey(o);
                 else if (o instanceof ExtractedContent)
                     this.refreshKey(o);
             }

Core/src/org/sleuthkit/autopsy/datamodel/Tags.java

@@ -1,7 +1,7 @@
 /*
  * Autopsy Forensic Browser
  * 
- * Copyright 2012 Basis Technology Corp.
+ * Copyright 2013 Basis Technology Corp.
  * Contact: carrier <at> sleuthkit <dot> org
  * 
  * Licensed under the Apache License, Version 2.0 (the "License");
@@ -21,8 +21,17 @@ package org.sleuthkit.autopsy.datamodel;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
+import java.util.Random;
 import java.util.logging.Level;
+import org.openide.nodes.ChildFactory;
+import org.openide.nodes.Children;
+import org.openide.nodes.Node;
+import org.openide.nodes.Sheet;
+import org.openide.util.lookup.Lookups;
 import org.sleuthkit.autopsy.casemodule.Case;
 import org.sleuthkit.autopsy.coreutils.Logger;
 import org.sleuthkit.datamodel.AbstractFile;
@@ -32,15 +41,195 @@ import org.sleuthkit.datamodel.BlackboardAttribute.ATTRIBUTE_TYPE;
 import org.sleuthkit.datamodel.SleuthkitCase;
 import org.sleuthkit.datamodel.TskCoreException;
 
-public class Tags {
+public class Tags implements AutopsyVisitableItem {
     private static final Logger logger = Logger.getLogger(Tags.class.getName());
+    private SleuthkitCase skCase;
     
+    public static final String NAME = "Tags";
+    private static final String TAG_ICON_PATH = "org/sleuthkit/autopsy/images/tag-folder-blue-icon-16.png";
+    private Map<String, List<BlackboardArtifact>> tags = new HashMap<String, List<BlackboardArtifact>>();
+
+    Tags(SleuthkitCase skCase) {
+        this.skCase = skCase;
+    }
+
+    @Override
+    public <T> T accept(AutopsyItemVisitor<T> v) {
+        return v.visit(this);
+    }
+    
+    /**
+     * Root of all Tag nodes. This node is shown directly under Results
+     * in the directory tree.
+     */
+    public class TagsRootNode extends DisplayableItemNode {
+
+        public TagsRootNode() {
+            super(Children.create(new Tags.TagsRootChildren(), true), Lookups.singleton(NAME));
+            super.setName(NAME);
+            super.setDisplayName(NAME);
+            this.setIconBaseWithExtension(TAG_ICON_PATH);
+            initData();
+        }
+
+        private void initData() {
+            try {
+                // Get all file and artifact tags
+                tags = new HashMap<String, List<BlackboardArtifact>>();
+                List<BlackboardArtifact> tagArtifacts = skCase.getBlackboardArtifacts(BlackboardArtifact.ARTIFACT_TYPE.TSK_TAG_FILE);
+                tagArtifacts.addAll(skCase.getBlackboardArtifacts(BlackboardArtifact.ARTIFACT_TYPE.TSK_TAG_ARTIFACT));
+                
+                for (BlackboardArtifact artifact : tagArtifacts) {
+                    for (BlackboardAttribute attribute : artifact.getAttributes()) {
+                        if (attribute.getAttributeTypeID() == ATTRIBUTE_TYPE.TSK_TAG_NAME.getTypeID()) {
+                            String tagName = attribute.getValueString();
+                            if (tagName.equals(Bookmarks.BOOKMARK_TAG_NAME)) {
+                                break; // Don't add bookmarks
+                            } else if (tags.containsKey(tagName)) {
+                                List<BlackboardArtifact> list = new ArrayList<BlackboardArtifact>(tags.get(tagName));
+                                list.add(artifact);
+                                tags.put(tagName, list);
+                            } else {
+                                tags.put(tagName, Arrays.asList(artifact));
+                            }
+                            break;
+                        }
+                    }
+                }
+                
+            } catch (TskCoreException ex) {
+                logger.log(Level.WARNING, "Count not initialize bookmark nodes, ", ex);
+            }
+        }
+
+        @Override
+        public <T> T accept(DisplayableItemNodeVisitor<T> v) {
+            return v.visit(this);
+        }
+
+        @Override
+        protected Sheet createSheet() {
+            Sheet s = super.createSheet();
+            Sheet.Set ss = s.get(Sheet.PROPERTIES);
+            if (ss == null) {
+                ss = Sheet.createPropertiesSet();
+                s.put(ss);
+            }
+
+            ss.put(new NodeProperty("Name",
+                    "Name",
+                    "no description",
+                    getName()));
+
+            return s;
+        }
+
+        @Override
+        public DisplayableItemNode.TYPE getDisplayableItemNodeType() {
+            return DisplayableItemNode.TYPE.ARTIFACT;
+        }
+    }
+
+    /**
+     * Child factory to add all the Tag artifacts to a TagsRootNode
+     * with the tag name.
+     */
+    private class TagsRootChildren extends ChildFactory<String> {
+
+        @Override
+        protected boolean createKeys(List<String> list) {
+            for (String tagName : tags.keySet()) {
+                list.add(tagName);
+            }
+
+            return true;
+        }
+
+        @Override
+        protected Node createNodeForKey(String key) {
+            return new Tags.TagsNodeRoot(key, tags.get(key));
+        }
+    }
+
+    /**
+     * Node for each unique tag name. Shown directly under Results > Tags.
+     */
+    public class TagsNodeRoot extends DisplayableItemNode {
+
+        public TagsNodeRoot(String tagName, List<BlackboardArtifact> artifacts) {
+            super(Children.create(new Tags.TagsChildrenNode(artifacts), true), Lookups.singleton(tagName));
+
+            super.setName(tagName);
+            super.setDisplayName(tagName + " (" + tags.get(tagName).size() + ")");
+
+            this.setIconBaseWithExtension(TAG_ICON_PATH);
+        }
+
+        @Override
+        protected Sheet createSheet() {
+            Sheet s = super.createSheet();
+            Sheet.Set ss = s.get(Sheet.PROPERTIES);
+            if (ss == null) {
+                ss = Sheet.createPropertiesSet();
+                s.put(ss);
+            }
+
+            ss.put(new NodeProperty("Name",
+                    "Name",
+                    "no description",
+                    getName()));
+
+            return s;
+        }
+
+        @Override
+        public <T> T accept(DisplayableItemNodeVisitor<T> v) {
+            return v.visit(this);
+        }
+
+        @Override
+        public DisplayableItemNode.TYPE getDisplayableItemNodeType() {
+            return DisplayableItemNode.TYPE.ARTIFACT;
+        }
+
+        @Override
+        public boolean isLeafTypeNode() {
+            return true;
+        }
+    }
+
+    /**
+     * Node representing an individual Tag artifact. For each TagsNodeRoot
+     * under Results > Tags, this is one of the nodes listed in the result viewer.
+     */
+    private class TagsChildrenNode extends ChildFactory<BlackboardArtifact> {
+
+        private List<BlackboardArtifact> artifacts;
+
+        private TagsChildrenNode(List<BlackboardArtifact> artifacts) {
+            super();
+            this.artifacts = artifacts;
+        }
+
+        @Override
+        protected boolean createKeys(List<BlackboardArtifact> list) {
+            list.addAll(artifacts);
+            return true;
+        }
+
+        @Override
+        protected Node createNodeForKey(BlackboardArtifact artifact) {
+            return new BlackboardArtifactNode(artifact, TAG_ICON_PATH);
+        }
+    }
+        
     /**
      * Create a tag for a file with TSK_TAG_NAME as tagName.
      * @param file to create tag for
      * @param tagName TSK_TAG_NAME
+     * @param comment the tag comment
      */
-    static void createTag(AbstractFile file, String tagName, String comment) {
+    public static void createTag(AbstractFile file, String tagName, String comment) {
         try {
             final BlackboardArtifact bookArt = file.newArtifact(BlackboardArtifact.ARTIFACT_TYPE.TSK_TAG_FILE);
             List<BlackboardAttribute> attrs = new ArrayList<BlackboardAttribute>();
@@ -62,8 +251,9 @@ public class Tags {
      * Create a tag for an artifact with TSK_TAG_NAME as tagName.
      * @param artifact to create tag for
      * @param tagName TSK_TAG_NAME
+     * @param comment the tag comment
      */
-    static void createTag(BlackboardArtifact artifact, String tagName, String comment) {
+    public static void createTag(BlackboardArtifact artifact, String tagName, String comment) {
         try {
             Case currentCase = Case.getCurrentCase();
             SleuthkitCase skCase = currentCase.getSleuthkitCase();
@@ -91,6 +281,7 @@ public class Tags {
     /**
      * Create a bookmark tag for a file.
      * @param file to create bookmark tag for
+     * @param comment the bookmark comment
      */
     public static void createBookmark(AbstractFile file, String comment) {
         createTag(file, Bookmarks.BOOKMARK_TAG_NAME, comment);
@@ -99,6 +290,7 @@ public class Tags {
     /**
      * Create a bookmark tag for an artifact.
      * @param artifact to create bookmark tag for
+     * @param comment the bookmark comment
      */
     public static void createBookmark(BlackboardArtifact artifact, String comment) {
         createTag(artifact, Bookmarks.BOOKMARK_TAG_NAME, comment);
@@ -124,6 +316,7 @@ public class Tags {
      * Uses a custom query for speed when dealing with thousands of Tags.
      * @return a list of all tag names.
      */
+    @SuppressWarnings("deprecation")
     public static List<String> getTagNames() {
         Case currentCase = Case.getCurrentCase();
         SleuthkitCase skCase = currentCase.getSleuthkitCase();
@@ -145,6 +338,7 @@ public class Tags {
                 try {
                     skCase.closeRunQuery(rs);
                 } catch (SQLException ex) {
+                    logger.log(Level.SEVERE, "Failed to close the query for blackboard for tag names.");
                 }
             }
         }

Core/src/org/sleuthkit/autopsy/directorytree/BookmarkAction.java

@@ -1,122 +0,0 @@
-/*
- * Autopsy Forensic Browser
- * 
- * Copyright 2011 Basis Technology Corp.
- * Contact: carrier <at> sleuthkit <dot> org
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *     http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.sleuthkit.autopsy.directorytree;
-
-import java.awt.event.ActionEvent;
-import javax.swing.AbstractAction;
-import javax.swing.JOptionPane;
-import org.openide.nodes.Node;
-import org.sleuthkit.autopsy.coreutils.Logger;
-import org.sleuthkit.autopsy.datamodel.ContentUtils;
-import org.sleuthkit.autopsy.datamodel.Tags;
-import org.sleuthkit.datamodel.AbstractFile;
-import org.sleuthkit.datamodel.BlackboardArtifact;
-import org.sleuthkit.datamodel.Content;
-import org.sleuthkit.datamodel.ContentVisitor;
-import org.sleuthkit.datamodel.Directory;
-
-/**
- * Action on a file or artifact that bookmarks a file and/or artifact
- * and reloads the bookmark view.
- * Supports bookmarking of a fs file, directory and layout file and layout
- * directory (virtual files/dirs for unalloc content) 
- * 
- * TODO add use enters description and hierarchy (TSK_TAG_NAME with slashes)
- */
-public class BookmarkAction extends AbstractAction {
-
-    private static final Logger logger = Logger.getLogger(BookmarkAction.class.getName());
-    //content to bookmark
-    private AbstractFile bookmarkFile;
-    private BlackboardArtifact bookmarkArtifact;
-    private final InitializeBookmarkFileV initializer = new InitializeBookmarkFileV();
-
-    public BookmarkAction(String title, Node contentNode) {
-        super(title);
-        Content content = contentNode.getLookup().lookup(Content.class);
-
-        bookmarkArtifact = null;
-        bookmarkFile = content.accept(initializer);
-        this.setEnabled(bookmarkFile != null);
-    }
-    
-    public BookmarkAction(String title, Content content) {
-        super(title);
-
-        bookmarkArtifact = null;
-        bookmarkFile = content.accept(initializer);
-        this.setEnabled(bookmarkFile != null);
-    }
-
-    public BookmarkAction(String title, BlackboardArtifact art) {
-        super(title);
-        
-        bookmarkArtifact = art;
-        bookmarkFile = null;
-        this.setEnabled(bookmarkArtifact != null);
-    }
-
-    /**
-     * Returns the FsContent if it is supported, otherwise null
-     */
-    private static class InitializeBookmarkFileV extends ContentVisitor.Default<AbstractFile> {
-
-        @Override
-        public AbstractFile visit(org.sleuthkit.datamodel.File f) {
-            return f;
-        }
-
-        @Override
-        public AbstractFile visit(org.sleuthkit.datamodel.LayoutFile lf) {
-            return lf;
-        }
-
-        @Override
-        public AbstractFile visit(org.sleuthkit.datamodel.VirtualDirectory ld) {
-            return ld;
-        }
-
-        @Override
-        public AbstractFile visit(Directory dir) {
-            return ContentUtils.isDotDirectory(dir) ? null : dir;
-        }
-
-        @Override
-        protected AbstractFile defaultVisit(Content cntnt) {
-            return null;
-        }
-    }
-
-    @Override
-    public void actionPerformed(ActionEvent e) {         
-        String comment = JOptionPane.showInputDialog(null, "Please enter a comment for the bookmark:", "Bookmark Comment", JOptionPane.PLAIN_MESSAGE);
-        if(comment == null || comment.isEmpty()) {
-            comment = "No Comment";
-        }
-        if(bookmarkArtifact != null) {
-            Tags.createBookmark(bookmarkArtifact, comment);
-        } else if(bookmarkFile != null) {
-            Tags.createBookmark(bookmarkFile, comment);
-        }
-        
-        DirectoryTreeTopComponent viewer = DirectoryTreeTopComponent.findInstance();  
-        viewer.refreshTree(BlackboardArtifact.ARTIFACT_TYPE.TSK_TAG_FILE);
-        viewer.refreshTree(BlackboardArtifact.ARTIFACT_TYPE.TSK_TAG_ARTIFACT);
-    }
-}

Core/src/org/sleuthkit/autopsy/directorytree/Bundle.properties

@@ -47,3 +47,11 @@ ImageDetailsPanel.imgSectorSizeLabel.text=Sector Size:
 ImageDetailsPanel.imgSectorSizeValue.text=...
 DirectoryTreeTopComponent.backButton.text=
 DirectoryTreeTopComponent.forwardButton.text=
+CreateTagDialog.cancelButton.text=Cancel
+CreateTagDialog.okButton.text=OK
+CreateTagDialog.tagNameField.text=
+CreateTagDialog.tagCommentField.text=
+CreateTagDialog.tagNameLabel.text=Tag Name:
+CreateTagDialog.tagCommentLabel.text=Tag Comment:
+CreateTagDialog.preexistingLabel.text=Pre-existing Tags:
+CreateTagDialog.newTagPanel.border.title=New Tag

Core/src/org/sleuthkit/autopsy/directorytree/CreateTagDialog.form

@@ -0,0 +1,212 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+
+<Form version="1.5" maxVersion="1.8" type="org.netbeans.modules.form.forminfo.JDialogFormInfo">
+  <Properties>
+    <Property name="defaultCloseOperation" type="int" value="2"/>
+  </Properties>
+  <SyntheticProperties>
+    <SyntheticProperty name="formSizePolicy" type="int" value="1"/>
+  </SyntheticProperties>
+  <Events>
+    <EventHandler event="keyReleased" listener="java.awt.event.KeyListener" parameters="java.awt.event.KeyEvent" handler="formKeyReleased"/>
+  </Events>
+  <AuxValues>
+    <AuxValue name="FormSettings_autoResourcing" type="java.lang.Integer" value="1"/>
+    <AuxValue name="FormSettings_autoSetComponentName" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_generateFQN" type="java.lang.Boolean" value="true"/>
+    <AuxValue name="FormSettings_generateMnemonicsCode" type="java.lang.Boolean" value="true"/>
+    <AuxValue name="FormSettings_i18nAutoMode" type="java.lang.Boolean" value="true"/>
+    <AuxValue name="FormSettings_layoutCodeTarget" type="java.lang.Integer" value="1"/>
+    <AuxValue name="FormSettings_listenerGenerationStyle" type="java.lang.Integer" value="0"/>
+    <AuxValue name="FormSettings_variablesLocal" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_variablesModifier" type="java.lang.Integer" value="2"/>
+  </AuxValues>
+
+  <Layout>
+    <DimensionLayout dim="0">
+      <Group type="103" groupAlignment="0" attributes="0">
+          <Group type="102" attributes="0">
+              <EmptySpace max="-2" attributes="0"/>
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Component id="jScrollPane1" alignment="0" min="-2" pref="198" max="-2" attributes="0"/>
+                  <Component id="preexistingLabel" alignment="0" min="-2" max="-2" attributes="0"/>
+              </Group>
+              <EmptySpace type="unrelated" max="-2" attributes="0"/>
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" attributes="0">
+                      <EmptySpace min="0" pref="233" max="32767" attributes="0"/>
+                      <Component id="okButton" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace type="unrelated" max="-2" attributes="0"/>
+                      <Component id="cancelButton" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <Component id="newTagPanel" max="32767" attributes="0"/>
+              </Group>
+              <EmptySpace max="-2" attributes="0"/>
+          </Group>
+      </Group>
+    </DimensionLayout>
+    <DimensionLayout dim="1">
+      <Group type="103" groupAlignment="0" attributes="0">
+          <Group type="102" alignment="0" attributes="0">
+              <EmptySpace max="-2" attributes="0"/>
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" attributes="0">
+                      <Component id="preexistingLabel" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="jScrollPane1" pref="0" max="32767" attributes="0"/>
+                  </Group>
+                  <Component id="newTagPanel" max="32767" attributes="0"/>
+              </Group>
+              <EmptySpace max="-2" attributes="0"/>
+              <Group type="103" groupAlignment="3" attributes="0">
+                  <Component id="cancelButton" alignment="3" min="-2" max="-2" attributes="0"/>
+                  <Component id="okButton" alignment="3" min="-2" max="-2" attributes="0"/>
+              </Group>
+              <EmptySpace max="-2" attributes="0"/>
+          </Group>
+      </Group>
+    </DimensionLayout>
+  </Layout>
+  <SubComponents>
+    <Component class="javax.swing.JButton" name="cancelButton">
+      <Properties>
+        <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
+          <ResourceString bundle="org/sleuthkit/autopsy/directorytree/Bundle.properties" key="CreateTagDialog.cancelButton.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
+        </Property>
+      </Properties>
+      <Events>
+        <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="cancelButtonActionPerformed"/>
+      </Events>
+    </Component>
+    <Component class="javax.swing.JButton" name="okButton">
+      <Properties>
+        <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
+          <ResourceString bundle="org/sleuthkit/autopsy/directorytree/Bundle.properties" key="CreateTagDialog.okButton.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
+        </Property>
+      </Properties>
+      <Events>
+        <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="okButtonActionPerformed"/>
+      </Events>
+    </Component>
+    <Container class="javax.swing.JScrollPane" name="jScrollPane1">
+      <Properties>
+        <Property name="background" type="java.awt.Color" editor="org.netbeans.beaninfo.editors.ColorEditor">
+          <Color blue="ff" green="ff" red="ff" type="rgb"/>
+        </Property>
+      </Properties>
+      <AuxValues>
+        <AuxValue name="autoScrollPane" type="java.lang.Boolean" value="true"/>
+      </AuxValues>
+
+      <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
+      <SubComponents>
+        <Component class="javax.swing.JTable" name="tagsTable">
+          <Properties>
+            <Property name="model" type="javax.swing.table.TableModel" editor="org.netbeans.modules.form.editors2.TableModelEditor">
+              <Table columnCount="0" rowCount="0"/>
+            </Property>
+            <Property name="columnModel" type="javax.swing.table.TableColumnModel" editor="org.netbeans.modules.form.editors2.TableColumnModelEditor">
+              <TableColumnModel selectionModel="0"/>
+            </Property>
+            <Property name="showHorizontalLines" type="boolean" value="false"/>
+            <Property name="showVerticalLines" type="boolean" value="false"/>
+            <Property name="tableHeader" type="javax.swing.table.JTableHeader" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+              <Connection code="null" type="code"/>
+            </Property>
+          </Properties>
+        </Component>
+      </SubComponents>
+    </Container>
+    <Component class="javax.swing.JLabel" name="preexistingLabel">
+      <Properties>
+        <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
+          <ResourceString bundle="org/sleuthkit/autopsy/directorytree/Bundle.properties" key="CreateTagDialog.preexistingLabel.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
+        </Property>
+      </Properties>
+    </Component>
+    <Container class="javax.swing.JPanel" name="newTagPanel">
+      <Properties>
+        <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+          <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+            <TitledBorder title="New Tag">
+              <ResourceString PropertyName="titleX" bundle="org/sleuthkit/autopsy/directorytree/Bundle.properties" key="CreateTagDialog.newTagPanel.border.title" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
+            </TitledBorder>
+          </Border>
+        </Property>
+      </Properties>
+
+      <Layout>
+        <DimensionLayout dim="0">
+          <Group type="103" groupAlignment="0" attributes="0">
+              <Group type="102" attributes="0">
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="0" attributes="0">
+                      <Component id="tagCommentLabel" alignment="0" min="-2" max="-2" attributes="0"/>
+                      <Component id="tagNameLabel" alignment="0" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace type="separate" max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="0" attributes="0">
+                      <Component id="tagNameField" max="32767" attributes="0"/>
+                      <Component id="tagCommentField" max="32767" attributes="0"/>
+                  </Group>
+                  <EmptySpace max="-2" attributes="0"/>
+              </Group>
+          </Group>
+        </DimensionLayout>
+        <DimensionLayout dim="1">
+          <Group type="103" groupAlignment="0" attributes="0">
+              <Group type="102" attributes="0">
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="3" attributes="0">
+                      <Component id="tagNameLabel" alignment="3" min="-2" max="-2" attributes="0"/>
+                      <Component id="tagNameField" alignment="3" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="3" attributes="0">
+                      <Component id="tagCommentLabel" alignment="3" min="-2" max="-2" attributes="0"/>
+                      <Component id="tagCommentField" alignment="3" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace pref="138" max="32767" attributes="0"/>
+              </Group>
+          </Group>
+        </DimensionLayout>
+      </Layout>
+      <SubComponents>
+        <Component class="javax.swing.JTextField" name="tagCommentField">
+          <Properties>
+            <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
+              <ResourceString bundle="org/sleuthkit/autopsy/directorytree/Bundle.properties" key="CreateTagDialog.tagCommentField.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
+            </Property>
+          </Properties>
+          <Events>
+            <EventHandler event="keyReleased" listener="java.awt.event.KeyListener" parameters="java.awt.event.KeyEvent" handler="tagCommentFieldKeyReleased"/>
+          </Events>
+        </Component>
+        <Component class="javax.swing.JLabel" name="tagNameLabel">
+          <Properties>
+            <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
+              <ResourceString bundle="org/sleuthkit/autopsy/directorytree/Bundle.properties" key="CreateTagDialog.tagNameLabel.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
+            </Property>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JLabel" name="tagCommentLabel">
+          <Properties>
+            <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
+              <ResourceString bundle="org/sleuthkit/autopsy/directorytree/Bundle.properties" key="CreateTagDialog.tagCommentLabel.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
+            </Property>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JTextField" name="tagNameField">
+          <Properties>
+            <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
+              <ResourceString bundle="org/sleuthkit/autopsy/directorytree/Bundle.properties" key="CreateTagDialog.tagNameField.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
+            </Property>
+          </Properties>
+          <Events>
+            <EventHandler event="keyReleased" listener="java.awt.event.KeyListener" parameters="java.awt.event.KeyEvent" handler="tagNameFieldKeyReleased"/>
+          </Events>
+        </Component>
+      </SubComponents>
+    </Container>
+  </SubComponents>
+</Form>

Core/src/org/sleuthkit/autopsy/directorytree/CreateTagDialog.java

@@ -0,0 +1,319 @@
+/*
+ * Autopsy Forensic Browser
+ * 
+ * Copyright 2013 Basis Technology Corp.
+ * Contact: carrier <at> sleuthkit <dot> org
+ * 
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.sleuthkit.autopsy.directorytree;
+
+import java.awt.Dimension;
+import java.awt.Toolkit;
+import java.awt.event.KeyEvent;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import javax.swing.JOptionPane;
+import javax.swing.ListSelectionModel;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.table.AbstractTableModel;
+import org.sleuthkit.autopsy.datamodel.Tags;
+
+public class CreateTagDialog extends javax.swing.JDialog {
+    private Map<String, String> tagMap = null;
+    TagsTableModel tagsTableModel;
+    TagSelectionListener tagSelectionListener;
+
+    /**
+     * Creates new form CreateTagDialog
+     */
+    public CreateTagDialog(java.awt.Frame parent, boolean modal) {
+        super(parent, modal);
+        initComponents();
+        
+        tagsTableModel = new TagsTableModel();
+        tagSelectionListener = new TagSelectionListener();
+        tagsTable.setModel(tagsTableModel);
+        tagsTable.getSelectionModel().addListSelectionListener(tagSelectionListener);
+        tagsTable.setTableHeader(null);
+        tagsTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+        tagsTable.setRowHeight(tagsTable.getRowHeight() + 5);
+    }
+    
+    public Map<String, String> display() {
+        this.setTitle("Create a new tag");
+        
+        Dimension screenDimension = Toolkit.getDefaultToolkit().getScreenSize();
+        // set the popUp window / JFrame
+        int w = this.getSize().width;
+        int h = this.getSize().height;
+
+        // set the location of the popUp Window on the center of the screen
+        setLocation((screenDimension.width - w) / 2, (screenDimension.height - h) / 2);
+        this.setVisible(true);
+        
+        return this.tagMap;
+    }
+    
+    private boolean containsIllegalCharacters(String content) {
+        if ((content.contains("\\") || content.contains(":") || content.contains("*")
+                || content.contains("?") || content.contains("\"") || content.contains("<")
+                || content.contains(">") || content.contains("|"))) {
+            return true;
+        }
+        return false;
+    }
+
+    /**
+     * This method is called from within the constructor to initialize the form.
+     * WARNING: Do NOT modify this code. The content of this method is always
+     * regenerated by the Form Editor.
+     */
+    @SuppressWarnings("unchecked")
+    // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
+    private void initComponents() {
+
+        cancelButton = new javax.swing.JButton();
+        okButton = new javax.swing.JButton();
+        jScrollPane1 = new javax.swing.JScrollPane();
+        tagsTable = new javax.swing.JTable();
+        preexistingLabel = new javax.swing.JLabel();
+        newTagPanel = new javax.swing.JPanel();
+        tagCommentField = new javax.swing.JTextField();
+        tagNameLabel = new javax.swing.JLabel();
+        tagCommentLabel = new javax.swing.JLabel();
+        tagNameField = new javax.swing.JTextField();
+
+        setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+        addKeyListener(new java.awt.event.KeyAdapter() {
+            public void keyReleased(java.awt.event.KeyEvent evt) {
+                formKeyReleased(evt);
+            }
+        });
+
+        org.openide.awt.Mnemonics.setLocalizedText(cancelButton, org.openide.util.NbBundle.getMessage(CreateTagDialog.class, "CreateTagDialog.cancelButton.text")); // NOI18N
+        cancelButton.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                cancelButtonActionPerformed(evt);
+            }
+        });
+
+        org.openide.awt.Mnemonics.setLocalizedText(okButton, org.openide.util.NbBundle.getMessage(CreateTagDialog.class, "CreateTagDialog.okButton.text")); // NOI18N
+        okButton.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                okButtonActionPerformed(evt);
+            }
+        });
+
+        jScrollPane1.setBackground(new java.awt.Color(255, 255, 255));
+
+        tagsTable.setModel(new javax.swing.table.DefaultTableModel(
+            new Object [][] {
+
+            },
+            new String [] {
+
+            }
+        ));
+        tagsTable.setShowHorizontalLines(false);
+        tagsTable.setShowVerticalLines(false);
+        tagsTable.setTableHeader(null);
+        jScrollPane1.setViewportView(tagsTable);
+
+        org.openide.awt.Mnemonics.setLocalizedText(preexistingLabel, org.openide.util.NbBundle.getMessage(CreateTagDialog.class, "CreateTagDialog.preexistingLabel.text")); // NOI18N
+
+        newTagPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(org.openide.util.NbBundle.getMessage(CreateTagDialog.class, "CreateTagDialog.newTagPanel.border.title"))); // NOI18N
+
+        tagCommentField.setText(org.openide.util.NbBundle.getMessage(CreateTagDialog.class, "CreateTagDialog.tagCommentField.text")); // NOI18N
+        tagCommentField.addKeyListener(new java.awt.event.KeyAdapter() {
+            public void keyReleased(java.awt.event.KeyEvent evt) {
+                tagCommentFieldKeyReleased(evt);
+            }
+        });
+
+        org.openide.awt.Mnemonics.setLocalizedText(tagNameLabel, org.openide.util.NbBundle.getMessage(CreateTagDialog.class, "CreateTagDialog.tagNameLabel.text")); // NOI18N
+
+        org.openide.awt.Mnemonics.setLocalizedText(tagCommentLabel, org.openide.util.NbBundle.getMessage(CreateTagDialog.class, "CreateTagDialog.tagCommentLabel.text")); // NOI18N
+
+        tagNameField.setText(org.openide.util.NbBundle.getMessage(CreateTagDialog.class, "CreateTagDialog.tagNameField.text")); // NOI18N
+        tagNameField.addKeyListener(new java.awt.event.KeyAdapter() {
+            public void keyReleased(java.awt.event.KeyEvent evt) {
+                tagNameFieldKeyReleased(evt);
+            }
+        });
+
+        javax.swing.GroupLayout newTagPanelLayout = new javax.swing.GroupLayout(newTagPanel);
+        newTagPanel.setLayout(newTagPanelLayout);
+        newTagPanelLayout.setHorizontalGroup(
+            newTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(newTagPanelLayout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(newTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addComponent(tagCommentLabel)
+                    .addComponent(tagNameLabel))
+                .addGap(18, 18, 18)
+                .addGroup(newTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addComponent(tagNameField)
+                    .addComponent(tagCommentField))
+                .addContainerGap())
+        );
+        newTagPanelLayout.setVerticalGroup(
+            newTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(newTagPanelLayout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(newTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(tagNameLabel)
+                    .addComponent(tagNameField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(newTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(tagCommentLabel)
+                    .addComponent(tagCommentField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addContainerGap(138, Short.MAX_VALUE))
+        );
+
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
+        getContentPane().setLayout(layout);
+        layout.setHorizontalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(layout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addComponent(jScrollPane1, javax.swing.GroupLayout.PREFERRED_SIZE, 198, javax.swing.GroupLayout.PREFERRED_SIZE)
+                    .addComponent(preexistingLabel))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
+                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addGroup(layout.createSequentialGroup()
+                        .addGap(0, 233, Short.MAX_VALUE)
+                        .addComponent(okButton)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
+                        .addComponent(cancelButton))
+                    .addComponent(newTagPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+                .addContainerGap())
+        );
+        layout.setVerticalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(layout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addGroup(layout.createSequentialGroup()
+                        .addComponent(preexistingLabel)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(jScrollPane1, javax.swing.GroupLayout.PREFERRED_SIZE, 0, Short.MAX_VALUE))
+                    .addComponent(newTagPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(cancelButton)
+                    .addComponent(okButton))
+                .addContainerGap())
+        );
+
+        pack();
+    }// </editor-fold>//GEN-END:initComponents
+
+    private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_cancelButtonActionPerformed
+        this.tagMap = null;
+        this.dispose();
+    }//GEN-LAST:event_cancelButtonActionPerformed
+
+    private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_okButtonActionPerformed
+        String tagName = tagNameField.getText();
+        String tagComment = tagCommentField.getText();
+        if (tagName.isEmpty()) {
+            JOptionPane.showMessageDialog(null, "Must supply a tag name to continue.", "Tag Name", JOptionPane.ERROR_MESSAGE);
+        } else if (containsIllegalCharacters(tagName)) {
+            JOptionPane.showMessageDialog(null, "The tag name contains illegal characters.\nCannot contain any of the following symbols: \\ : * ? \" < > |",
+                    "Illegal Characters", JOptionPane.ERROR_MESSAGE);
+        } else {
+            this.tagMap = new HashMap<String, String>();
+            tagMap.put("Name", tagName);
+            tagMap.put("Comment", tagComment.isEmpty() ? "No Comment" : tagComment);
+            this.dispose();
+        }
+    }//GEN-LAST:event_okButtonActionPerformed
+
+    private void formKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_formKeyReleased
+        if (evt.getKeyCode() == KeyEvent.VK_ENTER) {
+            okButtonActionPerformed(null);
+        }
+    }//GEN-LAST:event_formKeyReleased
+
+    private void tagNameFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_tagNameFieldKeyReleased
+        if (evt.getKeyCode() == KeyEvent.VK_ENTER) {
+            okButtonActionPerformed(null);
+        }
+    }//GEN-LAST:event_tagNameFieldKeyReleased
+
+    private void tagCommentFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_tagCommentFieldKeyReleased
+        if (evt.getKeyCode() == KeyEvent.VK_ENTER) {
+            okButtonActionPerformed(null);
+        }
+    }//GEN-LAST:event_tagCommentFieldKeyReleased
+
+    // Variables declaration - do not modify//GEN-BEGIN:variables
+    private javax.swing.JButton cancelButton;
+    private javax.swing.JScrollPane jScrollPane1;
+    private javax.swing.JPanel newTagPanel;
+    private javax.swing.JButton okButton;
+    private javax.swing.JLabel preexistingLabel;
+    private javax.swing.JTextField tagCommentField;
+    private javax.swing.JLabel tagCommentLabel;
+    private javax.swing.JTextField tagNameField;
+    private javax.swing.JLabel tagNameLabel;
+    private javax.swing.JTable tagsTable;
+    // End of variables declaration//GEN-END:variables
+
+    private class TagsTableModel extends AbstractTableModel {
+        List<String> tagNames;
+        
+        TagsTableModel() {
+            tagNames = Tags.getTagNames();
+        }
+
+        @Override
+        public int getRowCount() {
+            return tagNames.size();
+        }
+
+        @Override
+        public boolean isCellEditable(int rowIndex, int columnIndex) {
+            return false;
+        }
+
+        @Override
+        public int getColumnCount() {
+            return 1;
+        }
+
+        @Override
+        public String getValueAt(int rowIndex, int columnIndex) {
+            return tagNames.get(rowIndex);
+        }
+        
+    }
+    
+    private class TagSelectionListener implements ListSelectionListener {
+
+        @Override
+        public void valueChanged(ListSelectionEvent e) {
+            Object row = tagsTable.getValueAt(tagsTable.getSelectedRow(), 0);
+            if (row != null) {
+                String tagName = row.toString();
+                tagNameField.setText(tagName);
+            }
+        }
+        
+    }
+
+}

Core/src/org/sleuthkit/autopsy/directorytree/DataResultFilterNode.java

@@ -174,7 +174,7 @@ public class DataResultFilterNode extends FilterNode {
             actions.add(null); // creates a menu separator
             actions.add(new ExtractAction("Extract Directory", dir));
             actions.add(null); // creates a menu separator
-            actions.add(new BookmarkAction("Bookmark Directory", dir));
+            actions.add(new TagFileAction(dir));
             return actions;
         }
         
@@ -187,7 +187,7 @@ public class DataResultFilterNode extends FilterNode {
             actions.add(null); // creates a menu separator
             actions.add(new ExtractAction("Extract File", lf));
             actions.add(null); // creates a menu separator
-            actions.add(new BookmarkAction("Bookmark File", lf));
+            actions.add(new TagFileAction(lf));
             return actions;
         }
         
@@ -195,7 +195,7 @@ public class DataResultFilterNode extends FilterNode {
         public List<Action> visit(VirtualDirectoryNode ld) {
             List<Action> actions = new ArrayList<Action>();
            
-            actions.add(new BookmarkAction("Bookmark Directory", ld));
+            actions.add(new TagFileAction(ld));
             return actions;
         }
 
@@ -212,7 +212,7 @@ public class DataResultFilterNode extends FilterNode {
             actions.add(new ExtractAction("Extract File", f));
             actions.add(new HashSearchAction("Search for files with the same MD5 hash", f));
             actions.add(null); // creates a menu separator
-            actions.add(new BookmarkAction("Bookmark File", f));
+            actions.add(new TagFileAction(f));
             return actions;
         }
 
@@ -246,8 +246,8 @@ public class DataResultFilterNode extends FilterNode {
                 //add file bookmark if itself is not a file bookmark
                 if (artifactTypeID != BlackboardArtifact.ARTIFACT_TYPE.TSK_TAG_FILE.getTypeID()) {
                     actions.add(null); // creates a menu separator
-                    actions.add(new BookmarkAction("Bookmark File", f));
-                    actions.add(new BookmarkAction("Bookmark Result", ba));
+                    actions.add(new TagFileAction(f));
+                    actions.add(new TagResultAction(ba));
                 }
             }
              if (( d = ban.getLookup().lookup(Directory.class)) != null) {
@@ -260,8 +260,8 @@ public class DataResultFilterNode extends FilterNode {
                 //add file bookmark if itself is not a file bookmark
                 if (artifactTypeID != BlackboardArtifact.ARTIFACT_TYPE.TSK_TAG_FILE.getTypeID()) {
                     actions.add(null); // creates a menu separator
-                    actions.add(new BookmarkAction("Bookmark Directory", d));
-                    actions.add(new BookmarkAction("Bookmark Result Directory", ba));
+                    actions.add(new TagFileAction( d));
+                    actions.add(new TagResultAction(ba));
                 }
             }
             else if ( ( lf = ban.getLookup().lookup(LayoutFile.class)) != null) {
@@ -274,8 +274,8 @@ public class DataResultFilterNode extends FilterNode {
                 //add file bookmark if itself is not a file bookmark
                 if (artifactTypeID != BlackboardArtifact.ARTIFACT_TYPE.TSK_TAG_FILE.getTypeID()) {
                     actions.add(null); // creates a menu separator
-                     actions.add(new BookmarkAction("Bookmark File", lf));
-                    actions.add(new BookmarkAction("Bookmark Result", ba));
+                     actions.add(new TagFileAction(lf));
+                    actions.add(new TagResultAction(ba));
                 }
             }
             //if (artifactTypeID == BlackboardArtifact.ARTIFACT_TYPE.TSK_KEYWORD_HIT.getTypeID()) {

Core/src/org/sleuthkit/autopsy/directorytree/ExtractUnallocAction.java

@@ -378,7 +378,7 @@ public final class ExtractUnallocAction extends AbstractAction {
         /**
          * LayoutDirectory has all the Layout(Unallocated) files
          *
-         * @param ld LayoutDirectory the visitor encountered
+         * @param vd VirtualDirectory the visitor encountered
          * @return A list<LayoutFile> containing all the LayoutFile in ld,
          * returns null if it fails
          */

Core/src/org/sleuthkit/autopsy/directorytree/ResultDeleteAction.java

@@ -33,7 +33,9 @@ import org.sleuthkit.datamodel.SleuthkitCase;
 
 /**
  * Action that deletes blackboard artifacts requested and reloads the view
+ * @deprecated do not use, it is here in case we ever pick up on this work
  */
+@Deprecated
 public class ResultDeleteAction extends AbstractAction {
 
     private enum ActionType {
@@ -100,6 +102,7 @@ public class ResultDeleteAction extends AbstractAction {
     }
 
     //TODO should be moved to SleuthkitCase and BlackboardArtifact API
+    @SuppressWarnings("deprecation")
     private static void deleteArtifact(BlackboardArtifact art) {
         final SleuthkitCase skCase = Case.getCurrentCase().getSleuthkitCase();
         final long artId = art.getArtifactID();
@@ -117,15 +120,17 @@ public class ResultDeleteAction extends AbstractAction {
     }
 
 
+    @SuppressWarnings("deprecation")
     private static void deleteArtifactsByAttributeValue(BlackboardArtifact.ARTIFACT_TYPE artType,
             BlackboardAttribute.ATTRIBUTE_TYPE attrType, String value) {
 
         final SleuthkitCase skCase = Case.getCurrentCase().getSleuthkitCase();
+        ResultSet rs = null;
         try {
             //first to select to get artifact ids to delete
             //then join delete attrs
             //then delete arts by id
-            ResultSet rs = skCase.runQuery("DELETE FROM blackboard_attributes WHERE artifact_id IN "
+                    rs = skCase.runQuery("DELETE FROM blackboard_attributes WHERE artifact_id IN "
                     + "(SELECT blackboard_artifacts.artifact_id FROM blackboard_artifacts "
                     + "INNER JOIN blackboard_attributes ON (blackboard_attributes.artifact_id = blackboard_artifacts.artifact_id) "
                     + "WHERE blackboard_artifacts.artifact_type_id = "
@@ -134,7 +139,7 @@ public class ResultDeleteAction extends AbstractAction {
                     + " AND blackboard_attributes.value_type = " + BlackboardAttribute.TSK_BLACKBOARD_ATTRIBUTE_VALUE_TYPE.STRING.getType()
                     + " AND blackboard_attributes.value_text = '" + value + "'"
                     + ")");
-            skCase.closeRunQuery(rs);
+        
 
             //rs = skCase.runQuery("DELETE from blackboard_artifacts where artifact_type_id = "
               //      + Integer.toString(artType.getTypeID()));
@@ -143,10 +148,20 @@ public class ResultDeleteAction extends AbstractAction {
         } catch (SQLException ex) {
             logger.log(Level.WARNING, "Could not delete artifacts by type id: " + artType.getTypeID(), ex);
         }
+        finally {
+            if (rs != null) {
+                try {
+                    skCase.closeRunQuery(rs);
+                } catch (SQLException ex) {
+                    logger.log(Level.WARNING, "Error closing result set after deleting", ex);
+                }
+            }
+        }
 
     }
 
     //TODO should be moved to SleuthkitCase
+    @SuppressWarnings("deprecation")
     private static void deleteArtifacts(BlackboardArtifact.ARTIFACT_TYPE artType) {
         // SELECT * from blackboard_attributes INNER JOIN blackboard_artifacts ON blackboard_artifacts.artifact_id = blackboard_attributes.artifact_ID AND blackboard_artifacts.artifact_type_id = 9;
         final SleuthkitCase skCase = Case.getCurrentCase().getSleuthkitCase();

Core/src/org/sleuthkit/autopsy/directorytree/TagFileAction.java

@@ -0,0 +1,179 @@
+/*
+ * Autopsy Forensic Browser
+ * 
+ * Copyright 2013 Basis Technology Corp.
+ * Contact: carrier <at> sleuthkit <dot> org
+ * 
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.sleuthkit.autopsy.directorytree;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.List;
+import java.util.Map;
+import javax.swing.AbstractAction;
+import javax.swing.JFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import org.openide.nodes.Node;
+import org.openide.util.actions.Presenter;
+import org.sleuthkit.autopsy.coreutils.Logger;
+import org.sleuthkit.autopsy.datamodel.Bookmarks;
+import org.sleuthkit.autopsy.datamodel.ContentUtils;
+import org.sleuthkit.autopsy.datamodel.Tags;
+import org.sleuthkit.datamodel.AbstractFile;
+import org.sleuthkit.datamodel.BlackboardArtifact;
+import org.sleuthkit.datamodel.Content;
+import org.sleuthkit.datamodel.ContentVisitor;
+import org.sleuthkit.datamodel.Directory;
+
+/**
+ * Action on a file or artifact that bookmarks a file and/or artifact
+ * and reloads the bookmark view.
+ * Supports bookmarking of a fs file, directory and layout file and layout
+ * directory (virtual files/dirs for unalloc content) 
+ * 
+ * TODO add use enters description and hierarchy (TSK_TAG_NAME with slashes)
+ */
+public class TagFileAction extends AbstractAction implements Presenter.Popup {
+
+    private static final Logger logger = Logger.getLogger(TagFileAction.class.getName());
+    //content to bookmark
+    private AbstractFile tagFile;
+    private final InitializeBookmarkFileV initializer = new InitializeBookmarkFileV();
+
+    public TagFileAction(Node contentNode) {
+        Content content = contentNode.getLookup().lookup(Content.class);
+        tagFile = content.accept(initializer);
+    }
+    
+    public TagFileAction(Content content) {
+        tagFile = content.accept(initializer);
+    }
+    
+    private String getComment() {
+        String comment = JOptionPane.showInputDialog(null,
+                "Please enter a comment for the tag (optional):",
+                "Tag Comment",
+                JOptionPane.PLAIN_MESSAGE);
+        if(comment == null || comment.isEmpty()) {
+            comment = "No Comment";
+        }
+        return comment;
+    }
+    
+    private void refreshDirectoryTree() {
+        DirectoryTreeTopComponent viewer = DirectoryTreeTopComponent.findInstance();  
+        viewer.refreshTree(BlackboardArtifact.ARTIFACT_TYPE.TSK_TAG_FILE);
+        viewer.refreshTree(BlackboardArtifact.ARTIFACT_TYPE.TSK_TAG_ARTIFACT);
+    }
+
+    @Override
+    public JMenuItem getPopupPresenter() {
+        JMenu result = new JMenu("Tag File");
+        
+        JMenuItem contentItem = new JMenuItem("Bookmark File");
+        contentItem.addActionListener(new ActionListener() {
+
+            @Override
+            public void actionPerformed(ActionEvent e) {
+                Tags.createBookmark(tagFile, getComment());
+                refreshDirectoryTree();
+            }
+            
+        });
+        result.add(contentItem);
+        result.addSeparator();
+        
+        JMenuItem newTagItem = new JMenuItem("Create a new tag");
+        newTagItem.addActionListener(new ActionListener() {
+                
+            @Override
+            public void actionPerformed(ActionEvent e) {
+                Map<String, String> tagMap = new CreateTagDialog(new JFrame(), true).display();
+                if (tagMap != null) {
+                    Tags.createTag(tagFile, tagMap.get("Name"), tagMap.get("Comment"));
+                    refreshDirectoryTree();
+                }
+            }
+
+        });
+        result.add(newTagItem);
+        result.addSeparator();
+        
+        List<String> tagNames = Tags.getTagNames();
+        if (tagNames.isEmpty()) {
+            JMenuItem empty = new JMenuItem("No tags");
+            empty.setEnabled(false);
+            result.add(empty);
+        } else {
+            for (final String tagName : tagNames) {
+                if (tagName.equals(Bookmarks.BOOKMARK_TAG_NAME)) {
+                    continue;
+                }
+                JMenuItem tagItem = new JMenuItem(tagName);
+                tagItem.addActionListener(new ActionListener() {
+
+                    @Override
+                    public void actionPerformed(ActionEvent e) {
+                        Tags.createTag(tagFile, tagName, getComment());
+                        refreshDirectoryTree();
+                    }
+
+                });
+                result.add(tagItem);
+            }
+        }
+        
+        return result;
+    }
+
+    /**
+     * Returns the FsContent if it is supported, otherwise null
+     */
+    private static class InitializeBookmarkFileV extends ContentVisitor.Default<AbstractFile> {
+
+        @Override
+        public AbstractFile visit(org.sleuthkit.datamodel.File f) {
+            return f;
+        }
+
+        @Override
+        public AbstractFile visit(org.sleuthkit.datamodel.LayoutFile lf) {
+            return lf;
+        }
+
+        @Override
+        public AbstractFile visit(org.sleuthkit.datamodel.VirtualDirectory ld) {
+            return ld;
+        }
+
+        @Override
+        public AbstractFile visit(Directory dir) {
+            return ContentUtils.isDotDirectory(dir) ? null : dir;
+        }
+
+        @Override
+        protected AbstractFile defaultVisit(Content cntnt) {
+            return null;
+        }
+    }
+
+    @Override
+    public void actionPerformed(ActionEvent e) {
+        // Do nothing - this action should never be performed
+        // Submenu actions are invoked instead
+    }
+}

Core/src/org/sleuthkit/autopsy/directorytree/TagResultAction.java

@@ -0,0 +1,136 @@
+/*
+ * Autopsy Forensic Browser
+ * 
+ * Copyright 2013 Basis Technology Corp.
+ * Contact: carrier <at> sleuthkit <dot> org
+ * 
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.sleuthkit.autopsy.directorytree;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.List;
+import java.util.Map;
+import javax.swing.AbstractAction;
+import javax.swing.JFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import org.openide.util.actions.Presenter;
+import org.sleuthkit.autopsy.coreutils.Logger;
+import org.sleuthkit.autopsy.datamodel.Bookmarks;
+import org.sleuthkit.autopsy.datamodel.Tags;
+import org.sleuthkit.datamodel.BlackboardArtifact;
+
+/**
+ * Action on a file or artifact that bookmarks a file and/or artifact
+ * and reloads the bookmark view.
+ * Supports bookmarking of a fs file, directory and layout file and layout
+ * directory (virtual files/dirs for unalloc content) 
+ * 
+ * TODO add use enters description and hierarchy (TSK_TAG_NAME with slashes)
+ */
+public class TagResultAction extends AbstractAction implements Presenter.Popup {
+
+    private static final Logger logger = Logger.getLogger(TagFileAction.class.getName());
+    //content to bookmark
+    private BlackboardArtifact tagArtifact;
+    
+    public TagResultAction(BlackboardArtifact artifact) {
+        tagArtifact = artifact;
+    }
+    
+    private String getComment() {
+        String comment = JOptionPane.showInputDialog(null,
+                "Please enter a comment for the tag (optional):",
+                "Tag Comment",
+                JOptionPane.PLAIN_MESSAGE);
+        if(comment == null || comment.isEmpty()) {
+            comment = "No Comment";
+        }
+        return comment;
+    }
+    
+    private void refreshDirectoryTree() {
+        DirectoryTreeTopComponent viewer = DirectoryTreeTopComponent.findInstance();  
+        viewer.refreshTree(BlackboardArtifact.ARTIFACT_TYPE.TSK_TAG_FILE);
+        viewer.refreshTree(BlackboardArtifact.ARTIFACT_TYPE.TSK_TAG_ARTIFACT);
+    }
+
+    @Override
+    public JMenuItem getPopupPresenter() {
+        JMenu result = new JMenu("Tag Result");
+        
+        JMenuItem contentItem = new JMenuItem("Bookmark Result");
+        contentItem.addActionListener(new ActionListener() {
+
+            @Override
+            public void actionPerformed(ActionEvent e) {
+                Tags.createBookmark(tagArtifact, getComment());
+                refreshDirectoryTree();
+            }
+            
+        });
+        result.add(contentItem);
+        result.addSeparator();
+        
+        JMenuItem newTagItem = new JMenuItem("Create a new tag");
+        newTagItem.addActionListener(new ActionListener() {
+                
+            @Override
+            public void actionPerformed(ActionEvent e) {
+                Map<String, String> tagMap = new CreateTagDialog(new JFrame(), true).display();
+                if (tagMap != null) {
+                    Tags.createTag(tagArtifact, tagMap.get("Name"), tagMap.get("Comment"));
+                    refreshDirectoryTree();
+                }
+            }
+
+        });
+        result.add(newTagItem);
+        result.addSeparator();
+        
+        List<String> tagNames = Tags.getTagNames();
+        if (tagNames.isEmpty()) {
+            JMenuItem empty = new JMenuItem("No tags");
+            empty.setEnabled(false);
+            result.add(empty);
+        } else {
+            for (final String tagName : Tags.getTagNames()) {
+                if (tagName.equals(Bookmarks.BOOKMARK_TAG_NAME)) {
+                    continue;
+                }
+                JMenuItem tagItem = new JMenuItem(tagName);
+                tagItem.addActionListener(new ActionListener() {
+
+                    @Override
+                    public void actionPerformed(ActionEvent e) {
+                        Tags.createTag(tagArtifact, tagName, getComment());
+                        refreshDirectoryTree();
+                    }
+
+                });
+                result.add(tagItem);
+            }
+        }
+        
+        return result;
+    }
+
+    @Override
+    public void actionPerformed(ActionEvent e) {
+        // Do nothing - this action should never be performed
+        // Submenu actions are invoked instead
+    }
+}

Core/src/org/sleuthkit/autopsy/filesearch/FileSearchPanel.java

@@ -153,6 +153,7 @@ public class FileSearchPanel extends javax.swing.JPanel {
      * Action when the "Search" button is pressed.
      *
      */
+    @SuppressWarnings("deprecation")
     private void search() {
         // change the cursor to "waiting cursor" for this operation
         this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
@@ -170,16 +171,12 @@ public class FileSearchPanel extends javax.swing.JPanel {
                     SleuthkitCase tempDb = currentCase.getSleuthkitCase();
                     ResultSet rs = tempDb.runQuery(this.getQuery("count(*) as TotalMatches"));
                     totalMatches = totalMatches + rs.getInt("TotalMatches");
-                    Statement s = rs.getStatement();
-                    rs.close();
-                    if (s != null)
-                        s.close();
+                    tempDb.closeRunQuery(rs);
+                    
                     rs = tempDb.runQuery(this.getQuery(null));
                     currentDbList = tempDb.resultSetToFsContents(rs);
-                    s = rs.getStatement();
-                    rs.close();
-                    if (s != null)
-                        s.close();
+                    tempDb.closeRunQuery(rs);
+                    
                     fsContentList.addAll(currentDbList);
                 } catch (SQLException ex) {
                     Logger logger = Logger.getLogger(this.getClass().getName());

Core/src/org/sleuthkit/autopsy/filesearch/FileSearchTopComponent.java

@@ -150,6 +150,7 @@ public final class FileSearchTopComponent extends TopComponent implements DataEx
      * Action when the "Search" button is pressed.
      *
      */
+    @SuppressWarnings("deprecation")
     private void search() {
         // change the cursor to "waiting cursor" for this operation
         this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
@@ -167,16 +168,12 @@ public final class FileSearchTopComponent extends TopComponent implements DataEx
                     SleuthkitCase tempDb = currentCase.getSleuthkitCase();
                     ResultSet rs = tempDb.runQuery(this.getQuery("count(*) as TotalMatches"));
                     totalMatches = totalMatches + rs.getInt("TotalMatches");
-                    Statement s = rs.getStatement();
-                    rs.close();
-                    if (s != null)
-                        s.close();
+                    tempDb.closeRunQuery(rs);
+                    
                     rs = tempDb.runQuery(this.getQuery(null));
                     currentDbList = tempDb.resultSetToFsContents(rs);
-                    s = rs.getStatement();
-                    rs.close();
-                    if (s != null)
-                        s.close();
+                    tempDb.closeRunQuery(rs);
+                    
                     fsContentList.addAll(currentDbList);
                 } catch (SQLException ex) {
                     Logger logger = Logger.getLogger(this.getClass().getName());

Core/src/org/sleuthkit/autopsy/ingest/IngestManager.java

@@ -690,7 +690,16 @@ public class IngestManager {
                 sb.append("Errors per module:");
                 for (IngestModuleAbstract module : errors.keySet()) {
                     final int errorsModule = errors.get(module);
-                    sb.append("\t").append(module.getName()).append(": ").append(errorsModule).append(EOL);
+                    String moduleName;
+                    if (module != null) {
+                        moduleName = module.getName();
+                    }
+                    else {
+                        //manager message
+                        moduleName = "System";
+                    }
+                    
+                    sb.append("\t").append(moduleName).append(": ").append(errorsModule).append(EOL);
                 }
             }
             return sb.toString();

Core/src/org/sleuthkit/autopsy/ingest/IngestMessage.java

@@ -241,4 +241,8 @@ public class IngestMessage {
     static IngestMessage createManagerMessage(String subject, String detailsHtml) {
         return new IngestMessage(++managerMessageId, MessageType.INFO, null, subject, detailsHtml, null);
     }
+    
+    static IngestMessage createManagerErrorMessage(String subject, String detailsHtml) {
+        return new IngestMessage(++managerMessageId, MessageType.ERROR, null, subject, detailsHtml, null);
+    }
 }

Core/src/org/sleuthkit/autopsy/ingest/IngestMessageTopComponent.java

@@ -18,10 +18,14 @@
  */
 package org.sleuthkit.autopsy.ingest;
 
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.util.List;
 import java.util.logging.Level;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 import org.sleuthkit.autopsy.coreutils.Logger;
 import javax.swing.Action;
 import javax.swing.BoxLayout;
@@ -33,6 +37,8 @@ import org.openide.windows.Mode;
 import org.openide.windows.TopComponent;
 import org.openide.windows.WindowManager;
 import org.sleuthkit.autopsy.casemodule.Case;
+import org.sleuthkit.autopsy.coreutils.MessageNotifyUtil;
+import org.sleuthkit.autopsy.ingest.IngestMessage.MessageType;
 import org.sleuthkit.datamodel.Image;
 
 /**
@@ -45,6 +51,8 @@ public final class IngestMessageTopComponent extends TopComponent implements Ing
     private IngestMessageMainPanel messagePanel;
     private IngestManager manager;
     private static String PREFERRED_ID = "IngestMessageTopComponent";
+    private ActionListener showIngestInboxAction;
+    private static final Pattern tagRemove = Pattern.compile("<.+?>");
 
     public IngestMessageTopComponent() {
         initComponents();
@@ -54,6 +62,13 @@ public final class IngestMessageTopComponent extends TopComponent implements Ing
         setToolTipText(NbBundle.getMessage(IngestMessageTopComponent.class, "HINT_IngestMessageTopComponent"));
         //putClientProperty(TopComponent.PROP_CLOSING_DISABLED, Boolean.TRUE);
 
+        showIngestInboxAction = new ActionListener() {
+            @Override
+            public void actionPerformed(ActionEvent e) {
+                IngestMessagesToolbar.getDefault().showIngestMessages();
+            }
+        };
+
     }
 
     private static synchronized IngestMessageTopComponent getDefault() {
@@ -79,13 +94,11 @@ public final class IngestMessageTopComponent extends TopComponent implements Ing
     protected String preferredID() {
         return PREFERRED_ID;
     }
-    
-    
 
-    /** This method is called from within the constructor to
-     * initialize the form.
-     * WARNING: Do NOT modify this code. The content of this method is
-     * always regenerated by the Form Editor.
+    /**
+     * This method is called from within the constructor to initialize the form.
+     * WARNING: Do NOT modify this code. The content of this method is always
+     * regenerated by the Form Editor.
      */
     // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
     private void initComponents() {
@@ -124,11 +137,11 @@ public final class IngestMessageTopComponent extends TopComponent implements Ing
         super.componentClosed();
 
         /*
-        Mode mode = WindowManager.getDefault().findMode("dockedBottom");
-        if (mode != null) {
-        mode.dockInto(this);
-        this.open();
-        }
+         Mode mode = WindowManager.getDefault().findMode("dockedBottom");
+         if (mode != null) {
+         mode.dockInto(this);
+         this.open();
+         }
          * */
 
         //this.close();
@@ -204,7 +217,6 @@ public final class IngestMessageTopComponent extends TopComponent implements Ing
     private void registerListeners() {
         //handle case change
         Case.addPropertyChangeListener(new PropertyChangeListener() {
-
             @Override
             public void propertyChange(PropertyChangeEvent evt) {
                 if (evt.getPropertyName().equals(Case.CASE_CURRENT_CASE)) {
@@ -219,8 +231,7 @@ public final class IngestMessageTopComponent extends TopComponent implements Ing
                     }
                     try {
                         manager.stopAll();
-                    }
-                    finally {
+                    } finally {
                         //clear inbox 
                         clearMessages();
                     }
@@ -257,7 +268,7 @@ public final class IngestMessageTopComponent extends TopComponent implements Ing
 
         final String reportActionName = "org.sleuthkit.autopsy.report.ReportAction";
         Action reportAction = null;
-        
+
         //find action by name from action lookup, without introducing cyclic dependency
         if (choice == JOptionPane.NO_OPTION) {
             List<? extends Action> actions = Utilities.actionsForPath("Toolbars/File");
@@ -270,11 +281,13 @@ public final class IngestMessageTopComponent extends TopComponent implements Ing
                     }
                 }
             }
-            
-            if (reportAction == null)
+
+            if (reportAction == null) {
                 logger.log(Level.SEVERE, "Could not locate Action: " + reportActionName);
-            else reportAction.actionPerformed(null);
-        
+            } else {
+                reportAction.actionPerformed(null);
+            }
+
         }
 
     }
@@ -285,6 +298,28 @@ public final class IngestMessageTopComponent extends TopComponent implements Ing
     @Override
     public void displayMessage(IngestMessage ingestMessage) {
         messagePanel.addMessage(ingestMessage);
+
+
+        //post special messages to notification area
+        MessageType ingestMessageType = ingestMessage.getMessageType();
+        if (ingestMessageType.equals(MessageType.ERROR)
+                || ingestMessageType.equals(MessageType.WARNING)) {
+            MessageNotifyUtil.MessageType notifyMessageType =
+                    ingestMessageType.equals(MessageType.ERROR)
+                    ? MessageNotifyUtil.MessageType.ERROR
+                    : MessageNotifyUtil.MessageType.WARNING;
+
+            String subject = ingestMessage.getSubject();
+            String details = ingestMessage.getDetails();
+            if (details == null) {
+                details = "";
+            }
+            //strip html tags in case they are present in ingest message
+            details  = stripHtmlTags(details);
+
+            MessageNotifyUtil.Notify.show(subject, details,
+                    notifyMessageType, showIngestInboxAction);
+        }
     }
 
     @Override
@@ -292,8 +327,6 @@ public final class IngestMessageTopComponent extends TopComponent implements Ing
         return messagePanel.getMessagesCount();
     }
 
-    
-
     @Override
     public void clearMessages() {
         messagePanel.clearMessages();
@@ -302,9 +335,9 @@ public final class IngestMessageTopComponent extends TopComponent implements Ing
     @Override
     public void displayIngestDialog(final Image image) {
         /*
-        final IngestDialog ingestDialog = new IngestDialog();
-        ingestDialog.setImage(image);
-        ingestDialog.display();    
+         final IngestDialog ingestDialog = new IngestDialog();
+         ingestDialog.setImage(image);
+         ingestDialog.display();    
          */
     }
 
@@ -318,4 +351,13 @@ public final class IngestMessageTopComponent extends TopComponent implements Ing
         //disable TC toolbar actions
         return new Action[0];
     }
+
+    private static String stripHtmlTags(String string) {
+        if (string == null || string.length() == 0) {
+            return string;
+        }
+
+        Matcher m = tagRemove.matcher(string);
+        return m.replaceAll("");
+    }
 }

Core/src/org/sleuthkit/autopsy/ingest/IngestMessagesToolbar.java

@@ -130,7 +130,10 @@ public class IngestMessagesToolbar extends javax.swing.JPanel {
         });
     }
 
-    private void showIngestMessages() {
+    /**
+     * Pop up and show ingest messages window
+     */
+    void showIngestMessages() {
         IngestMessageTopComponent tc = IngestMessageTopComponent.findInstance();
 
         Mode mode = WindowManager.getDefault().findMode("floatingLeftBottom");

Core/src/org/sleuthkit/autopsy/ingest/IngestMonitor.java

@@ -118,7 +118,10 @@ public class IngestMonitor {
                 final String diskPath = root.getAbsolutePath();
                 logger.log(Level.SEVERE, "Stopping ingest due to low disk space on disk " + diskPath);
                 manager.stopAll();
-                manager.postMessage(IngestMessage.createManagerMessage("Stopping ingest due to low disk space on disk " + diskPath, "Stopping ingest due to low disk space on disk " + diskPath + ". Please ensure the drive where Case is located has at least 1GB free space (more for large images) and restart ingest."));
+                manager.postMessage(IngestMessage.createManagerErrorMessage
+                        ("Ingest stopped - low disk space on " + diskPath, 
+                        "Stopping ingest due to low disk space on disk " + diskPath 
+                        + ". \nEnsure the Case drive has at least 1GB free space and restart ingest."));
             }
         }
 

Core/src/org/sleuthkit/autopsy/report/ReportExcel.java

@@ -123,6 +123,7 @@ public class ReportExcel implements TableReportModule {
             }
         }
     }
+    
 
     /**
      * Start a new sheet for the given data type.
@@ -130,6 +131,7 @@ public class ReportExcel implements TableReportModule {
      */
     @Override
     public void startDataType(String title) {
+        title = escapeForExcel(title);
         sheet = wb.createSheet(title);
         sheet.setAutobreaks(true);
         currentDataType = title;
@@ -154,6 +156,7 @@ public class ReportExcel implements TableReportModule {
      */
     @Override
     public void startSet(String setName) {
+        setName = escapeForExcel(setName);
         Row temp = sheet.createRow(rowCount);
         temp.setRowStyle(setStyle);
         temp.createCell(0).setCellValue(setName);
@@ -179,6 +182,7 @@ public class ReportExcel implements TableReportModule {
      */
     @Override
     public void addSetElement(String elementName) {
+        elementName = escapeForExcel(elementName);
         Row temp = sheet.createRow(rowCount);
         temp.setRowStyle(elementStyle);
         temp.createCell(0).setCellValue(elementName);
@@ -248,4 +252,13 @@ public class ReportExcel implements TableReportModule {
         return "Excel.xlsx";
     }
     
+    /**
+     * Escape special chars for Excel that would cause errors/hangs in generating report
+     * The following are not valid for sheet names: ? / \ * :
+     * @param text
+     * @return 
+     */
+    private static String escapeForExcel(String text) {
+         return text.replaceAll("[\\/\\:\\?\\*\\\\]", "_");
+    }
 }

Core/src/org/sleuthkit/autopsy/report/ReportHTML.java

@@ -98,7 +98,6 @@ public class ReportHTML implements TableReportModule {
      * Start this report by setting the path, refreshing member variables,
      * and writing the skeleton for the HTML report.
      * @param path path to save the report
-     * @param info map of info to display in the summary
      */
     @Override
     public void startReport(String path) {
@@ -140,9 +139,12 @@ public class ReportHTML implements TableReportModule {
      */
     @Override
     public void startDataType(String title) {        
+        String fTitle = org.sleuthkit.autopsy.coreutils.FileUtil.escapeFileName(title);
         // Make a new out for this page
         try {
-            out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(path + title + getExtension()), "UTF-8"));
+            //escape out slashes tha that appear in title
+            
+            out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(path + fTitle + getExtension()), "UTF-8"));
         } catch (FileNotFoundException ex) {
             logger.log(Level.SEVERE, "File not found: {0}", ex);
         } catch (UnsupportedEncodingException ex) {
@@ -425,7 +427,12 @@ public class ReportHTML implements TableReportModule {
             nav.append("<li style=\"background: url(summary.png) left center no-repeat;\"><a href=\"summary.html\" target=\"content\">Case Summary</a></li>\n");
             
             for (String dataType : dataTypes.keySet()) {
-                nav.append("<li style=\"background: url('").append(dataType).append(".png') left center no-repeat;\"><a href=\"").append(dataType).append(".html\" target=\"content\">").append(dataType).append(" (").append(dataTypes.get(dataType)).append(")</a></li>\n");
+                String dataTypeEsc = org.sleuthkit.autopsy.coreutils.FileUtil.escapeFileName(dataType);
+                nav.append("<li style=\"background: url('").append(dataType)
+                        .append(".png') left center no-repeat;\"><a href=\"")
+                        .append(dataTypeEsc).append(".html\" target=\"content\">")
+                        .append(dataType).append(" (").append(dataTypes.get(dataType))
+                        .append(")</a></li>\n");
             }
             nav.append("</ul>\n");
             nav.append("</div>\n</body>\n</html>");

ExifParser/manifest.mf

@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 AutoUpdate-Show-In-Client: true
 OpenIDE-Module: org.sleuthkit.autopsy.exifparser/3
-OpenIDE-Module-Implementation-Version: 3
+OpenIDE-Module-Implementation-Version: 4
 OpenIDE-Module-Layer: org/sleuthkit/autopsy/exifparser/layer.xml
 OpenIDE-Module-Localizing-Bundle: org/sleuthkit/autopsy/exifparser/Bundle.properties

ExifParser/nbproject/project.xml

@@ -11,8 +11,8 @@
                     <build-prerequisite/>
                     <compile-dependency/>
                     <run-dependency>
-                        <release-version>5</release-version>
-                        <specification-version>3.0</specification-version>
+                        <release-version>6</release-version>
+                        <specification-version>4.0</specification-version>
                     </run-dependency>
                 </dependency>
             </module-dependencies>

HashDatabase/manifest.mf

@@ -1,7 +1,7 @@
 Manifest-Version: 1.0
 AutoUpdate-Show-In-Client: true
 OpenIDE-Module: org.sleuthkit.autopsy.hashdatabase/3
-OpenIDE-Module-Implementation-Version: 3
+OpenIDE-Module-Implementation-Version: 4
 OpenIDE-Module-Layer: org/sleuthkit/autopsy/hashdatabase/layer.xml
 OpenIDE-Module-Localizing-Bundle: org/sleuthkit/autopsy/hashdatabase/Bundle.properties
 

HashDatabase/nbproject/project.xml

@@ -77,8 +77,8 @@
                     <build-prerequisite/>
                     <compile-dependency/>
                     <run-dependency>
-                        <release-version>5</release-version>
-                        <specification-version>3.0</specification-version>
+                        <release-version>6</release-version>
+                        <specification-version>4.0</specification-version>
                     </run-dependency>
                 </dependency>
             </module-dependencies>

HashDatabase/src/org/sleuthkit/autopsy/hashdatabase/KeyValueFileNode.java

@@ -1,6 +1,20 @@
 /*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
+ * Autopsy Forensic Browser
+ *
+ * Copyright 2011 Basis Technology Corp.
+ * Contact: carrier <at> sleuthkit <dot> org
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  */
 package org.sleuthkit.autopsy.hashdatabase;
 
@@ -13,7 +27,7 @@ import org.openide.util.lookup.Lookups;
 import org.sleuthkit.autopsy.datamodel.DirectoryNode;
 import org.sleuthkit.autopsy.datamodel.FileNode;
 import org.sleuthkit.autopsy.datamodel.KeyValueNode;
-import org.sleuthkit.autopsy.directorytree.BookmarkAction;
+import org.sleuthkit.autopsy.directorytree.TagFileAction;
 import org.sleuthkit.autopsy.directorytree.ExternalViewerAction;
 import org.sleuthkit.autopsy.directorytree.ExtractAction;
 import org.sleuthkit.autopsy.directorytree.HashSearchAction;
@@ -75,7 +89,7 @@ public class KeyValueFileNode extends KeyValueNode {
             actions.add(new ExtractAction("Extract File", new FileNode(f)));
             actions.add(new HashSearchAction("Search for files with the same MD5 hash", new FileNode(f)));
             actions.add(null); // creates a menu separator
-            actions.add(new BookmarkAction("Bookmark File", new FileNode(f)));
+            actions.add(new TagFileAction(new FileNode(f)));
             return actions;
         }
         

KeywordSearch/ivy.xml

@@ -17,9 +17,14 @@
         <dependency conf="autopsy->*" org="org.apache.solr" name="solr-solrj" rev="4.0.0"/>
         <dependency conf="autopsy->*" org="commons-lang" name="commons-lang" rev="2.4"/>
         <dependency conf="autopsy->*" org="org.apache.tika" name="tika-parsers" rev="1.2"/>
+        <!-- icu4j for pdfbox bidirectional text support, needs to be defined explicitely (it is optional) -->
+        <dependency conf="autopsy->*" org="com.ibm.icu" name="icu4j" rev="3.8"/>
+        
+        <!-- TODO update jetty to eclipse.jetty 8 -->
         <dependency conf="start-solr->default" org="org.mortbay.jetty" name="start" rev="6.1.26"/>
         <dependency conf="jetty-libs->default" org="org.mortbay.jetty" name="jetty" rev="6.1.26"/>
         <dependency conf="jetty-libs->default" org="org.mortbay.jetty" name="jsp-2.1" rev="6.1.14"/>
+        
         <dependency conf="autopsy->*" org="net.htmlparser.jericho" name="jericho-html" rev="3.3"/>
     </dependencies>
 </ivy-module>

KeywordSearch/manifest.mf

@@ -1,7 +1,7 @@
 Manifest-Version: 1.0
 AutoUpdate-Show-In-Client: true
 OpenIDE-Module: org.sleuthkit.autopsy.keywordsearch/4
-OpenIDE-Module-Implementation-Version: 3
+OpenIDE-Module-Implementation-Version: 4
 OpenIDE-Module-Install: org/sleuthkit/autopsy/keywordsearch/Installer.class
 OpenIDE-Module-Layer: org/sleuthkit/autopsy/keywordsearch/layer.xml
 OpenIDE-Module-Localizing-Bundle: org/sleuthkit/autopsy/keywordsearch/Bundle.properties

KeywordSearch/nbproject/project.properties

@@ -3,4 +3,4 @@ javac.compilerargs=-Xlint -Xlint:-serial
 license.file=../LICENSE-2.0.txt
 nbm.homepage=http://www.sleuthkit.org/autopsy/
 nbm.needs.restart=true
-spec.version.base=2.0
+spec.version.base=2.1

KeywordSearch/nbproject/project.xml

@@ -95,8 +95,8 @@
                     <build-prerequisite/>
                     <compile-dependency/>
                     <run-dependency>
-                        <release-version>5</release-version>
-                        <specification-version>3.0</specification-version>
+                        <release-version>6</release-version>
+                        <specification-version>4.0</specification-version>
                     </run-dependency>
                 </dependency>
             </module-dependencies>
@@ -144,21 +144,29 @@
                 <binary-origin>release/modules/ext/vorbis-java-core-0.1-tests.jar</binary-origin>
             </class-path-extension>
             <class-path-extension>
-                <runtime-relative-path>ext/log4j-over-slf4j-1.6.4.jar</runtime-relative-path>
-                <binary-origin>release/modules/ext/log4j-over-slf4j-1.6.4.jar</binary-origin>
+                <runtime-relative-path>ext/tika-parsers-1.2-javadoc.jar</runtime-relative-path>
+                <binary-origin>release/modules/ext/tika-parsers-1.2-javadoc.jar</binary-origin>
             </class-path-extension>
             <class-path-extension>
-                <runtime-relative-path>ext/isoparser-1.0-RC-1.jar</runtime-relative-path>
-                <binary-origin>release/modules/ext/isoparser-1.0-RC-1.jar</binary-origin>
+                <runtime-relative-path>ext/log4j-over-slf4j-1.6.4.jar</runtime-relative-path>
+                <binary-origin>release/modules/ext/log4j-over-slf4j-1.6.4.jar</binary-origin>
             </class-path-extension>
             <class-path-extension>
                 <runtime-relative-path>ext/vorbis-java-tika-0.1.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/vorbis-java-tika-0.1.jar</binary-origin>
             </class-path-extension>
+            <class-path-extension>
+                <runtime-relative-path>ext/isoparser-1.0-RC-1.jar</runtime-relative-path>
+                <binary-origin>release/modules/ext/isoparser-1.0-RC-1.jar</binary-origin>
+            </class-path-extension>
             <class-path-extension>
                 <runtime-relative-path>ext/httpcore-4.1.4.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/httpcore-4.1.4.jar</binary-origin>
             </class-path-extension>
+            <class-path-extension>
+                <runtime-relative-path>ext/tika-parsers-1.2-sources.jar</runtime-relative-path>
+                <binary-origin>release/modules/ext/tika-parsers-1.2-sources.jar</binary-origin>
+            </class-path-extension>
             <class-path-extension>
                 <runtime-relative-path>ext/aspectjrt-1.6.11.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/aspectjrt-1.6.11.jar</binary-origin>
@@ -187,6 +195,10 @@
                 <runtime-relative-path>ext/httpclient-4.1.3.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/httpclient-4.1.3.jar</binary-origin>
             </class-path-extension>
+            <class-path-extension>
+                <runtime-relative-path>ext/icu4j-3.8.jar</runtime-relative-path>
+                <binary-origin>release/modules/ext/icu4j-3.8.jar</binary-origin>
+            </class-path-extension>
             <class-path-extension>
                 <runtime-relative-path>ext/juniversalchardet-1.0.3.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/juniversalchardet-1.0.3.jar</binary-origin>
@@ -195,6 +207,10 @@
                 <runtime-relative-path>ext/pdfbox-1.7.0.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/pdfbox-1.7.0.jar</binary-origin>
             </class-path-extension>
+            <class-path-extension>
+                <runtime-relative-path>ext/jericho-html-3.3-sources.jar</runtime-relative-path>
+                <binary-origin>release/modules/ext/jericho-html-3.3-sources.jar</binary-origin>
+            </class-path-extension>
             <class-path-extension>
                 <runtime-relative-path>ext/jdom-1.0.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/jdom-1.0.jar</binary-origin>
@@ -227,10 +243,18 @@
                 <runtime-relative-path>ext/slf4j-api-1.7.2.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/slf4j-api-1.7.2.jar</binary-origin>
             </class-path-extension>
+            <class-path-extension>
+                <runtime-relative-path>ext/commons-lang-2.4-javadoc.jar</runtime-relative-path>
+                <binary-origin>release/modules/ext/commons-lang-2.4-javadoc.jar</binary-origin>
+            </class-path-extension>
             <class-path-extension>
                 <runtime-relative-path>ext/jempbox-1.7.0.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/jempbox-1.7.0.jar</binary-origin>
             </class-path-extension>
+            <class-path-extension>
+                <runtime-relative-path>ext/jericho-html-3.3-javadoc.jar</runtime-relative-path>
+                <binary-origin>release/modules/ext/jericho-html-3.3-javadoc.jar</binary-origin>
+            </class-path-extension>
             <class-path-extension>
                 <runtime-relative-path>ext/wstx-asl-3.2.7.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/wstx-asl-3.2.7.jar</binary-origin>
@@ -239,6 +263,10 @@
                 <runtime-relative-path>ext/netcdf-4.2-min.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/netcdf-4.2-min.jar</binary-origin>
             </class-path-extension>
+            <class-path-extension>
+                <runtime-relative-path>ext/solr-solrj-4.0.0-javadoc.jar</runtime-relative-path>
+                <binary-origin>release/modules/ext/solr-solrj-4.0.0-javadoc.jar</binary-origin>
+            </class-path-extension>
             <class-path-extension>
                 <runtime-relative-path>ext/xmlbeans-2.3.0.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/xmlbeans-2.3.0.jar</binary-origin>
@@ -287,18 +315,26 @@
                 <runtime-relative-path>ext/poi-ooxml-schemas-3.8.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/poi-ooxml-schemas-3.8.jar</binary-origin>
             </class-path-extension>
-            <class-path-extension>
-                <runtime-relative-path>ext/jericho-html-3.3.jar</runtime-relative-path>
-                <binary-origin>release/modules/ext/jericho-html-3.3.jar</binary-origin>
-            </class-path-extension>
             <class-path-extension>
                 <runtime-relative-path>ext/bcprov-jdk15-1.45.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/bcprov-jdk15-1.45.jar</binary-origin>
             </class-path-extension>
+            <class-path-extension>
+                <runtime-relative-path>ext/jericho-html-3.3.jar</runtime-relative-path>
+                <binary-origin>release/modules/ext/jericho-html-3.3.jar</binary-origin>
+            </class-path-extension>
             <class-path-extension>
                 <runtime-relative-path>ext/solr-solrj-4.0.0.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/solr-solrj-4.0.0.jar</binary-origin>
             </class-path-extension>
+            <class-path-extension>
+                <runtime-relative-path>ext/commons-lang-2.4-sources.jar</runtime-relative-path>
+                <binary-origin>release/modules/ext/commons-lang-2.4-sources.jar</binary-origin>
+            </class-path-extension>
+            <class-path-extension>
+                <runtime-relative-path>ext/solr-solrj-4.0.0-sources.jar</runtime-relative-path>
+                <binary-origin>release/modules/ext/solr-solrj-4.0.0-sources.jar</binary-origin>
+            </class-path-extension>
             <class-path-extension>
                 <runtime-relative-path>ext/apache-mime4j-dom-0.7.2.jar</runtime-relative-path>
                 <binary-origin>release/modules/ext/apache-mime4j-dom-0.7.2.jar</binary-origin>

KeywordSearch/release/solr/solr/conf/solrconfig.xml

@@ -321,7 +321,7 @@
       -->
      <autoCommit> 
        <maxDocs>15000</maxDocs> 
-       <openSearcher>false</openSearcher> 
+       <openSearcher>true</openSearcher> 
      </autoCommit>
 
     <!-- softAutoCommit is like autoCommit except it causes a

KeywordSearch/src/org/sleuthkit/autopsy/keywordsearch/KeywordSearchFilterNode.java

@@ -28,7 +28,7 @@ import org.openide.nodes.PropertySupport;
 import org.openide.nodes.Sheet;
 import org.openide.util.lookup.Lookups;
 import org.openide.util.lookup.ProxyLookup;
-import org.sleuthkit.autopsy.directorytree.BookmarkAction;
+import org.sleuthkit.autopsy.directorytree.TagFileAction;
 import org.sleuthkit.autopsy.directorytree.ExternalViewerAction;
 import org.sleuthkit.autopsy.directorytree.ExtractAction;
 import org.sleuthkit.autopsy.directorytree.HashSearchAction;
@@ -144,7 +144,7 @@ class KeywordSearchFilterNode extends FilterNode {
             actions.add(new ExtractAction("Extract File", getOriginal()));
             actions.add(new HashSearchAction("Search for files with the same MD5 hash", getOriginal()));
             actions.add(null); // creates a menu separator
-            actions.add(new BookmarkAction("Bookmark File", getOriginal()));
+            actions.add(new TagFileAction(getOriginal()));
             return actions;
         }
 

KeywordSearch/src/org/sleuthkit/autopsy/keywordsearch/KeywordSearchIngestModule.java

@@ -252,9 +252,9 @@ public final class KeywordSearchIngestModule implements IngestModuleAbstractFile
             logger.log(Level.WARNING, "Error executing Solr query to check number of indexed files/chunks: ", ex);
         } catch (KeywordSearchModuleException se) {
             logger.log(Level.WARNING, "Error executing Solr query to check number of indexed files/chunks: ", se);
-        } finally {
-            cleanup();
         }
+        
+        //cleanup done in final searcher
 
         //postSummary();
     }
@@ -290,13 +290,13 @@ public final class KeywordSearchIngestModule implements IngestModuleAbstractFile
     }
 
     /**
-     * Common cleanup code when module stops or completes
+     * Common cleanup code when module stops or final searcher completes
      */
     private void cleanup() {
         ingestStatus.clear();
         currentResults.clear();
         currentSearcher = null;
-        finalSearcher = null;
+        //finalSearcher = null; //do not collect, might be finalizing
 
         commitTimer.stop();
         searchTimer.stop();
@@ -888,13 +888,16 @@ public final class KeywordSearchIngestModule implements IngestModuleAbstractFile
                         return null;
                     }
 
+                    final String queryStr = keywordQuery.getQuery();
+                    final KeywordSearchList list = keywordToList.get(queryStr);
+                    final String listName = list.getName();
+
+                    //new subProgress will be active after the initial query
+                    //when we know number of hits to start() with
                     if (keywordsSearched > 0) {
                         subProgresses[keywordsSearched - 1].finish();
                     }
 
-                    final String queryStr = keywordQuery.getQuery();
-                    final KeywordSearchList list = keywordToList.get(queryStr);
-                    final String listName = list.getName();
 
                     KeywordSearchQuery del = null;
 
@@ -1080,11 +1083,14 @@ public final class KeywordSearchIngestModule implements IngestModuleAbstractFile
                         if (!newArtifacts.isEmpty()) {
                             services.fireModuleDataEvent(new ModuleDataEvent(MODULE_NAME, ARTIFACT_TYPE.TSK_KEYWORD_HIT, newArtifacts));
                         }
-                    }
-
+                    } //if has results
+                                        
+                    //reset the status text before it goes away
+                    subProgresses[keywordsSearched].progress("");
+                    
                     ++keywordsSearched;
 
-                }
+                } //for each keyword
 
             } //end try block
             catch (Exception ex) {
@@ -1142,8 +1148,11 @@ public final class KeywordSearchIngestModule implements IngestModuleAbstractFile
                 //this is the final searcher
                 logger.log(Level.INFO, "The final searcher in this ingest done.");
                 finalSearcherDone = true;
-
+                
                 services.postMessage(IngestMessage.createMessage(++messageID, MessageType.INFO, KeywordSearchIngestModule.instance, "Completed"));
+                
+                //run module cleanup
+                cleanup();
             } else {
                 //start counting time for a new searcher to start
                 //unless final searcher is pending

KeywordSearch/src/org/sleuthkit/autopsy/keywordsearch/LuceneQuery.java

@@ -51,7 +51,7 @@ public class LuceneQuery implements KeywordSearchQuery {
     private Keyword keywordQuery = null;
     private KeywordQueryFilter filter = null;
     private String field = null;
-    private static final int MAX_RESULTS = 10000;
+    private static final int MAX_RESULTS = 20000;
     static final int SNIPPET_LENGTH = 50;
     //can use different highlight schema fields for regex and literal search
     static final String HIGHLIGHT_FIELD_LITERAL = Server.Schema.CONTENT.toString();

NEWS.txt

@@ -1,17 +1,31 @@
----------------- VERSION 3.0.3 --------------
+---------------- VERSION Current (development) --------------
+
+New features:
+- Results and files can be tagged with custom tags and assigned different categories, and 
+they can be reported on based on those categories.
 
 Improvements:
-- Keyword Search indexing and search speed improvements
-- Improved Keyword Search highlighting in Text View: highlighted tokens are no longer delimiter separated
-- Better progress updates from Keyword Search ingest
-- Upgrade to Solr4.0 / Tika 1.2
+- Better error reporting in the UI using the notification area.
+
+
+Bugfixes:
+- fixed crash and hang in html and excel report generation, due to special characters present
+
+
+---------------- VERSION 3.0.3 --------------
+
+*Note: Due to major changes in Keyword search module indexing this release is not fully backward compatible.
+As a workaround, you will need to rebuild index by re-running Keyword Search ingest on Cases created with previous versions.
+
+Improvements:
+- Upgrade to Solr4.0 / Tika 1.2: Improved performance and highlighting
 - Remake of reporting UI and functionality
 - Significant increase in reporting speed
 - New option to keep the most specific file viewer (default) or the lastly used viewer active.
 
 
 Bugfixes:
-- Keyword search now indexes and searches entire extracted content from files
+- Fixed bug that caused the ends of large amounts of text to not be indexed (occurs mostly in unallocated space).
 - Fix scrolling to first keyword hit when Text View is first loaded
 - Imported keyword lists are now always enabled for ingest by default
 

RecentActivity/manifest.mf

@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 OpenIDE-Module: org.sleuthkit.autopsy.recentactivity/4
-OpenIDE-Module-Implementation-Version: 3
+OpenIDE-Module-Implementation-Version: 4
 OpenIDE-Module-Layer: org/sleuthkit/autopsy/recentactivity/layer.xml
 OpenIDE-Module-Localizing-Bundle: org/sleuthkit/autopsy/recentactivity/Bundle.properties
 OpenIDE-Module-Requires: 

RecentActivity/nbproject/project.xml

@@ -35,8 +35,8 @@
                     <build-prerequisite/>
                     <compile-dependency/>
                     <run-dependency>
-                        <release-version>5</release-version>
-                        <specification-version>3.0</specification-version>
+                        <release-version>6</release-version>
+                        <specification-version>4.0</specification-version>
                     </run-dependency>
                 </dependency>
             </module-dependencies>

RecentActivity/src/org/sleuthkit/autopsy/recentactivity/Extract.java

@@ -58,6 +58,7 @@ abstract public class Extract implements IngestModuleImage{
      * @param  query is a sql string query that is to be run
      * @return  FFSqlitedb is a List of FsContent objects
      */
+    @SuppressWarnings("deprecation")
     public List<FsContent> extractFiles(Image image, String query) {
 
         Collection<FileSystem> imageFS = tskCase.getFileSystems(image);
@@ -78,20 +79,23 @@ abstract public class Extract implements IngestModuleImage{
             }
         }
         List<FsContent> FFSqlitedb = null;
+        ResultSet rs = null;
         try {
-            ResultSet rs = tskCase.runQuery(query + allFS);
+            rs = tskCase.runQuery(query + allFS);
             FFSqlitedb = tskCase.resultSetToFsContents(rs);
-            Statement s = rs.getStatement();
-            rs.close();
-            if (s != null) {
-                s.close();
-            }
-            rs.close();
-            rs.getStatement().close();
         } catch (SQLException ex) {
             logger.log(Level.SEVERE, "Error while trying to extract files for:" + this.getClass().getName(), ex);
             this.addErrorMessage(this.getName() + ": Error while trying to extract files to analyze.");
         }
+        finally {
+            if (rs != null) {
+                try {
+                    tskCase.closeRunQuery(rs);
+                } catch (SQLException ex) {
+                    logger.log(Level.SEVERE, "Error while trying to close result set after extract files for:" + this.getClass().getName(), ex);
+                }
+            }
+        }
         return FFSqlitedb;
     }
 

Testing/manifest.mf

@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 AutoUpdate-Show-In-Client: false
 OpenIDE-Module: org.sleuthkit.autopsy.testing/3
-OpenIDE-Module-Implementation-Version: 3
+OpenIDE-Module-Implementation-Version: 4
 OpenIDE-Module-Localizing-Bundle: org/sleuthkit/autopsy/testing/Bundle.properties
 

Testing/nbproject/project.xml

@@ -11,8 +11,8 @@
                     <build-prerequisite/>
                     <compile-dependency/>
                     <run-dependency>
-                        <release-version>5</release-version>
-                        <specification-version>3.0</specification-version>
+                        <release-version>6</release-version>
+                        <specification-version>4.0</specification-version>
                     </run-dependency>
                 </dependency>
             </module-dependencies>

thunderbirdparser/manifest.mf

@@ -1,7 +1,7 @@
 Manifest-Version: 1.0
 AutoUpdate-Show-In-Client: true
 OpenIDE-Module: org.sleuthkit.autopsy.thunderbirdparser/3
-OpenIDE-Module-Implementation-Version: 3
+OpenIDE-Module-Implementation-Version: 4
 OpenIDE-Module-Layer: org/sleuthkit/autopsy/thunderbirdparser/layer.xml
 OpenIDE-Module-Localizing-Bundle: org/sleuthkit/autopsy/thunderbirdparser/Bundle.properties
 

thunderbirdparser/nbproject/project.xml

@@ -11,8 +11,8 @@
                     <build-prerequisite/>
                     <compile-dependency/>
                     <run-dependency>
-                        <release-version>5</release-version>
-                        <specification-version>3.0</specification-version>
+                        <release-version>6</release-version>
+                        <specification-version>4.0</specification-version>
                     </run-dependency>
                 </dependency>
             </module-dependencies>