Merge branch 'develop' of https://github.com/briangsweeney/autopsy into 3788-intercase-intracase-merge

# Conflicts:
#	Core/src/org/sleuthkit/autopsy/commonfilesearch/CommonAttributesSearchResultsViewerTable.java
#	Core/src/org/sleuthkit/autopsy/commonfilesearch/CommonFilesPanel.java
#	Core/src/org/sleuthkit/autopsy/commonfilesearch/CommonFilesSearchAction.java
#	Core/src/org/sleuthkit/autopsy/datamodel/DisplayableItemNodeVisitor.java

Core/src/org/sleuthkit/autopsy/actions/ReplaceBlackboardArtifactTagAction.java

@@ -64,14 +64,14 @@ public final class ReplaceBlackboardArtifactTagAction extends ReplaceTagAction<B
      * 
      * @param oldArtifactTag tag to be replaced
      * @param newTagName name of the tag to replace with
-     * @param comment the comment for the tag use an empty string for no comment
+     * @param newComment the newComment for the tag use an empty string for no newComment
      */
     @NbBundle.Messages({
         "# {0} - old tag name",
         "# {1} - artifactID",
         "ReplaceBlackboardArtifactTagAction.replaceTag.alert=Unable to replace tag {0} for artifact {1}."})
     @Override
-    protected void replaceTag( BlackboardArtifactTag oldArtifactTag, TagName newTagName, String comment) {
+    protected void replaceTag( BlackboardArtifactTag oldArtifactTag, TagName newTagName, String newComment) {
         new SwingWorker<Void, Void>() {
             
             @Override
@@ -91,7 +91,7 @@ public final class ReplaceBlackboardArtifactTagAction extends ReplaceTagAction<B
                     logger.log(Level.INFO, "Replacing tag {0}  with tag {1} for artifact {2}", new Object[]{oldArtifactTag.getName().getDisplayName(), newTagName.getDisplayName(), oldArtifactTag.getContent().getName()}); //NON-NLS
 
                     tagsManager.deleteBlackboardArtifactTag(oldArtifactTag);
-                    tagsManager.addBlackboardArtifactTag(oldArtifactTag.getArtifact(), newTagName, comment);
+                    tagsManager.addBlackboardArtifactTag(oldArtifactTag.getArtifact(), newTagName, newComment);
 
                 } catch (TskCoreException tskCoreException) {
                     logger.log(Level.SEVERE, "Error replacing artifact tag", tskCoreException); //NON-NLS

Core/src/org/sleuthkit/autopsy/actions/ReplaceContentTagAction.java

@@ -64,7 +64,7 @@ public final class ReplaceContentTagAction extends ReplaceTagAction<ContentTag>
         "# {1} - content obj id",
         "ReplaceContentTagAction.replaceTag.alert=Unable to replace tag {0} for {1}."})
     @Override
-    protected void replaceTag(ContentTag oldTag, TagName newTagName, String comment) {
+    protected void replaceTag(ContentTag oldTag, TagName newTagName, String newComment) {
         new SwingWorker<Void, Void>() {
 
             @Override
@@ -84,7 +84,7 @@ public final class ReplaceContentTagAction extends ReplaceTagAction<ContentTag>
                     logger.log(Level.INFO, "Replacing tag {0}  with tag {1} for artifact {2}", new Object[]{oldTag.getName().getDisplayName(), newTagName.getDisplayName(), oldTag.getContent().getName()}); //NON-NLS
 
                     tagsManager.deleteContentTag(oldTag);
-                    tagsManager.addContentTag(oldTag.getContent(), newTagName, comment);
+                    tagsManager.addContentTag(oldTag.getContent(), newTagName, newComment);
 
                 } catch (TskCoreException tskCoreException) {
                     logger.log(Level.SEVERE, "Error replacing artifact tag", tskCoreException); //NON-NLS

Core/src/org/sleuthkit/autopsy/actions/ReplaceTagAction.java

@@ -141,7 +141,7 @@ abstract class ReplaceTagAction<T extends Tag> extends AbstractAction implements
                     // Add action to replace the tag
                     tagNameItem.addActionListener((ActionEvent event) -> {
                         selectedTags.forEach((oldtag) -> {
-                            replaceTag(oldtag, entry.getValue(), "");
+                            replaceTag(oldtag, entry.getValue(), oldtag.getComment());
                         });
                     });
 
@@ -178,7 +178,7 @@ abstract class ReplaceTagAction<T extends Tag> extends AbstractAction implements
                 TagName newTagName = GetTagNameDialog.doDialog();
                 if (null != newTagName) {
                     selectedTags.forEach((oldtag) -> {
-                        replaceTag(oldtag, newTagName, "");
+                        replaceTag(oldtag, newTagName, oldtag.getComment());
                     });
                 }
             });

Core/src/org/sleuthkit/autopsy/casemodule/Case.java

@@ -129,6 +129,7 @@ public class Case {
     private static final String EXPORT_FOLDER = "Export"; //NON-NLS
     private static final String LOG_FOLDER = "Log"; //NON-NLS
     private static final String REPORTS_FOLDER = "Reports"; //NON-NLS
+    private static final String CONFIG_FOLDER = "Config"; // NON-NLS
     private static final String TEMP_FOLDER = "Temp"; //NON-NLS
     private static final String MODULE_FOLDER = "ModuleOutput"; //NON-NLS
     private static final String CASE_ACTION_THREAD_NAME = "%s-case-action";
@@ -291,9 +292,10 @@ public class Case {
          */
         ADDING_DATA_SOURCE_FAILED,
         /**
-         * A new data source has been added to the current case. The old value
+         * A new data source or series of data sources have been added to the
-         * of the PropertyChangeEvent is null, the new value is the newly-added
+         * current case. The old value of the PropertyChangeEvent is null, the
-         * data source (type: Content). Cast the PropertyChangeEvent to
+         * new value is the newly-added data source (type: Content). Cast the
+         * PropertyChangeEvent to
          * org.sleuthkit.autopsy.casemodule.events.DataSourceAddedEvent to
          * access additional event data.
          */
@@ -1098,6 +1100,10 @@ public class Case {
                 /*
                  * Open the top components (windows within the main application
                  * window).
+                 * 
+                 * Note: If the core windows are not opened here, they will be
+                 * opened via the DirectoryTreeTopComponent 'propertyChange()'
+                 * method on a DATA_SOURCE_ADDED event.
                  */
                 if (newCurrentCase.hasData()) {
                     CoreComponentControl.openCoreWindows();
@@ -1351,6 +1357,16 @@ public class Case {
         return getOrCreateSubdirectory(REPORTS_FOLDER);
     }
 
+    /**
+     * Gets the full path to the config directory for this case, creating it if
+     * it does not exist.
+     *
+     * @return The config directory path.
+     */
+    public String getConfigDirectory() {
+        return getOrCreateSubdirectory(CONFIG_FOLDER);
+    }
+
     /**
      * Gets the full path to the module output directory for this case, creating
      * it if it does not exist.

Core/src/org/sleuthkit/autopsy/casemodule/services/Bundle.properties

@@ -1,6 +1,5 @@
 OptionsCategory_Name_TagNamesOptions=Tags
 OptionsCategory_TagNames=TagNames
-Blackboard.unableToIndexArtifact.error.msg=Unable to index blackboard artifact {0}
 TagNameDialog.title.text=New Tag
 TagNameDialog.JOptionPane.tagNameIllegalCharacters.message=Tag name may not contain any of the following symbols\: \\ \: * ? " < > | , ;
 TagNameDialog.JOptionPane.tagNameIllegalCharacters.title=Invalid character in tag name

Core/src/org/sleuthkit/autopsy/centralrepository/AddEditCentralRepoCommentAction.java

@@ -105,7 +105,7 @@ public final class AddEditCentralRepoCommentAction extends AbstractAction {
                     dbManager.updateAttributeInstanceComment(correlationAttribute);
                 }
             } catch (EamDbException ex) {
-                logger.log(Level.SEVERE, "Error connecting to Central Repository database.", ex);
+                logger.log(Level.SEVERE, "Error adding comment", ex);
             }
         }
         return centralRepoCommentDialog.getComment();

Core/src/org/sleuthkit/autopsy/centralrepository/datamodel/AbstractSqlEamDb.java

@@ -58,6 +58,9 @@ abstract class AbstractSqlEamDb implements EamDb {
     protected int bulkArtifactsThreshold;
     private final Map<String, Collection<CorrelationAttribute>> bulkArtifacts;
 
+    // Maximum length for the value column in the instance tables
+    static final int MAX_VALUE_LENGTH = 256;
+
     // number of instances to keep in bulk queue before doing an insert.
     // Update Test code if this changes.  It's hard coded there.
     static final int DEFAULT_BULK_THRESHHOLD = 1000;
@@ -472,7 +475,8 @@ abstract class AbstractSqlEamDb implements EamDb {
         if (eamDataSource.getCaseID() == -1) {
             throw new EamDbException("Case ID is -1");
         } else if (eamDataSource.getID() != -1) {
-            throw new EamDbException("Database ID is already set in object");
+            // This data source is already in the central repo
+            return;
         }
         Connection conn = connect();
 
@@ -632,6 +636,13 @@ abstract class AbstractSqlEamDb implements EamDb {
         if (eamArtifact.getCorrelationValue() == null) {
             throw new EamDbException("Correlation value is null");
         }
+        if (eamArtifact.getCorrelationValue().length() >= MAX_VALUE_LENGTH) {
+            throw new EamDbException("Artifact value too long for central repository."
+                    + "\nCorrelationArtifact ID: " + eamArtifact.getID()
+                    + "\nCorrelationArtifact Type: " + eamArtifact.getCorrelationType().getDisplayName()
+                    + "\nCorrelationArtifact Value: " + eamArtifact.getCorrelationValue());
+
+        }
 
         Connection conn = connect();
 
@@ -1056,27 +1067,50 @@ abstract class AbstractSqlEamDb implements EamDb {
                             if (!eamArtifact.getCorrelationValue().isEmpty()) {
 
                                 if (eamInstance.getCorrelationCase() == null) {
-                                    throw new EamDbException("CorrelationAttributeInstance case is null");
+                                    throw new EamDbException("CorrelationAttributeInstance case is null for: "
+                                            + "\n\tCorrelationArtifact ID: " + eamArtifact.getID()
+                                            + "\n\tCorrelationArtifact Type: " + eamArtifact.getCorrelationType().getDisplayName()
+                                            + "\n\tCorrelationArtifact Value: " + eamArtifact.getCorrelationValue());
                                 }
                                 if (eamInstance.getCorrelationDataSource() == null) {
-                                    throw new EamDbException("CorrelationAttributeInstance data source is null");
+                                    throw new EamDbException("CorrelationAttributeInstance data source is null for: "
+                                            + "\n\tCorrelationArtifact ID: " + eamArtifact.getID()
+                                            + "\n\tCorrelationArtifact Type: " + eamArtifact.getCorrelationType().getDisplayName()
+                                            + "\n\tCorrelationArtifact Value: " + eamArtifact.getCorrelationValue());
                                 }
                                 if (eamInstance.getKnownStatus() == null) {
-                                    throw new EamDbException("CorrelationAttributeInstance known status is null");
+                                    throw new EamDbException("CorrelationAttributeInstance known status is null for: "
+                                            + "\n\tCorrelationArtifact ID: " + eamArtifact.getID()
+                                            + "\n\tCorrelationArtifact Type: " + eamArtifact.getCorrelationType().getDisplayName()
+                                            + "\n\tCorrelationArtifact Value: " + eamArtifact.getCorrelationValue() 
+                                            + "\n\tEam Instance: "
+                                            + "\n\t\tCaseId: " + eamInstance.getCorrelationDataSource().getCaseID()
+                                            + "\n\t\tDeviceID: " + eamInstance.getCorrelationDataSource().getDeviceID());
                                 }
 
-                                bulkPs.setString(1, eamInstance.getCorrelationCase().getCaseUUID());
+                                if (eamArtifact.getCorrelationValue().length() < MAX_VALUE_LENGTH) {
-                                bulkPs.setString(2, eamInstance.getCorrelationDataSource().getDeviceID());
+                                    bulkPs.setString(1, eamInstance.getCorrelationCase().getCaseUUID());
-                                bulkPs.setInt(3, eamInstance.getCorrelationDataSource().getCaseID());
+                                    bulkPs.setString(2, eamInstance.getCorrelationDataSource().getDeviceID());
-                                bulkPs.setString(4, eamArtifact.getCorrelationValue());
+                                    bulkPs.setInt(3, eamInstance.getCorrelationDataSource().getCaseID());
-                                bulkPs.setString(5, eamInstance.getFilePath());
+                                    bulkPs.setString(4, eamArtifact.getCorrelationValue());
-                                bulkPs.setByte(6, eamInstance.getKnownStatus().getFileKnownValue());
+                                    bulkPs.setString(5, eamInstance.getFilePath());
-                                if ("".equals(eamInstance.getComment())) {
+                                    bulkPs.setByte(6, eamInstance.getKnownStatus().getFileKnownValue());
-                                    bulkPs.setNull(7, Types.INTEGER);
+                                    if ("".equals(eamInstance.getComment())) {
+                                        bulkPs.setNull(7, Types.INTEGER);
+                                    } else {
+                                        bulkPs.setString(7, eamInstance.getComment());
+                                    }
+                                    bulkPs.addBatch();
                                 } else {
-                                    bulkPs.setString(7, eamInstance.getComment());
+                                    logger.log(Level.WARNING, ("Artifact value too long for central repository."
+                                            + "\n\tCorrelationArtifact ID: " + eamArtifact.getID()
+                                            + "\n\tCorrelationArtifact Type: " + eamArtifact.getCorrelationType().getDisplayName()
+                                            + "\n\tCorrelationArtifact Value: " + eamArtifact.getCorrelationValue())
+                                            + "\n\tEam Instance: "
+                                            + "\n\t\tCaseId: " + eamInstance.getCorrelationDataSource().getCaseID()
+                                            + "\n\t\tDeviceID: " + eamInstance.getCorrelationDataSource().getDeviceID()
+                                            + "\n\t\tFilePath: " + eamInstance.getFilePath());
                                 }
-                                bulkPs.addBatch();
                             }
                         }
                     }
@@ -1821,11 +1855,13 @@ abstract class AbstractSqlEamDb implements EamDb {
 
         return 0 < badInstances;
     }
+
     /**
      * Process the Artifact instance in the EamDb
      *
-     * @param type EamArtifact.Type to search for
+     * @param type                  EamArtifact.Type to search for
      * @param instanceTableCallback callback to process the instance
+     *
      * @throws EamDbException
      */
     @Override

Core/src/org/sleuthkit/autopsy/centralrepository/datamodel/CorrelationDataSource.java

@@ -67,6 +67,7 @@ public class CorrelationDataSource implements Serializable {
 
     /**
      * Create a CorrelationDataSource object from a TSK Content object.
+     * This will add it to the central repository.
      *
      * @param correlationCase the current CorrelationCase used for ensuring
      *                        uniqueness of DataSource

Core/src/org/sleuthkit/autopsy/centralrepository/eventlisteners/CaseEventListener.java

@@ -450,10 +450,10 @@ final class CaseEventListener implements PropertyChangeListener {
                     correlationCase = dbManager.newCase(openCase);
                 }
                 if (null == dbManager.getDataSource(correlationCase, deviceId)) {
-                    dbManager.newDataSource(CorrelationDataSource.fromTSKDataSource(correlationCase, newDataSource));
+                    CorrelationDataSource.fromTSKDataSource(correlationCase, newDataSource);
                 }
             } catch (EamDbException ex) {
-                LOGGER.log(Level.SEVERE, "Error connecting to Central Repository database.", ex); //NON-NLS
+                LOGGER.log(Level.SEVERE, "Error adding new data source to the central repository", ex); //NON-NLS
             } catch (TskCoreException | TskDataException ex) {
                 LOGGER.log(Level.SEVERE, "Error getting data source from DATA_SOURCE_ADDED event content.", ex); //NON-NLS
             }

Core/src/org/sleuthkit/autopsy/centralrepository/eventlisteners/IngestEventsListener.java

@@ -276,12 +276,12 @@ public class IngestEventsListener {
                 }
             }
             if (FALSE == eamArtifacts.isEmpty()) {
-                try {
+                for (CorrelationAttribute eamArtifact : eamArtifacts) {
-                    for (CorrelationAttribute eamArtifact : eamArtifacts) {
+                    try {
                         dbManager.addArtifact(eamArtifact);
+                    } catch (EamDbException ex) {
+                        LOGGER.log(Level.SEVERE, "Error adding artifact to database.", ex); //NON-NLS
                     }
-                } catch (EamDbException ex) {
-                    LOGGER.log(Level.SEVERE, "Error connecting to Central Repository database.", ex); //NON-NLS
                 }
             } // DATA_ADDED
         }

Core/src/org/sleuthkit/autopsy/commonfilesearch/CommonAttributesSearchResultsViewerTable.java

@@ -23,6 +23,8 @@ import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.Map;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 import javax.swing.table.TableColumn;
 import javax.swing.table.TableColumnModel;
 import org.openide.util.NbBundle;
@@ -36,10 +38,14 @@ import org.sleuthkit.autopsy.corecomponents.DataResultViewerTable;
  * rows and looking for wide cells.  Rather, we just pick some reasonable values.
  */
 public class CommonAttributesSearchResultsViewerTable extends DataResultViewerTable {
-    
+
     private static final Map<String, Integer> COLUMN_WIDTHS;
     private static final long serialVersionUID = 1L;
+
+    private static final Logger LOGGER = Logger.getLogger(CommonFilesSearchResultsViewerTable.class.getName());
     
+    private static final int DEFAULT_WIDTH = 100;
+
     static {
         Map<String, Integer> map = new HashMap<>();
         map.put(Bundle.CommonFilesSearchResultsViewerTable_filesColLbl(), 260);
@@ -50,10 +56,10 @@ public class CommonAttributesSearchResultsViewerTable extends DataResultViewerTa
         map.put(Bundle.CommonFilesSearchResultsViewerTable_hashsetHitsColLbl(), 100);
         map.put(Bundle.CommonFilesSearchResultsViewerTable_mimeTypeColLbl(), 130);
         map.put(Bundle.CommonFilesSearchResultsViewerTable_tagsColLbl1(), 300);;
-        
+
         COLUMN_WIDTHS = Collections.unmodifiableMap(map);
     }
-    
+
     @NbBundle.Messages({
         "CommonFilesSearchResultsViewerTable.noDescText= ",
         "CommonFilesSearchResultsViewerTable.filesColLbl=Files",
@@ -66,18 +72,24 @@ public class CommonAttributesSearchResultsViewerTable extends DataResultViewerTa
         "CommonFilesSearchResultsViewerTable.tagsColLbl1=Tags"
     })
     @Override
-    protected void setColumnWidths(){
+    protected void setColumnWidths() {
         TableColumnModel model = this.getColumnModel();
-        
+
         Enumeration<TableColumn> columnsEnumerator = model.getColumns();
-        while(columnsEnumerator.hasMoreElements()){
+        while (columnsEnumerator.hasMoreElements()) {
-            
+
             TableColumn column = columnsEnumerator.nextElement();
-            
+
             final String headerValue = column.getHeaderValue().toString();
-            final Integer get = COLUMN_WIDTHS.get(headerValue);
+
-                        
+            final Integer defaultWidth = COLUMN_WIDTHS.get(headerValue);
-            column.setPreferredWidth(get);
+            
+            if(defaultWidth == null){
+                column.setPreferredWidth(DEFAULT_WIDTH);
+                LOGGER.log(Level.SEVERE, String.format("Tried to set width on a column not supported by the CommonFilesSearchResultsViewerTable: %s", headerValue));
+            } else {
+                column.setPreferredWidth(defaultWidth);
+            }
         }
     }
 }

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

@@ -88,7 +88,21 @@ final public class CoreComponentControl {
         TopComponent directoryTree = null;
         TopComponent favorites = null;
         final WindowManager windowManager = WindowManager.getDefault();
+        
+        // Set the UI selections to null before closing the top components.
+        // Otherwise it may experience errors trying to load data for the closed case.
         for (Mode mode : windowManager.getModes()) {
+            for (TopComponent tc : windowManager.getOpenedTopComponents(mode)) {
+                if(tc instanceof DataContent) {
+                    ((DataContent) tc).setNode(null);
+                } else if(tc instanceof DataResult) {
+                    ((DataResult) tc).setNode(null);
+                }
+            }
+        }
+        
+        for (Mode mode : windowManager.getModes()) {
+            
             for (TopComponent tc : windowManager.getOpenedTopComponents(mode)) {
                 String tcName = tc.getName();
 
@@ -105,7 +119,7 @@ final public class CoreComponentControl {
                 }
             }
         }
-
+        
         if (directoryTree != null) {
             directoryTree.close();
         }

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

@@ -249,7 +249,7 @@ public final class FileTypes implements AutopsyVisitableItem {
             if (typesRoot.showCounts) {
                 //only show "(counting...)" the first time, otherwise it is distracting.
                 setDisplayName(getDisplayNameBase() + ((childCount < 0) ? Bundle.FileTypes_bgCounting_placeholder()
-                        : ("(" + childCount + ")"))); //NON-NLS
+                        : (" (" + childCount + ")"))); //NON-NLS
                 new SwingWorker<Long, Void>() {
                     @Override
                     protected Long doInBackground() throws Exception {

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

@@ -120,3 +120,8 @@ AddExternalViewerRulePanel.exePathTextField.text=
 AddExternalViewerRulePanel.exePathLabel.text=Path of the program to use for files with this type or extension
 AddExternalViewerRulePanel.extRadioButton.text=Extension
 DirectoryTreeTopComponent.groupByDatasourceCheckBox.text=Group by Data Source
+GroupDataSourcesDialog.dataSourceCountLabel.text=jLabel1
+GroupDataSourcesDialog.queryLabel.text=Would you like to group by data source for faster loading?
+GroupDataSourcesDialog.yesButton.text=Yes
+GroupDataSourcesDialog.noButton.text=No
+GroupDataSourcesDialog.title=Group by Data Source?

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

@@ -24,6 +24,11 @@ import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.beans.PropertyVetoException;
 import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.EnumSet;
@@ -35,6 +40,7 @@ import java.util.concurrent.ExecutionException;
 import java.util.logging.Level;
 import java.util.prefs.PreferenceChangeEvent;
 import java.util.prefs.PreferenceChangeListener;
+import java.util.Properties;
 import javax.swing.Action;
 import javax.swing.SwingUtilities;
 import javax.swing.SwingWorker;
@@ -62,6 +68,7 @@ import org.sleuthkit.autopsy.corecomponentinterfaces.DataExplorer;
 import org.sleuthkit.autopsy.corecomponents.DataResultTopComponent;
 import org.sleuthkit.autopsy.corecomponents.TableFilterNode;
 import org.sleuthkit.autopsy.coreutils.Logger;
+import org.sleuthkit.autopsy.coreutils.ModuleSettings;
 import org.sleuthkit.autopsy.datamodel.ArtifactNodeSelectionInfo;
 import org.sleuthkit.autopsy.datamodel.BlackboardArtifactNode;
 import org.sleuthkit.autopsy.datamodel.CreditCards;
@@ -103,6 +110,9 @@ public final class DirectoryTreeTopComponent extends TopComponent implements Dat
     private static final Logger LOGGER = Logger.getLogger(DirectoryTreeTopComponent.class.getName());
     private AutopsyTreeChildrenFactory autopsyTreeChildrenFactory;
     private Children autopsyTreeChildren;
+    private static final long DEFAULT_DATASOURCE_GROUPING_THRESHOLD = 5; // Threshold for prompting the user about grouping by data source
+    private static final String GROUPING_THRESHOLD_NAME = "GroupDataSourceThreshold";
+    private static final String SETTINGS_FILE = "CasePreferences.properties"; //NON-NLS
 
     /**
      * the constructor
@@ -125,7 +135,7 @@ public final class DirectoryTreeTopComponent extends TopComponent implements Dat
         this.forwardList = new LinkedList<>();
         backButton.setEnabled(false);
         forwardButton.setEnabled(false);
-        
+
         groupByDatasourceCheckBox.setSelected(UserPreferences.groupItemsInTreeByDatasource());
     }
 
@@ -149,7 +159,7 @@ public final class DirectoryTreeTopComponent extends TopComponent implements Dat
                 }
             }
         });
-        
+
         Case.addEventTypeSubscriber(EnumSet.of(Case.Events.CURRENT_CASE, Case.Events.DATA_SOURCE_ADDED), this);
         this.em.addPropertyChangeListener(this);
         IngestManager.getInstance().addIngestJobEventListener(this);
@@ -370,6 +380,51 @@ public final class DirectoryTreeTopComponent extends TopComponent implements Dat
         return TopComponent.PERSISTENCE_NEVER;
     }
 
+    /**
+     * Ask the user if they want to group by data source when opening a large
+     * case.
+     *
+     * @param currentCase
+     * @param dataSourceCount
+     */
+    private void promptForDataSourceGrouping(Case currentCase, int dataSourceCount) {
+        Path settingsFile = Paths.get(currentCase.getConfigDirectory(), SETTINGS_FILE); //NON-NLS
+        if (settingsFile.toFile().exists()) {
+            // Read the setting
+            try (InputStream inputStream = Files.newInputStream(settingsFile)) {
+                Properties props = new Properties();
+                props.load(inputStream);
+                if (props.getProperty("groupByDataSource", "false").equals("true")) {
+                    UserPreferences.setGroupItemsInTreeByDatasource(true);
+                    groupByDatasourceCheckBox.setSelected(true);
+                }
+            } catch (IOException ex) {
+                LOGGER.log(Level.SEVERE, "Error reading settings file", ex);
+            }
+        } else {
+            GroupDataSourcesDialog dialog = new GroupDataSourcesDialog(dataSourceCount);
+            dialog.display();
+            if (dialog.groupByDataSourceSelected()) {
+                UserPreferences.setGroupItemsInTreeByDatasource(true);
+                groupByDatasourceCheckBox.setSelected(true);
+            }
+
+            // Save the response
+            Properties props = new Properties();
+            if (dialog.groupByDataSourceSelected()) {
+                props.setProperty("groupByDataSource", "true");
+            } else {
+                props.setProperty("groupByDataSource", "false");
+            }
+
+            try (OutputStream fos = Files.newOutputStream(settingsFile)) {
+                props.store(fos, ""); //NON-NLS
+            } catch (IOException ex) {
+                LOGGER.log(Level.SEVERE, "Error writing settings file", ex);
+            }
+        }
+    }
+
     /**
      * Called only when top component was closed on all workspaces before and
      * now is opened for the first time on some workspace. The intent is to
@@ -377,6 +432,9 @@ public final class DirectoryTreeTopComponent extends TopComponent implements Dat
      * existing workspaces. Subclasses will usually perform initializing tasks
      * here.
      */
+    @NbBundle.Messages({"# {0} - dataSourceCount",
+        "DirectoryTreeTopComponent.componentOpened.groupDataSources.text=This case contains {0} data sources. Would you like to group by data source for faster loading?",
+        "DirectoryTreeTopComponent.componentOpened.groupDataSources.title=Group by data source?"})
     @Override
     public void componentOpened() {
         // change the cursor to "waiting cursor" for this operation
@@ -392,9 +450,34 @@ public final class DirectoryTreeTopComponent extends TopComponent implements Dat
         if (null == currentCase || currentCase.hasData() == false) {
             getTree().setRootVisible(false); // hide the root
         } else {
+            // If the case contains a lot of data sources, and they aren't already grouping
+            // by data source, give the user the option to do so before loading the tree.
+            if (RuntimeProperties.runningWithGUI()) {
+                long threshold = DEFAULT_DATASOURCE_GROUPING_THRESHOLD;
+                if (ModuleSettings.settingExists(ModuleSettings.MAIN_SETTINGS, GROUPING_THRESHOLD_NAME)) {
+                    try {
+                        threshold = Long.parseLong(ModuleSettings.getConfigSetting(ModuleSettings.MAIN_SETTINGS, GROUPING_THRESHOLD_NAME));
+                    } catch (NumberFormatException ex) {
+                        LOGGER.log(Level.SEVERE, "Group data sources threshold is not a number", ex);
+                    }
+                } else {
+                    ModuleSettings.setConfigSetting(ModuleSettings.MAIN_SETTINGS, GROUPING_THRESHOLD_NAME, String.valueOf(threshold));
+                }
+
+                try {
+                    int dataSourceCount = currentCase.getDataSources().size();
+                    if (!UserPreferences.groupItemsInTreeByDatasource()
+                            && dataSourceCount > threshold) {
+                        promptForDataSourceGrouping(currentCase, dataSourceCount);
+                    }
+                } catch (TskCoreException ex) {
+                    LOGGER.log(Level.SEVERE, "Error loading data sources", ex);
+                }
+            }
+
             // if there's at least one image, load the image and open the top componen
             autopsyTreeChildrenFactory = new AutopsyTreeChildrenFactory();
-            autopsyTreeChildren = Children.create(autopsyTreeChildrenFactory, true);     
+            autopsyTreeChildren = Children.create(autopsyTreeChildrenFactory, true);
             Node root = new AbstractNode(autopsyTreeChildren) {
                 //JIRA-2807: What is the point of these overrides?
                 /**
@@ -453,9 +536,9 @@ public final class DirectoryTreeTopComponent extends TopComponent implements Dat
                         tree.collapseNode(views);
                     }
                     /*
-                     * JIRA-2806: What is this supposed to do? Right now it selects
+                     * JIRA-2806: What is this supposed to do? Right now it
-                     * the data sources node, but the comment seems to indicate
+                     * selects the data sources node, but the comment seems to
-                     * it is supposed to select the first datasource.
+                     * indicate it is supposed to select the first datasource.
                      */
                     // select the first image node, if there is one
                     // (this has to happen after dataResult is opened, because the event
@@ -484,7 +567,7 @@ public final class DirectoryTreeTopComponent extends TopComponent implements Dat
                     // dataResult active)
                     try {
                         Node[] selections = get();
-                        if (selections != null && selections.length > 0){
+                        if (selections != null && selections.length > 0) {
                             em.setSelectedNodes(selections);
                         }
                     } catch (PropertyVetoException ex) {
@@ -592,15 +675,15 @@ public final class DirectoryTreeTopComponent extends TopComponent implements Dat
     }
 
     /**
-     * The "listener" that listens to any changes made in the Case.java class.
+     * The "listener" that monitors changes made in the Case class. This serves
-     * It will do something based on the changes in the Case.java class.
+     * the purpose of keeping the UI in sync with the data as it changes.
      *
-     * @param evt the property change event
+     * @param event The property change event.
      */
     @Override
-    public void propertyChange(PropertyChangeEvent evt) {
+    public void propertyChange(PropertyChangeEvent event) {
         if (RuntimeProperties.runningWithGUI()) {
-            String changed = evt.getPropertyName();
+            String changed = event.getPropertyName();
             if (changed.equals(Case.Events.CURRENT_CASE.toString())) { // changed current case
                 // When a case is closed, the old value of this property is the 
                 // closed Case object and the new value is null. When a case is 
@@ -610,15 +693,15 @@ public final class DirectoryTreeTopComponent extends TopComponent implements Dat
                 // opened events instead of property change events would be a better
                 // solution. Either way, more probably needs to be done to clean up
                 // data model objects when a case is closed.
-                if (evt.getOldValue() != null && evt.getNewValue() == null) {
+                if (event.getOldValue() != null && event.getNewValue() == null) {
                     // The current case has been closed. Reset the ExplorerManager.
                     SwingUtilities.invokeLater(() -> {
                         Node emptyNode = new AbstractNode(Children.LEAF);
                         em.setRootContext(emptyNode);
                     });
-                } else if (evt.getNewValue() != null) {
+                } else if (event.getNewValue() != null) {
                     // A new case has been opened. Reset the ExplorerManager. 
-                    Case newCase = (Case) evt.getNewValue();
+                    Case newCase = (Case) event.getNewValue();
                     final String newCaseName = newCase.getName();
                     SwingUtilities.invokeLater(() -> {
                         em.getRootContext().setName(newCaseName);
@@ -642,20 +725,27 @@ public final class DirectoryTreeTopComponent extends TopComponent implements Dat
                  * already closed.
                  */
                 try {
-                    Case currentCase = Case.getCurrentCaseThrows();
+                    Case.getCurrentCaseThrows();
-                    // We only need to trigger openCoreWindows() when the
+                    /*
-                    // first data source is added.
+                     * In case the Case 'updateGUIForCaseOpened()' method hasn't
-                    if (currentCase.getDataSources().size() == 1) {
+                     * already done so, open the tree and all other core
+                     * windows.
+                     *
+                     * TODO: (JIRA-4053) DirectoryTreeTopComponent should not be
+                     * responsible for opening core windows. Consider moving
+                     * this elsewhere.
+                     */
+                    if (!this.isOpened()) {
                         SwingUtilities.invokeLater(CoreComponentControl::openCoreWindows);
                     }
-                } catch (NoCurrentCaseException | TskCoreException notUsed) {
+                } catch (NoCurrentCaseException notUsed) {
                     /**
                      * Case is closed, do nothing.
                      */
                 }
             } // change in node selection
             else if (changed.equals(ExplorerManager.PROP_SELECTED_NODES)) {
-                respondSelection((Node[]) evt.getOldValue(), (Node[]) evt.getNewValue());
+                respondSelection((Node[]) event.getOldValue(), (Node[]) event.getNewValue());
             } else if (changed.equals(IngestManager.IngestModuleEvent.DATA_ADDED.toString())) {
                 // nothing to do here.
                 // all nodes should be listening for these events and update accordingly.
@@ -800,7 +890,7 @@ public final class DirectoryTreeTopComponent extends TopComponent implements Dat
 
     /**
      * Rebuilds the autopsy tree.
-     * 
+     *
      * Does nothing if there is no open case.
      */
     private void rebuildTree() {
@@ -813,9 +903,9 @@ public final class DirectoryTreeTopComponent extends TopComponent implements Dat
             return;
         }
         if (null == currentCase || currentCase.hasData() == false) {
-           return;
+            return;
         }
-        
+
         // refresh all children of the root.
         autopsyTreeChildrenFactory.refreshChildren();
 
@@ -842,14 +932,14 @@ public final class DirectoryTreeTopComponent extends TopComponent implements Dat
             }
         }.execute();
     }
-    
+
     /**
      * Selects the first node in the tree.
-     * 
+     *
      */
-    private void selectFirstChildNode () {
+    private void selectFirstChildNode() {
         Children rootChildren = em.getRootContext().getChildren();
-        
+
         if (rootChildren.getNodesCount() > 0) {
             Node firstNode = rootChildren.getNodeAt(0);
             if (firstNode != null) {
@@ -858,6 +948,7 @@ public final class DirectoryTreeTopComponent extends TopComponent implements Dat
             }
         }
     }
+
     /**
      * Set the selected node using a path to a previously selected node.
      *

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

@@ -18,8 +18,6 @@
  */
 package org.sleuthkit.autopsy.filesearch;
 
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseMotionListener;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -29,7 +27,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import java.util.logging.Level;
-import javax.swing.JList;
 import javax.swing.event.ListSelectionEvent;
 import org.sleuthkit.autopsy.casemodule.Case;
 import org.sleuthkit.autopsy.casemodule.NoCurrentCaseException;
@@ -47,38 +44,28 @@ public class DataSourcePanel extends javax.swing.JPanel {
     private static final Logger logger = Logger.getLogger(DataSourcePanel.class.getName());
     private static final long serialVersionUID = 1L;
     private final Map<Long, String> dataSourceMap = new HashMap<>();
-    private final List<String> toolTipList = new ArrayList<>();
 
     /**
      * Creates new form DataSourcePanel
      */
     public DataSourcePanel() {
         initComponents();
-        this.dataSourceList.addListSelectionListener((ListSelectionEvent evt) -> {
+        if (this.dataSourceList.getModel().getSize() > 1) {
-            firePropertyChange(FileSearchPanel.EVENT.CHECKED.toString(), null, null);
+            this.dataSourceList.addListSelectionListener((ListSelectionEvent evt) -> {
-        });
+                firePropertyChange(FileSearchPanel.EVENT.CHECKED.toString(), null, null);
-        this.dataSourceList.addMouseMotionListener(new MouseMotionListener() {
+            });
-
+        } else {
-            @Override
+            /*
-            public void mouseDragged(MouseEvent evt) {
+             * Disable data source filtering since there aren't multiple data
-                //Unused by now
+             * sources to choose from.
-            }
+             */
-
+            this.dataSourceCheckBox.setEnabled(false);
-            @Override
+            this.dataSourceList.setEnabled(false);
-            public void mouseMoved(MouseEvent evt) {
+        }
-                if (evt.getSource() instanceof JList<?>) {
-                    JList<?> dsList = (JList<?>) evt.getSource();
-                    int index = dsList.locationToIndex(evt.getPoint());
-                    if (index > -1) {
-                        dsList.setToolTipText(toolTipList.get(index));
-                    }
-                }
-            }
-    });
     }
 
     /**
-     * Get dataSourceMap with object id and data source display name. Add the data source full name to toolTipList
+     * Get dataSourceMap with object id and data source display name.
      *
      * @return The list of data source name
      */
@@ -93,8 +80,7 @@ public class DataSourcePanel extends javax.swing.JPanel {
                 String dsName = ds.getName();
                 File dataSourceFullName = new File(dsName);
                 String displayName = dataSourceFullName.getName();
-                dataSourceMap.put(ds.getId(), displayName);  
+                dataSourceMap.put(ds.getId(), displayName);
-                toolTipList.add(dsName);
                 dsList.add(displayName);
             }
         } catch (NoCurrentCaseException ex) {
@@ -107,7 +93,8 @@ public class DataSourcePanel extends javax.swing.JPanel {
 
     /**
      * Get a set of data source object ids that are selected.
-     * @return A set of selected object ids. 
+     *
+     * @return A set of selected object ids.
      */
     Set<Long> getDataSourcesSelected() {
         Set<Long> dataSourceObjIdSet = new HashSet<>();
@@ -124,6 +111,7 @@ public class DataSourcePanel extends javax.swing.JPanel {
 
     /**
      * Is dataSourceCheckBox selected
+     *
      * @return true if the dataSoureCheckBox is selected
      */
     boolean isSelected() {
@@ -131,7 +119,8 @@ public class DataSourcePanel extends javax.swing.JPanel {
     }
 
     /**
-     * Enable the dsList and dataSourceNoteLable if the dataSourceCheckBox is checked.
+     * Enable the dsList and dataSourceNoteLable if the dataSourceCheckBox is
+     * checked.
      */
     final void setComponentsEnabled() {
         boolean enabled = this.isSelected();

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

@@ -556,17 +556,29 @@ class ReportHTML implements TableReportModule {
     }
 
     /**
-     * Add a row to the current table.
+     * Add a row to the current table, escaping the text to be contained in the
+     * row.
      *
      * @param row values for each cell in the row
      */
     @Override
     public void addRow(List<String> row) {
+        addRow(row, true);
+    }
+
+    /**
+     * Add a row to the current table.
+     *
+     * @param row        values for each cell in the row
+     * @param escapeText whether or not the text of the row should be escaped,
+     *                   true for escaped, false for not escaped
+     */
+    private void addRow(List<String> row, boolean escapeText) {
         StringBuilder builder = new StringBuilder();
         builder.append("\t<tr>\n"); //NON-NLS
         for (String cell : row) {
-            String escapeHTMLCell = EscapeUtil.escapeHtml(cell);
+            String cellText = escapeText ? EscapeUtil.escapeHtml(cell) : cell;
-            builder.append("\t\t<td>").append(escapeHTMLCell).append("</td>\n"); //NON-NLS
+            builder.append("\t\t<td>").append(cellText).append("</td>\n"); //NON-NLS
         }
         builder.append("\t</tr>\n"); //NON-NLS
         rowCount++;
@@ -593,7 +605,7 @@ class ReportHTML implements TableReportModule {
     public void addRowWithTaggedContentHyperlink(List<String> row, ContentTag contentTag) {
         Content content = contentTag.getContent();
         if (content instanceof AbstractFile == false) {
-            addRow(row);
+            addRow(row, true);
             return;
         }
         AbstractFile file = (AbstractFile) content;
@@ -647,7 +659,7 @@ class ReportHTML implements TableReportModule {
         int pages = 1;
         for (Content content : images) {
             if (currentRow.size() == THUMBNAIL_COLUMNS) {
-                addRow(currentRow);
+                addRow(currentRow, false);
                 currentRow.clear();
             }
 
@@ -727,7 +739,7 @@ class ReportHTML implements TableReportModule {
                 // Finish out the row.
                 currentRow.add("");
             }
-            addRow(currentRow);
+            addRow(currentRow, false);
         }
 
         // manually set rowCount to be the total number of images.
@@ -1094,8 +1106,8 @@ class ReportHTML implements TableReportModule {
             summary.append("<div class=\"title\">\n"); //NON-NLS
             summary.append(writeSummaryCaseDetails());
             summary.append(writeSummaryImageInfo());
-            summary.append(writeSummarySoftwareInfo(skCase,ingestJobs));
+            summary.append(writeSummarySoftwareInfo(skCase, ingestJobs));
-            summary.append(writeSummaryIngestHistoryInfo(skCase,ingestJobs));
+            summary.append(writeSummaryIngestHistoryInfo(skCase, ingestJobs));
             if (generatorLogoSet) {
                 summary.append("<div class=\"left\">\n"); //NON-NLS
                 summary.append("<img src=\"generator_logo.png\" />\n"); //NON-NLS
@@ -1126,14 +1138,13 @@ class ReportHTML implements TableReportModule {
             }
         }
     }
-    
+
     /**
      * Write the case details section of the summary for this report.
-     * 
+     *
      * @return StringBuilder updated html report with case details
      */
-    
+    private StringBuilder writeSummaryCaseDetails() {
-    private StringBuilder writeSummaryCaseDetails(){
         StringBuilder summary = new StringBuilder();
         String caseName = currentCase.getDisplayName();
         String caseNumber = currentCase.getNumber();
@@ -1146,40 +1157,39 @@ class ReportHTML implements TableReportModule {
             imagecount = 0;
         }
         summary.append("<div class=\"title\">\n"); //NON-NLS
-            if (agencyLogoSet) {
+        if (agencyLogoSet) {
-                summary.append("<div class=\"left\">\n"); //NON-NLS
+            summary.append("<div class=\"left\">\n"); //NON-NLS
-                summary.append("<img src=\"");
+            summary.append("<img src=\"");
-                summary.append(Paths.get(reportBranding.getAgencyLogoPath()).getFileName().toString());
+            summary.append(Paths.get(reportBranding.getAgencyLogoPath()).getFileName().toString());
-                summary.append("\" />\n"); //NON-NLS
+            summary.append("\" />\n"); //NON-NLS
-                summary.append("</div>\n"); //NON-NLS
-            }
-            final String align = agencyLogoSet ? "right" : "left"; //NON-NLS NON-NLS
-            summary.append("<div class=\"").append(align).append("\">\n"); //NON-NLS
-            summary.append("<table>\n"); //NON-NLS
-            summary.append("<tr><td>").append(NbBundle.getMessage(this.getClass(), "ReportHTML.writeSum.caseName")) //NON-NLS
-                    .append("</td><td>").append(caseName).append("</td></tr>\n"); //NON-NLS NON-NLS
-            summary.append("<tr><td>").append(NbBundle.getMessage(this.getClass(), "ReportHTML.writeSum.caseNum")) //NON-NLS
-                    .append("</td><td>").append(!caseNumber.isEmpty() ? caseNumber : NbBundle //NON-NLS
-                    .getMessage(this.getClass(), "ReportHTML.writeSum.noCaseNum")).append("</td></tr>\n"); //NON-NLS
-            summary.append("<tr><td>").append(NbBundle.getMessage(this.getClass(), "ReportHTML.writeSum.examiner")).append("</td><td>") //NON-NLS
-                    .append(!examiner.isEmpty() ? examiner : NbBundle
-                            .getMessage(this.getClass(), "ReportHTML.writeSum.noExaminer"))
-                    .append("</td></tr>\n"); //NON-NLS
-            summary.append("<tr><td>").append(NbBundle.getMessage(this.getClass(), "ReportHTML.writeSum.numImages")) //NON-NLS
-                    .append("</td><td>").append(imagecount).append("</td></tr>\n"); //NON-NLS
-            summary.append("</table>\n"); //NON-NLS
             summary.append("</div>\n"); //NON-NLS
-            summary.append("<div class=\"clear\"></div>\n"); //NON-NLS
+        }
-            summary.append("</div>\n"); //NON-NLS
+        final String align = agencyLogoSet ? "right" : "left"; //NON-NLS NON-NLS
-            return summary;
+        summary.append("<div class=\"").append(align).append("\">\n"); //NON-NLS
+        summary.append("<table>\n"); //NON-NLS
+        summary.append("<tr><td>").append(NbBundle.getMessage(this.getClass(), "ReportHTML.writeSum.caseName")) //NON-NLS
+                .append("</td><td>").append(caseName).append("</td></tr>\n"); //NON-NLS NON-NLS
+        summary.append("<tr><td>").append(NbBundle.getMessage(this.getClass(), "ReportHTML.writeSum.caseNum")) //NON-NLS
+                .append("</td><td>").append(!caseNumber.isEmpty() ? caseNumber : NbBundle //NON-NLS
+                .getMessage(this.getClass(), "ReportHTML.writeSum.noCaseNum")).append("</td></tr>\n"); //NON-NLS
+        summary.append("<tr><td>").append(NbBundle.getMessage(this.getClass(), "ReportHTML.writeSum.examiner")).append("</td><td>") //NON-NLS
+                .append(!examiner.isEmpty() ? examiner : NbBundle
+                        .getMessage(this.getClass(), "ReportHTML.writeSum.noExaminer"))
+                .append("</td></tr>\n"); //NON-NLS
+        summary.append("<tr><td>").append(NbBundle.getMessage(this.getClass(), "ReportHTML.writeSum.numImages")) //NON-NLS
+                .append("</td><td>").append(imagecount).append("</td></tr>\n"); //NON-NLS
+        summary.append("</table>\n"); //NON-NLS
+        summary.append("</div>\n"); //NON-NLS
+        summary.append("<div class=\"clear\"></div>\n"); //NON-NLS
+        summary.append("</div>\n"); //NON-NLS
+        return summary;
     }
-    
+
     /**
      * Write the Image Information section of the summary for this report.
-     * 
+     *
      * @return StringBuilder updated html report with Image Information
      */
-    
     private StringBuilder writeSummaryImageInfo() {
         StringBuilder summary = new StringBuilder();
         summary.append(NbBundle.getMessage(this.getClass(), "ReportHTML.writeSum.imageInfoHeading"));
@@ -1208,13 +1218,12 @@ class ReportHTML implements TableReportModule {
         summary.append("</div>\n"); //NON-NLS
         return summary;
     }
-    
+
     /**
      * Write the software information section of the summary for this report.
-     * 
+     *
      * @return StringBuilder updated html report with software information
      */
-    
     private StringBuilder writeSummarySoftwareInfo(SleuthkitCase skCase, List<IngestJobInfo> ingestJobs) {
         StringBuilder summary = new StringBuilder();
         summary.append(NbBundle.getMessage(this.getClass(), "ReportHTML.writeSum.softwareInfoHeading"));
@@ -1244,13 +1253,12 @@ class ReportHTML implements TableReportModule {
         summary.append("<div class=\"clear\"></div>\n"); //NON-NLS
         return summary;
     }
-    
+
     /**
      * Write the Ingest History section of the summary for this report.
-     * 
+     *
      * @return StringBuilder updated html report with ingest history
      */
-
     private StringBuilder writeSummaryIngestHistoryInfo(SleuthkitCase skCase, List<IngestJobInfo> ingestJobs) {
         StringBuilder summary = new StringBuilder();
         try {
@@ -1304,4 +1312,4 @@ class ReportHTML implements TableReportModule {
                 + thumbFile.getName();
     }
 
-}
+}

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

@@ -44,6 +44,7 @@ import org.sleuthkit.autopsy.casemodule.services.TagsManager;
 import org.sleuthkit.autopsy.coreutils.ImageUtils;
 import org.sleuthkit.autopsy.coreutils.Logger;
 import org.sleuthkit.autopsy.datamodel.ContentUtils;
+import static org.sleuthkit.autopsy.casemodule.services.TagsManager.getNotableTagLabel;
 import org.sleuthkit.datamodel.AbstractFile;
 import org.sleuthkit.datamodel.Account;
 import org.sleuthkit.datamodel.BlackboardArtifact;
@@ -53,6 +54,7 @@ import org.sleuthkit.datamodel.BlackboardAttribute.Type;
 import org.sleuthkit.datamodel.Content;
 import org.sleuthkit.datamodel.ContentTag;
 import org.sleuthkit.datamodel.SleuthkitCase;
+import org.sleuthkit.datamodel.TagName;
 import org.sleuthkit.datamodel.TskCoreException;
 import org.sleuthkit.datamodel.TskData;
 
@@ -538,6 +540,65 @@ class TableReportGenerator {
             logger.log(Level.SEVERE, "Exception while getting open case: ", ex); //NON-NLS
             return;
         }
+        
+        // Get a list of all selected tag IDs
+        String tagIDList = "";
+        if( ! tagNamesFilter.isEmpty()) {
+            try {
+                Map<String, TagName> tagNamesMap = Case.getCurrentCaseThrows().getServices().getTagsManager().getDisplayNamesToTagNamesMap();
+                for(String tagDisplayName : tagNamesFilter) {
+                    if(tagNamesMap.containsKey(tagDisplayName)) {
+                        if (! tagIDList.isEmpty()) {
+                            tagIDList += ",";
+                        }
+                        tagIDList += tagNamesMap.get(tagDisplayName).getId();
+                    } else {
+                        // If the tag name ends with "(Notable)", try stripping that off
+                        if(tagDisplayName.endsWith(getNotableTagLabel())) {
+                            String editedDisplayName = tagDisplayName.substring(0, tagDisplayName.length() - getNotableTagLabel().length());
+                            if(tagNamesMap.containsKey(editedDisplayName)) {
+                                if (! tagIDList.isEmpty()) {
+                                    tagIDList += ",";
+                                }
+                                tagIDList += tagNamesMap.get(editedDisplayName).getId();
+                            }
+                        }
+                    }
+                }
+            } catch (NoCurrentCaseException | TskCoreException ex) {
+                logger.log(Level.SEVERE, "Exception while getting tag info - proceeding without tag filter: ", ex); //NON-NLS
+                tagIDList = "";
+            }
+        }
+        
+        // Check if there are any ad-hoc results
+        String adHocCountQuery = "SELECT COUNT(*) FROM " + //NON-NLS
+                "(SELECT art.artifact_id FROM blackboard_artifacts AS art, blackboard_attributes AS att1 ";//NON-NLS
+        if (!tagIDList.isEmpty()) {
+            adHocCountQuery += ", blackboard_artifact_tags as tag "; //NON-NLS
+        }
+        adHocCountQuery += "WHERE (att1.artifact_id = art.artifact_id) AND (art.artifact_type_id = " + BlackboardArtifact.ARTIFACT_TYPE.TSK_KEYWORD_HIT.getTypeID() + ") "; // NON-NLS
+        if (!tagIDList.isEmpty()) {
+            adHocCountQuery += " AND (art.artifact_id = tag.artifact_id) AND (tag.tag_name_id IN (" + tagIDList + ")) "; //NON-NLS
+        }
+        adHocCountQuery += "EXCEPT " + // NON-NLS
+                "SELECT art.artifact_id FROM blackboard_artifacts AS art, blackboard_attributes AS att1 WHERE (att1.artifact_id = art.artifact_id) AND (art.artifact_type_id = " + BlackboardArtifact.ARTIFACT_TYPE.TSK_KEYWORD_HIT.getTypeID() + ") AND (att1.attribute_type_id = " + BlackboardAttribute.ATTRIBUTE_TYPE.TSK_SET_NAME.getTypeID() + ")) "; //NON-NLS
+
+        int adHocCount = 0;
+        try (SleuthkitCase.CaseDbQuery dbQuery = openCase.getSleuthkitCase().executeQuery(adHocCountQuery)) {
+            ResultSet adHocCountResultSet = dbQuery.getResultSet();
+            if (adHocCountResultSet.next()) {
+                adHocCount = adHocCountResultSet.getInt(1); //NON-NLS
+            } else {
+                throw new TskCoreException("Error counting ad hoc keywords");
+            }
+        } catch (TskCoreException | SQLException ex) {
+            errorList.add(NbBundle.getMessage(this.getClass(), "ReportGenerator.errList.failedQueryKWLists"));
+            logger.log(Level.SEVERE, "Failed to count ad hoc searches with query " + adHocCountQuery, ex); //NON-NLS
+            return;
+        }
+        
+        // Create the query to get the keyword list names
         if (openCase.getCaseType() == Case.CaseType.MULTI_USER_CASE) {
             orderByClause = "ORDER BY convert_to(att.value_text, 'SQL_ASCII') ASC NULLS FIRST"; //NON-NLS
         } else {
@@ -546,16 +607,25 @@ class TableReportGenerator {
         String keywordListQuery
                 = "SELECT att.value_text AS list "
                 + //NON-NLS
-                "FROM blackboard_attributes AS att, blackboard_artifacts AS art "
+                "FROM blackboard_attributes AS att, blackboard_artifacts AS art "; // NON-NLS
-                + //NON-NLS
+        if(! tagIDList.isEmpty()) {
-                "WHERE att.attribute_type_id = " + BlackboardAttribute.ATTRIBUTE_TYPE.TSK_SET_NAME.getTypeID() + " "
+            keywordListQuery += ", blackboard_artifact_tags as tag "; //NON-NLS
+        }
+        keywordListQuery += "WHERE att.attribute_type_id = " + BlackboardAttribute.ATTRIBUTE_TYPE.TSK_SET_NAME.getTypeID() + " "
                 + //NON-NLS
                 "AND art.artifact_type_id = " + BlackboardArtifact.ARTIFACT_TYPE.TSK_KEYWORD_HIT.getTypeID() + " "
                 + //NON-NLS
-                "AND att.artifact_id = art.artifact_id "
+                "AND att.artifact_id = art.artifact_id ";
-                + //NON-NLS
+        if (! tagIDList.isEmpty()) {
-                "GROUP BY list " + orderByClause; //NON-NLS
+            keywordListQuery += "AND (art.artifact_id = tag.artifact_id) " + //NON-NLS
+                    "AND (tag.tag_name_id IN (" + tagIDList + ")) "; //NON-NLS
+        }
+        if (adHocCount > 0) {
+            keywordListQuery += " UNION SELECT \"\" AS list ";
+        }
+        keywordListQuery += "GROUP BY list " + orderByClause; //NON-NLS
 
+        // Make the table of contents links for each list type
         try (SleuthkitCase.CaseDbQuery dbQuery = openCase.getSleuthkitCase().executeQuery(keywordListQuery)) {
             ResultSet listsRs = dbQuery.getResultSet();
             List<String> lists = new ArrayList<>();
@@ -579,6 +649,7 @@ class TableReportGenerator {
             return;
         }
 
+        // Query for keywords, grouped by list
         if (openCase.getCaseType() == Case.CaseType.MULTI_USER_CASE) {
             orderByClause = "ORDER BY convert_to(att3.value_text, 'SQL_ASCII') ASC NULLS FIRST, " //NON-NLS
                     + "convert_to(att1.value_text, 'SQL_ASCII') ASC NULLS FIRST, " //NON-NLS
@@ -588,9 +659,10 @@ class TableReportGenerator {
         } else {
             orderByClause = "ORDER BY list ASC, keyword ASC, parent_path ASC, name ASC, preview ASC"; //NON-NLS
         }
-        // Query for keywords, grouped by list
+        
-        String keywordsQuery
+        // Query for keywords that are part of a list
-                = "SELECT art.artifact_id, art.obj_id, att1.value_text AS keyword, att2.value_text AS preview, att3.value_text AS list, f.name AS name, f.parent_path AS parent_path "
+        String keywordListsQuery
+                = "SELECT art.artifact_id AS artifact_id, art.obj_id AS obj_id, att1.value_text AS keyword, att2.value_text AS preview, att3.value_text AS list, f.name AS name, f.parent_path AS parent_path "
                 + //NON-NLS
                 "FROM blackboard_artifacts AS art, blackboard_attributes AS att1, blackboard_attributes AS att2, blackboard_attributes AS att3, tsk_files AS f "
                 + //NON-NLS
@@ -608,9 +680,24 @@ class TableReportGenerator {
                 + //NON-NLS
                 "AND (att3.attribute_type_id = " + BlackboardAttribute.ATTRIBUTE_TYPE.TSK_SET_NAME.getTypeID() + ") "
                 + //NON-NLS
-                "AND (art.artifact_type_id = " + BlackboardArtifact.ARTIFACT_TYPE.TSK_KEYWORD_HIT.getTypeID() + ") "
+                "AND (art.artifact_type_id = " + BlackboardArtifact.ARTIFACT_TYPE.TSK_KEYWORD_HIT.getTypeID() + ") ";
-                + //NON-NLS
+        
-                orderByClause; //NON-NLS
+        // Query for keywords that are not part of a list
+        String keywordAdHocQuery =
+                "SELECT art.artifact_id AS artifact_id, art.obj_id AS obj_id, att1.value_text AS keyword, att2.value_text AS preview, \"\" AS list, f.name AS name, f.parent_path AS parent_path " + // NON-NLS
+                "FROM blackboard_artifacts AS art, blackboard_attributes AS att1, blackboard_attributes AS att2, tsk_files AS f " + // NON-NLS
+                "WHERE " + // NON-NLS
+                " (art.artifact_id IN (SELECT art.artifact_id FROM blackboard_artifacts AS art, blackboard_attributes AS att1 WHERE (att1.artifact_id = art.artifact_id) AND (art.artifact_type_id = " + BlackboardArtifact.ARTIFACT_TYPE.TSK_KEYWORD_HIT.getTypeID() + ") " + // NON-NLS
+                "EXCEPT " + // NON-NLS
+                "SELECT art.artifact_id FROM blackboard_artifacts AS art, blackboard_attributes AS att1 WHERE (att1.artifact_id = art.artifact_id) AND (art.artifact_type_id = " + BlackboardArtifact.ARTIFACT_TYPE.TSK_KEYWORD_HIT.getTypeID() + ") AND (att1.attribute_type_id = " + BlackboardAttribute.ATTRIBUTE_TYPE.TSK_SET_NAME.getTypeID() + "))) " + //NON-NLS
+                "AND (att1.artifact_id = art.artifact_id) " + //NON-NLS
+                "AND (att2.artifact_id = art.artifact_id) " + //NON-NLS
+                "AND (f.obj_id = art.obj_id) " + //NON-NLS 
+                "AND (att1.attribute_type_id = " + BlackboardAttribute.ATTRIBUTE_TYPE.TSK_KEYWORD.getTypeID() + ") " +  // NON-NLS
+                "AND (att2.attribute_type_id = " + BlackboardAttribute.ATTRIBUTE_TYPE.TSK_KEYWORD_PREVIEW.getTypeID() + ") " + // NON-NLS
+                "AND (art.artifact_type_id = " + BlackboardArtifact.ARTIFACT_TYPE.TSK_KEYWORD_HIT.getTypeID() + ") "; // NON-NLS
+        
+        String keywordsQuery = keywordListsQuery + " UNION " + keywordAdHocQuery + orderByClause;
 
         try (SleuthkitCase.CaseDbQuery dbQuery = openCase.getSleuthkitCase().executeQuery(keywordsQuery)) {
             ResultSet resultSet = dbQuery.getResultSet();
@@ -1623,14 +1710,15 @@ class TableReportGenerator {
     private HashSet<String> getUniqueTagNames(long artifactId) throws TskCoreException {
         HashSet<String> uniqueTagNames = new HashSet<>();
 
-        String query = "SELECT display_name, artifact_id FROM tag_names AS tn, blackboard_artifact_tags AS bat "
+        String query = "SELECT display_name, artifact_id, knownStatus FROM tag_names AS tn, blackboard_artifact_tags AS bat "
                 + //NON-NLS 
                 "WHERE tn.tag_name_id = bat.tag_name_id AND bat.artifact_id = " + artifactId; //NON-NLS
 
         try (SleuthkitCase.CaseDbQuery dbQuery = Case.getCurrentCaseThrows().getSleuthkitCase().executeQuery(query)) {
             ResultSet tagNameRows = dbQuery.getResultSet();
             while (tagNameRows.next()) {
-                uniqueTagNames.add(tagNameRows.getString("display_name")); //NON-NLS
+                String notableString = tagNameRows.getInt("knownStatus") == TskData.FileKnown.BAD.ordinal() ? getNotableTagLabel() : "";
+                uniqueTagNames.add(tagNameRows.getString("display_name") + notableString); //NON-NLS
             }
         } catch (TskCoreException | SQLException | NoCurrentCaseException ex) {
             throw new TskCoreException("Error getting tag names for artifact: ", ex);

Core/test/qa-functional/src/org/sleuthkit/autopsy/commonfilessearch/IntraCaseUtils.java

@@ -104,16 +104,36 @@ class IntraCaseUtils {
     }
 
     void setUp() {
-        CaseUtils.createAsCurrentCase(this.caseName);
+        this.createAsCurrentCase();
 
         final ImageDSProcessor imageDSProcessor = new ImageDSProcessor();
 
-        IngestUtils.addDataSource(imageDSProcessor, imagePath1);
+        this.addImageOne(imageDSProcessor);
-        IngestUtils.addDataSource(imageDSProcessor, imagePath2);
+        this.addImageTwo(imageDSProcessor);
-        IngestUtils.addDataSource(imageDSProcessor, imagePath3);
+        this.addImageThree(imageDSProcessor);
+        this.addImageFour(imageDSProcessor);
+    }
+
+    void addImageFour(final ImageDSProcessor imageDSProcessor) {
         IngestUtils.addDataSource(imageDSProcessor, imagePath4);
     }
 
+    void addImageThree(final ImageDSProcessor imageDSProcessor) {
+        IngestUtils.addDataSource(imageDSProcessor, imagePath3);
+    }
+
+    void addImageTwo(final ImageDSProcessor imageDSProcessor) {
+        IngestUtils.addDataSource(imageDSProcessor, imagePath2);
+    }
+
+    void addImageOne(final ImageDSProcessor imageDSProcessor) {
+        IngestUtils.addDataSource(imageDSProcessor, imagePath1);
+    }
+
+    void createAsCurrentCase() {
+        CaseUtils.createAsCurrentCase(this.caseName);
+    }
+
     Map<Long, String> getDataSourceMap() throws NoCurrentCaseException, TskCoreException, SQLException {
         return this.dataSourceLoader.getDataSourceMap();
     }

Experimental/src/org/sleuthkit/autopsy/experimental/autoingest/AddArchiveTask.java

@@ -33,7 +33,6 @@ import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
 import org.openide.util.Lookup;
 import org.sleuthkit.autopsy.casemodule.Case;
-import org.sleuthkit.autopsy.casemodule.LocalDiskDSProcessor;
 import org.sleuthkit.autopsy.casemodule.LocalFilesDSProcessor;
 import org.sleuthkit.autopsy.corecomponentinterfaces.DataSourceProcessorCallback;
 import static org.sleuthkit.autopsy.corecomponentinterfaces.DataSourceProcessorCallback.DataSourceProcessorResult.CRITICAL_ERRORS;

Experimental/src/org/sleuthkit/autopsy/experimental/autoingest/AutoIngestAdminActions.java

@@ -338,7 +338,7 @@ final class AutoIngestAdminActions {
                         dashboard.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
                         AutoIngestManager.CaseDeletionResult result = dashboard.getMonitor().deleteCase(job);
 
-                        dashboard.getCompletedJobsPanel().refresh(new AutoIngestNodeRefreshEvents.RefreshChildrenEvent(dashboard.getMonitor().getJobsSnapshot()));
+                        dashboard.getCompletedJobsPanel().refresh(new AutoIngestNodeRefreshEvents.RefreshChildrenEvent(dashboard.getMonitor()));
                         dashboard.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
                         if (AutoIngestManager.CaseDeletionResult.FAILED == result) {
                             JOptionPane.showMessageDialog(dashboard,

Experimental/src/org/sleuthkit/autopsy/experimental/autoingest/AutoIngestDashboard.java

@@ -38,7 +38,6 @@ import org.openide.util.NbBundle;
 import org.openide.util.NbBundle.Messages;
 import org.sleuthkit.autopsy.core.ServicesMonitor;
 import org.sleuthkit.autopsy.coreutils.Logger;
-import org.sleuthkit.autopsy.experimental.autoingest.AutoIngestMonitor.JobsSnapshot;
 import org.sleuthkit.autopsy.experimental.autoingest.AutoIngestNodeRefreshEvents.RefreshChildrenEvent;
 
 /**
@@ -257,7 +256,7 @@ final class AutoIngestDashboard extends JPanel implements Observer {
 
     @Override
     public void update(Observable observable, Object arg) {
-        if (arg instanceof JobsSnapshot) {
+        if (arg == null ) {
             EventQueue.invokeLater(() -> {
                 refreshTables();
             });
@@ -271,9 +270,9 @@ final class AutoIngestDashboard extends JPanel implements Observer {
      * @param nodeStateSnapshot The jobs snapshot.
      */
     void refreshTables() {
-        pendingJobsPanel.refresh(new RefreshChildrenEvent(autoIngestMonitor.getJobsSnapshot()));
+        pendingJobsPanel.refresh(new RefreshChildrenEvent(autoIngestMonitor));
-        runningJobsPanel.refresh(new RefreshChildrenEvent(autoIngestMonitor.getJobsSnapshot()));
+        runningJobsPanel.refresh(new RefreshChildrenEvent(autoIngestMonitor));
-        completedJobsPanel.refresh(new RefreshChildrenEvent(autoIngestMonitor.getJobsSnapshot()));
+        completedJobsPanel.refresh(new RefreshChildrenEvent(autoIngestMonitor));
     }
 
     /**

Experimental/src/org/sleuthkit/autopsy/experimental/autoingest/AutoIngestJobsNode.java

@@ -33,7 +33,6 @@ import org.openide.nodes.Node;
 import org.openide.nodes.Sheet;
 import org.openide.util.NbBundle.Messages;
 import org.sleuthkit.autopsy.datamodel.NodeProperty;
-import org.sleuthkit.autopsy.experimental.autoingest.AutoIngestMonitor.JobsSnapshot;
 import org.sleuthkit.autopsy.guiutils.DurationCellRenderer;
 import org.sleuthkit.autopsy.guiutils.StatusIconCellRenderer;
 
@@ -61,13 +60,13 @@ final class AutoIngestJobsNode extends AbstractNode {
     /**
      * Construct a new AutoIngestJobsNode.
      *
-     * @param snapshot the snapshot which contains the AutoIngestJobs
+     * @param monitor  the monitor which gives access to the AutoIngestJobs
      * @param status   the status of the jobs being displayed
      * @param eventBus the event bus which will be used to send and receive
      *                 refresh events
      */
-    AutoIngestJobsNode(JobsSnapshot jobsSnapshot, AutoIngestJobStatus status, EventBus eventBus) {
+    AutoIngestJobsNode(AutoIngestMonitor monitor, AutoIngestJobStatus status, EventBus eventBus) {
-        super(Children.create(new AutoIngestNodeChildren(jobsSnapshot, status, eventBus), false));
+        super(Children.create(new AutoIngestNodeChildren(monitor, status, eventBus), false));
         refreshChildrenEventBus = eventBus;
     }
 
@@ -84,7 +83,7 @@ final class AutoIngestJobsNode extends AbstractNode {
     static final class AutoIngestNodeChildren extends ChildFactory<AutoIngestJob> {
 
         private final AutoIngestJobStatus autoIngestJobStatus;
-        private JobsSnapshot jobsSnapshot;
+        private AutoIngestMonitor monitor;
         private final RefreshChildrenSubscriber refreshChildrenSubscriber = new RefreshChildrenSubscriber();
         private final EventBus refreshEventBus;
 
@@ -92,13 +91,13 @@ final class AutoIngestJobsNode extends AbstractNode {
          * Create children nodes for the AutoIngestJobsNode which will each
          * represent a single AutoIngestJob
          *
-         * @param snapshot the snapshot which contains the AutoIngestJobs
+         * @param monitor  the monitor which gives access to the AutoIngestJobs
          * @param status   the status of the jobs being displayed
          * @param eventBus the event bus which the class registers to for
          *                 refresh events
          */
-        AutoIngestNodeChildren(JobsSnapshot snapshot, AutoIngestJobStatus status, EventBus eventBus) {
+        AutoIngestNodeChildren(AutoIngestMonitor monitor, AutoIngestJobStatus status, EventBus eventBus) {
-            jobsSnapshot = snapshot;
+            this.monitor = monitor;
             autoIngestJobStatus = status;
             refreshEventBus = eventBus;
             refreshChildrenSubscriber.register(refreshEventBus);
@@ -109,14 +108,14 @@ final class AutoIngestJobsNode extends AbstractNode {
             List<AutoIngestJob> jobs;
             switch (autoIngestJobStatus) {
                 case PENDING_JOB:
-                    jobs = jobsSnapshot.getPendingJobs();
+                    jobs = monitor.getPendingJobs();
                     Collections.sort(jobs);
                     break;
                 case RUNNING_JOB:
-                    jobs = jobsSnapshot.getRunningJobs();
+                    jobs = monitor.getRunningJobs();
                     break;
                 case COMPLETED_JOB:
-                    jobs = jobsSnapshot.getCompletedJobs();
+                    jobs = monitor.getCompletedJobs();
                     break;
                 default:
                     jobs = new ArrayList<>();
@@ -167,7 +166,7 @@ final class AutoIngestJobsNode extends AbstractNode {
                 //Ignore netbeans suggesting this isn't being used, it is used behind the scenes by the EventBus
                 //RefreshChildrenEvents can change which children are present however
                 //RefreshJobEvents and RefreshCaseEvents can still change the order we want to display them in
-                jobsSnapshot = refreshEvent.getJobsSnapshot();
+                monitor = refreshEvent.getMonitor();
                 refresh(true);
             }
 

Experimental/src/org/sleuthkit/autopsy/experimental/autoingest/AutoIngestJobsPanel.java

@@ -171,7 +171,7 @@ final class AutoIngestJobsPanel extends javax.swing.JPanel implements ExplorerMa
                 ((AutoIngestJobsNode) explorerManager.getRootContext()).refresh(refreshEvent);
             } else {
                 //Make a new AutoIngestJobsNode with it's own EventBus and set it as the root context
-                explorerManager.setRootContext(new AutoIngestJobsNode(refreshEvent.getJobsSnapshot(), status, new EventBus("AutoIngestJobsNodeEventBus")));
+                explorerManager.setRootContext(new AutoIngestJobsNode(refreshEvent.getMonitor(), status, new EventBus("AutoIngestJobsNodeEventBus")));
             }
             outline.setRowSelectionAllowed(true);
             outline.setFocusable(true);

Experimental/src/org/sleuthkit/autopsy/experimental/autoingest/AutoIngestManager.java

@@ -490,6 +490,14 @@ final class AutoIngestManager extends Observable implements PropertyChangeListen
                     break;
                 case RESUME:
                     resume();
+
+                    /**
+                     * Kick off an immediate scan so that the next pending job
+                     * will be picked up sooner than having to wait for the
+                     * InputDirScannerTask to run again.
+                     */
+                    scanInputDirsNow();
+
                     break;
                 case SHUTDOWN:
                     shutDown();
@@ -1840,13 +1848,13 @@ final class AutoIngestManager extends Observable implements PropertyChangeListen
                      */
                     setChanged();
                     notifyObservers(Event.RESUMED);
-
-                    /**
-                     * Publish an event to let remote listeners know that the
-                     * node has been resumed.
-                     */
-                    eventPublisher.publishRemotely(lastPublishedStateEvent = new AutoIngestNodeStateEvent(Event.RESUMED, AutoIngestManager.LOCAL_HOST_NAME));
                 }
+                /**
+                 * Publish an event to let remote listeners know that the node
+                 * has been resumed.
+                 */
+                eventPublisher.publishRemotely(lastPublishedStateEvent = new AutoIngestNodeStateEvent(Event.RESUMED, AutoIngestManager.LOCAL_HOST_NAME));
+
                 pauseLock.notifyAll();
             }
         }
@@ -2790,6 +2798,7 @@ final class AutoIngestManager extends Observable implements PropertyChangeListen
                             sysLogger.log(Level.INFO, "Finished ingest modules analysis for {0} ", manifestPath);
                             IngestJob.ProgressSnapshot jobSnapshot = ingestJob.getSnapshot();
                             for (IngestJob.ProgressSnapshot.DataSourceProcessingSnapshot snapshot : jobSnapshot.getDataSourceSnapshots()) {
+                                AutoIngestJobLogger nestedJobLogger = new AutoIngestJobLogger(manifestPath, snapshot.getDataSource(), caseDirectoryPath);
                                 if (!snapshot.isCancelled()) {
                                     List<String> cancelledModules = snapshot.getCancelledDataSourceIngestModules();
                                     if (!cancelledModules.isEmpty()) {
@@ -2798,15 +2807,15 @@ final class AutoIngestManager extends Observable implements PropertyChangeListen
                                         setCaseNodeDataErrorsOccurred(caseDirectoryPath);
                                         for (String module : snapshot.getCancelledDataSourceIngestModules()) {
                                             sysLogger.log(Level.WARNING, String.format("%s ingest module cancelled for %s", module, manifestPath));
-                                            jobLogger.logIngestModuleCancelled(module);
+                                            nestedJobLogger.logIngestModuleCancelled(module);
                                         }
                                     }
-                                    jobLogger.logAnalysisCompleted();
+                                    nestedJobLogger.logAnalysisCompleted();
                                 } else {
                                     currentJob.setProcessingStage(AutoIngestJob.Stage.CANCELLING, Date.from(Instant.now()));
                                     currentJob.setErrorsOccurred(true);
                                     setCaseNodeDataErrorsOccurred(caseDirectoryPath);
-                                    jobLogger.logAnalysisCancelled();
+                                    nestedJobLogger.logAnalysisCancelled();
                                     CancellationReason cancellationReason = snapshot.getCancellationReason();
                                     if (CancellationReason.NOT_CANCELLED != cancellationReason && CancellationReason.USER_CANCELLED != cancellationReason) {
                                         throw new AnalysisStartupException(String.format("Analysis cancelled due to %s for %s", cancellationReason.getDisplayName(), manifestPath));

Experimental/src/org/sleuthkit/autopsy/experimental/autoingest/AutoIngestMonitor.java

@@ -22,6 +22,7 @@ import com.google.common.util.concurrent.ThreadFactoryBuilder;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.nio.file.Path;
+import java.time.Duration;
 import java.time.Instant;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -116,11 +117,10 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
         } catch (AutopsyEventException ex) {
             throw new AutoIngestMonitorException("Failed to open auto ingest event channel", ex); //NON-NLS
         }
-        coordSvcQueryExecutor.scheduleWithFixedDelay(new CoordinationServiceQueryTask(), 0, CORRD_SVC_QUERY_INERVAL_MINS, TimeUnit.MINUTES);
+        coordSvcQueryExecutor.scheduleWithFixedDelay(new StateRefreshTask(), 0, CORRD_SVC_QUERY_INERVAL_MINS, TimeUnit.MINUTES);
         eventPublisher.addSubscriber(EVENT_LIST, this);
 
-        // Publish an event that asks running nodes to send their state.
+        refreshNodeState();
-        eventPublisher.publishRemotely(new AutoIngestRequestNodeStateEvent(AutoIngestManager.Event.REPORT_STATE));
     }
 
     /**
@@ -172,7 +172,7 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
             jobsSnapshot.removePendingJob(event.getJob());
             jobsSnapshot.addOrReplaceRunningJob(event.getJob());
             setChanged();
-            notifyObservers(jobsSnapshot);
+            notifyObservers();
         }
     }
 
@@ -190,7 +190,7 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
             jobsSnapshot.removePendingJob(job);
 
             // Update the state of the existing job in the running jobs table
-            for (AutoIngestJob runningJob : jobsSnapshot.getRunningJobs()) {
+            for (AutoIngestJob runningJob : getRunningJobs()) {
                 if (runningJob.equals(job)) {
                     runningJob.setIngestJobsSnapshot(job.getIngestJobSnapshots());
                     runningJob.setIngestThreadSnapshot(job.getIngestThreadActivitySnapshots());
@@ -200,7 +200,7 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
                 }
             }
             setChanged();
-            notifyObservers(jobsSnapshot);
+            notifyObservers();
         }
     }
 
@@ -216,7 +216,7 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
             jobsSnapshot.removeRunningJob(job);
             jobsSnapshot.addOrReplaceCompletedJob(job);
             setChanged();
-            notifyObservers(jobsSnapshot);
+            notifyObservers();
         }
     }
 
@@ -226,7 +226,7 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
      * @param event A job/case prioritization event.
      */
     private void handleCasePrioritizationEvent(AutoIngestCasePrioritizedEvent event) {
-        coordSvcQueryExecutor.submit(new CoordinationServiceQueryTask());
+        coordSvcQueryExecutor.submit(new StateRefreshTask());
     }
 
     /**
@@ -235,7 +235,7 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
      * @param event A job/case deletion event.
      */
     private void handleCaseDeletedEvent(AutoIngestCaseDeletedEvent event) {
-        coordSvcQueryExecutor.submit(new CoordinationServiceQueryTask());
+        coordSvcQueryExecutor.submit(new StateRefreshTask());
     }
 
     /**
@@ -259,15 +259,35 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
     }
 
     /**
-     * Gets the auto ingest monitor's current snapshot of the pending jobs
+     * Gets the snapshot of the pending jobs queue for an auto ingest cluster.
-     * queue, running jobs list, and completed jobs list for an auto ingest
-     * cluster.
      *
-     * @return The snapshot.
+     * @return The pending jobs queue.
      */
-    JobsSnapshot getJobsSnapshot() {
+    List<AutoIngestJob> getPendingJobs() {
         synchronized (jobsLock) {
-            return jobsSnapshot;
+            return new ArrayList<>(jobsSnapshot.pendingJobs);
+        }
+    }
+
+    /**
+     * Gets the snapshot of the running jobs list for an auto ingest cluster.
+     *
+     * @return The running jobs list.
+     */
+    List<AutoIngestJob> getRunningJobs() {
+        synchronized (jobsLock) {
+            return new ArrayList<>(jobsSnapshot.runningJobs);
+        }
+    }
+
+    /**
+     * Gets the snapshot of the completed jobs list for an auto ingest cluster.
+     *
+     * @return The completed jobs list.
+     */
+    List<AutoIngestJob> getCompletedJobs() {
+        synchronized (jobsLock) {
+            return new ArrayList<>(jobsSnapshot.completedJobs);
         }
     }
 
@@ -277,7 +297,12 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
      * @return
      */
     List<AutoIngestNodeState> getNodeStates() {
-        return nodeStates.values().stream().collect(Collectors.toList());
+        // We only report the state for nodes for which we have received
+        // a 'state' event in the last 15 minutes.
+        return nodeStates.values()
+                .stream()
+                .filter(s -> s.getLastSeenTime().isAfter(Instant.now().minus(Duration.ofMinutes(15))))
+                .collect(Collectors.toList());
     }
 
     /**
@@ -287,13 +312,20 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
      *
      * @return The refreshed snapshot.
      */
-    JobsSnapshot refreshJobsSnapshot() {
+    void refreshJobsSnapshot() {
         synchronized (jobsLock) {
             jobsSnapshot = queryCoordinationService();
-            return jobsSnapshot;
         }
     }
 
+    /**
+     * Ask running auto ingest nodes to report their state.
+     */
+    private void refreshNodeState() {
+        // Publish an event that asks running nodes to send their state.
+        eventPublisher.publishRemotely(new AutoIngestRequestNodeStateEvent(AutoIngestManager.Event.REPORT_STATE));
+    }
+
     /**
      * Gets a new snapshot of the pending jobs queue, running jobs list, and
      * completed jobs list for an auto ingest cluster.
@@ -358,13 +390,12 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
      * @throws AutoIngestMonitorException If there is an error removing the
      *                                    priority of the jobs for the case.
      *
-     * @return The latest jobs snapshot.
      */
-    JobsSnapshot deprioritizeCase(final String caseName) throws AutoIngestMonitorException {
+    void deprioritizeCase(final String caseName) throws AutoIngestMonitorException {
         List<AutoIngestJob> jobsToDeprioritize = new ArrayList<>();
 
         synchronized (jobsLock) {
-            for (AutoIngestJob pendingJob : jobsSnapshot.getPendingJobs()) {
+            for (AutoIngestJob pendingJob : getPendingJobs()) {
                 if (pendingJob.getManifest().getCaseName().equals(caseName)) {
                     jobsToDeprioritize.add(pendingJob);
                 }
@@ -395,7 +426,6 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
                         AutoIngestManager.getSystemUserNameProperty(), AutoIngestCasePrioritizedEvent.EventType.CASE_DEPRIORITIZED, ""));
                 }).start();
             }
-            return jobsSnapshot;
         }
     }
 
@@ -407,13 +437,12 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
      * @throws AutoIngestMonitorException If there is an error bumping the
      *                                    priority of the jobs for the case.
      *
-     * @return The latest jobs snapshot.
      */
-    JobsSnapshot prioritizeCase(final String caseName) throws AutoIngestMonitorException {
+    void prioritizeCase(final String caseName) throws AutoIngestMonitorException {
         List<AutoIngestJob> jobsToPrioritize = new ArrayList<>();
         int highestPriority = 0;
         synchronized (jobsLock) {
-            for (AutoIngestJob pendingJob : jobsSnapshot.getPendingJobs()) {
+            for (AutoIngestJob pendingJob : getPendingJobs()) {
                 if (pendingJob.getPriority() > highestPriority) {
                     highestPriority = pendingJob.getPriority();
                 }
@@ -448,7 +477,6 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
                         AutoIngestManager.getSystemUserNameProperty(), AutoIngestCasePrioritizedEvent.EventType.CASE_PRIORITIZED, ""));
                 }).start();
             }
-            return jobsSnapshot;
         }
     }
 
@@ -460,15 +488,14 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
      * @throws AutoIngestMonitorException If there is an error removing the
      *                                    priority of the job.
      *
-     * @return The latest jobs snapshot.
      */
-    JobsSnapshot deprioritizeJob(AutoIngestJob job) throws AutoIngestMonitorException {
+    void deprioritizeJob(AutoIngestJob job) throws AutoIngestMonitorException {
         synchronized (jobsLock) {
             AutoIngestJob jobToDeprioritize = null;
             /*
              * Make sure the job is still in the pending jobs queue.
              */
-            for (AutoIngestJob pendingJob : jobsSnapshot.getPendingJobs()) {
+            for (AutoIngestJob pendingJob : getPendingJobs()) {
                 if (pendingJob.equals(job)) {
                     jobToDeprioritize = job;
                     break;
@@ -506,7 +533,6 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
                 }).start();
 
             }
-            return jobsSnapshot;
         }
     }
 
@@ -518,9 +544,8 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
      * @throws AutoIngestMonitorException If there is an error bumping the
      *                                    priority of the job.
      *
-     * @return The latest jobs snapshot.
      */
-    JobsSnapshot prioritizeJob(AutoIngestJob job) throws AutoIngestMonitorException {
+    void prioritizeJob(AutoIngestJob job) throws AutoIngestMonitorException {
         synchronized (jobsLock) {
             int highestPriority = 0;
             AutoIngestJob jobToPrioritize = null;
@@ -528,7 +553,7 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
              * Get the highest known priority and make sure the job is still in
              * the pending jobs queue.
              */
-            for (AutoIngestJob pendingJob : jobsSnapshot.getPendingJobs()) {
+            for (AutoIngestJob pendingJob : getPendingJobs()) {
                 if (pendingJob.getPriority() > highestPriority) {
                     highestPriority = pendingJob.getPriority();
                 }
@@ -569,7 +594,6 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
                 }).start();
 
             }
-            return jobsSnapshot;
         }
     }
 
@@ -591,7 +615,7 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
      */
     void reprocessJob(AutoIngestJob job) throws AutoIngestMonitorException {
         synchronized (jobsLock) {
-            if (!jobsSnapshot.getCompletedJobs().contains(job)) {
+            if (!getCompletedJobs().contains(job)) {
                 return;
             }
 
@@ -660,7 +684,7 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
 
             // Update the state of completed jobs associated with this case to indicate
             // that the case has been deleted
-            for (AutoIngestJob completedJob : jobsSnapshot.getCompletedJobs()) {
+            for (AutoIngestJob completedJob : getCompletedJobs()) {
                 if (caseName.equals(completedJob.getManifest().getCaseName())) {
                     try {
                         completedJob.setProcessingStatus(DELETED);
@@ -724,25 +748,26 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
     }
 
     /**
-     * A task that queries the coordination service for auto ingest manifest
+     * A task that updates the state maintained by the monitor.
-     * node data and converts it to auto ingest jobs for publication top its
+     * At present this includes auto ingest job and auto ingest node data.
-     * observers.
+     * The job data is refreshed by querying the coordination service for
+     * auto ingest manifest nodes.
+     * The auto ingest node data is refreshed by publishing a message asking
+     * all nodes to report their state.
      */
-    private final class CoordinationServiceQueryTask implements Runnable {
+    private final class StateRefreshTask implements Runnable {
 
-        /**
-         * Queries the coordination service for auto ingest manifest node data
-         * and converts it to auto ingest jobs for publication top its
-         * observers.
-         */
         @Override
         public void run() {
             if (!Thread.currentThread().isInterrupted()) {
-                synchronized (jobsLock) {
+                // Query coordination service for jobs data.
-                    jobsSnapshot = queryCoordinationService();
+                refreshJobsSnapshot();
-                    setChanged();
+
-                    notifyObservers(jobsSnapshot);
+                // Ask running auto ingest nodes to report their status.
-                }
+                refreshNodeState();
+
+                setChanged();
+                notifyObservers();
             }
         }
 
@@ -752,42 +777,12 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
      * A snapshot of the pending jobs queue, running jobs list and completed
      * jobs list for an auto ingest cluster.
      */
-    static final class JobsSnapshot {
+    private static final class JobsSnapshot {
 
         private final Set<AutoIngestJob> pendingJobs = new HashSet<>();
         private final Set<AutoIngestJob> runningJobs = new HashSet<>();
         private final Set<AutoIngestJob> completedJobs = new HashSet<>();
 
-        /**
-         * Gets the snapshot of the pending jobs queue for an auto ingest
-         * cluster.
-         *
-         * @return The pending jobs queue.
-         */
-        List<AutoIngestJob> getPendingJobs() {
-            return new ArrayList<>(this.pendingJobs);
-        }
-
-        /**
-         * Gets the snapshot of the running jobs list for an auto ingest
-         * cluster.
-         *
-         * @return The running jobs list.
-         */
-        List<AutoIngestJob> getRunningJobs() {
-            return new ArrayList<>(this.runningJobs);
-        }
-
-        /**
-         * Gets the snapshot of the completed jobs list for an auto ingest
-         * cluster.
-         *
-         * @return The completed jobs list.
-         */
-        List<AutoIngestJob> getCompletedJobs() {
-            return new ArrayList<>(this.completedJobs);
-        }
-
         /**
          * Adds an auto job to the snapshot of the pending jobs queue for an
          * auto ingest cluster. If an equivalent job already exists, it is
@@ -886,6 +881,7 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
 
         private final String nodeName;
         private final State nodeState;
+        private final Instant lastSeenTime;
 
         AutoIngestNodeState(String name, Event event) {
             nodeName = name;
@@ -915,6 +911,7 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
                     nodeState = State.UNKNOWN;
                     break;
             }
+            lastSeenTime = Instant.now();
         }
 
         String getName() {
@@ -924,6 +921,10 @@ final class AutoIngestMonitor extends Observable implements PropertyChangeListen
         State getState() {
             return nodeState;
         }
+
+        Instant getLastSeenTime() {
+            return lastSeenTime;
+        }
     }
 
     /**

Experimental/src/org/sleuthkit/autopsy/experimental/autoingest/AutoIngestNodeRefreshEvents.java

@@ -18,8 +18,6 @@
  */
 package org.sleuthkit.autopsy.experimental.autoingest;
 
-import org.sleuthkit.autopsy.experimental.autoingest.AutoIngestMonitor.JobsSnapshot;
-
 /**
  * Class which contains events to identify what should be refreshed in the
  * AutoIngestJobsNode
@@ -31,19 +29,20 @@ class AutoIngestNodeRefreshEvents {
      */
     static class AutoIngestRefreshEvent {
 
-        private final JobsSnapshot jobsSnapshot;
+        private final AutoIngestMonitor monitor;
 
-        AutoIngestRefreshEvent(JobsSnapshot jobs) {
+        AutoIngestRefreshEvent(AutoIngestMonitor monitor) {
-            this.jobsSnapshot = jobs;
+            this.monitor = monitor;
         }
 
         /**
-         * Get the state of the jobs lists when the event was fired.
+         * Get the monitor which will provide access to the state of
+         * the jobs.
          *
          * @return
          */
-        JobsSnapshot getJobsSnapshot() {
+        AutoIngestMonitor getMonitor() {
-            return this.jobsSnapshot;
+            return this.monitor;
         }
     }
 
@@ -56,8 +55,8 @@ class AutoIngestNodeRefreshEvents {
         /**
          * Constructs a RefreshChildrenEvent.
          */
-        RefreshChildrenEvent(JobsSnapshot jobs) {
+        RefreshChildrenEvent(AutoIngestMonitor monitor) {
-            super(jobs);
+            super(monitor);
         }
     }
 
@@ -72,11 +71,11 @@ class AutoIngestNodeRefreshEvents {
         /**
          * Contructs a RefreshCaseEvent
          *
-         * @param jobs The current state of the jobs lists.
+         * @param monitor The monitor that will provide access to the current state of the jobs lists.
          * @param name The name of the case whose nodes should be refreshed.
          */
-        RefreshCaseEvent(JobsSnapshot jobs, String name) {
+        RefreshCaseEvent(AutoIngestMonitor monitor, String name) {
-            super(jobs);
+            super(monitor);
             caseName = name;
         }
 
@@ -103,11 +102,11 @@ class AutoIngestNodeRefreshEvents {
         /**
          * Constructs a RefreshJobEvent.
          *
-         * @param jobs The curent state of the jobs lists.
+         * @param monitor The monitor which will provide access to the current state of the jobs lists.
          * @param job  The job which should be refreshed.
          */
-        RefreshJobEvent(JobsSnapshot jobs, AutoIngestJob job) {
+        RefreshJobEvent(AutoIngestMonitor monitor, AutoIngestJob job) {
-            super(jobs);
+            super(monitor);
             autoIngestJob = job;
         }
 

Experimental/src/org/sleuthkit/autopsy/experimental/autoingest/PrioritizationAction.java

@@ -145,7 +145,7 @@ abstract class PrioritizationAction extends AbstractAction {
 
         @Override
         AutoIngestNodeRefreshEvents.AutoIngestRefreshEvent getRefreshEvent(AutoIngestMonitor monitor) {
-            return new AutoIngestNodeRefreshEvents.RefreshJobEvent(monitor.getJobsSnapshot(), getJob());
+            return new AutoIngestNodeRefreshEvents.RefreshJobEvent(monitor, getJob());
         }
     }
 
@@ -184,7 +184,7 @@ abstract class PrioritizationAction extends AbstractAction {
 
         @Override
         AutoIngestNodeRefreshEvents.AutoIngestRefreshEvent getRefreshEvent(AutoIngestMonitor monitor) {
-            return new AutoIngestNodeRefreshEvents.RefreshJobEvent(monitor.getJobsSnapshot(), getJob());
+            return new AutoIngestNodeRefreshEvents.RefreshJobEvent(monitor, getJob());
         }
     }
 
@@ -225,7 +225,7 @@ abstract class PrioritizationAction extends AbstractAction {
 
         @Override
         AutoIngestNodeRefreshEvents.AutoIngestRefreshEvent getRefreshEvent(AutoIngestMonitor monitor) {
-            return new AutoIngestNodeRefreshEvents.RefreshCaseEvent(monitor.getJobsSnapshot(), getJob().getManifest().getCaseName());
+            return new AutoIngestNodeRefreshEvents.RefreshCaseEvent(monitor, getJob().getManifest().getCaseName());
         }
     }
 
@@ -266,7 +266,7 @@ abstract class PrioritizationAction extends AbstractAction {
 
         @Override
         AutoIngestNodeRefreshEvents.AutoIngestRefreshEvent getRefreshEvent(AutoIngestMonitor monitor) {
-            return new AutoIngestNodeRefreshEvents.RefreshCaseEvent(monitor.getJobsSnapshot(), getJob().getManifest().getCaseName());
+            return new AutoIngestNodeRefreshEvents.RefreshCaseEvent(monitor, getJob().getManifest().getCaseName());
         }
     }
 }

Experimental/src/org/sleuthkit/autopsy/experimental/objectdetection/ObjectDetectectionFileIngestModule.java

@@ -106,10 +106,22 @@ public class ObjectDetectectionFileIngestModule extends FileIngestModuleAdapter
             try {
                 imageInMemory = IOUtils.toByteArray(inputStream);
             } catch (IOException ex) {
-                logger.log(Level.WARNING, "Unable to perform object detection on " + file.getName(), ex);
+                logger.log(Level.WARNING, "Unable to read image to byte array for performing object detection on " + file.getParentPath() + file.getName() + " with object id of " + file.getId(), ex);
                 return IngestModule.ProcessResult.ERROR;
             }
-            Mat originalImage = Highgui.imdecode(new MatOfByte(imageInMemory), Highgui.IMREAD_GRAYSCALE);
+            Mat originalImage;
+            try {
+                originalImage = Highgui.imdecode(new MatOfByte(imageInMemory), Highgui.IMREAD_GRAYSCALE);
+            } catch (CvException ex) {
+                //The image was something which could not be decoded by OpenCv, our isImageThumbnailSupported(file) check above failed us
+                logger.log(Level.WARNING, "Unable to decode image from byte array to perform object detection on " + file.getParentPath() + file.getName() + " with object id of " + file.getId(), ex); //NON-NLS
+                return IngestModule.ProcessResult.ERROR;
+            } catch (Exception unexpectedException) {
+                //hopefully an unnecessary generic exception catch but currently present to catch any exceptions OpenCv throws which may not be documented
+                logger.log(Level.SEVERE, "Unexpected Exception encountered attempting to use OpenCV to decode picture: " + file.getParentPath() + file.getName() + " with object id of " + file.getId(), unexpectedException);
+                return IngestModule.ProcessResult.ERROR;
+            }
+
             MatOfRect detectionRectangles = new MatOfRect(); //the rectangles which reprent the coordinates on the image for where objects were detected
             for (String classifierKey : classifiers.keySet()) {
                 //apply each classifier to the file
@@ -117,7 +129,10 @@ public class ObjectDetectectionFileIngestModule extends FileIngestModuleAdapter
                     classifiers.get(classifierKey).detectMultiScale(originalImage, detectionRectangles);
                 } catch (CvException ignored) {
                     //The image was likely an image which we are unable to generate a thumbnail for, and the classifier was likely one where that is not acceptable
-                    logger.log(Level.INFO, String.format("Classifier '%s' could not be applied to file '%s'.", classifierKey, file.getParentPath() + file.getName())); //NON-NLS
+                    continue;
+                } catch (Exception unexpectedException) {  
+                    //hopefully an unnecessary generic exception catch but currently present to catch any exceptions OpenCv throws which may not be documented
+                    logger.log(Level.SEVERE, "Unexpected Exception encountered for image " + file.getParentPath() + file.getName() + " with object id of " + file.getId() +" while trying to apply classifier " + classifierKey, unexpectedException);
                     continue;
                 }
 

ImageGallery/src/org/sleuthkit/autopsy/imagegallery/ImageGalleryOptionsPanel.java

@@ -203,17 +203,20 @@ final class ImageGalleryOptionsPanel extends javax.swing.JPanel {
     }
 
     void store() {
-        Case openCase;
-        try {
-            openCase = Case.getCurrentCaseThrows();
-        } catch (NoCurrentCaseException ex) {
-            Logger.getLogger(ImageGalleryOptionsPanel.class.getName()).log(Level.SEVERE, "Exception while getting open case.", ex); //NON-NLS
-            return;
-        }
         ImageGalleryPreferences.setEnabledByDefault(enabledByDefaultBox.isSelected());
         ImageGalleryController.getDefault().setListeningEnabled(enabledForCaseBox.isSelected());
-        new PerCaseProperties(openCase).setConfigSetting(ImageGalleryModule.getModuleName(), PerCaseProperties.ENABLED, Boolean.toString(enabledForCaseBox.isSelected()));
         ImageGalleryPreferences.setGroupCategorizationWarningDisabled(groupCategorizationWarningBox.isSelected());
+
+        // If a case is open, save the per case setting
+        try {
+            Case openCase = Case.getCurrentCaseThrows();
+            new PerCaseProperties(openCase).setConfigSetting(ImageGalleryModule.getModuleName(), PerCaseProperties.ENABLED, Boolean.toString(enabledForCaseBox.isSelected()));
+        } catch (NoCurrentCaseException ex) {
+            // It's not an error if there's no case open
+        }
+        
+        
+        
     }
 
     /**

ImageGallery/src/org/sleuthkit/autopsy/imagegallery/datamodel/grouping/GroupManager.java

@@ -360,7 +360,7 @@ public class GroupManager {
                             groupConcatClause = " array_to_string(array_agg(obj_id), ',') as object_ids";
                         }
                         else {
-                            groupConcatClause = "select group_concat(obj_id) as object_ids";
+                            groupConcatClause = " group_concat(obj_id) as object_ids";
                         }
                         String query = "select " + groupConcatClause + " , mime_type from tsk_files group by mime_type ";
                         try (SleuthkitCase.CaseDbQuery executeQuery = controller.getSleuthKitCase().executeQuery(query); //NON-NLS

InternalPythonModules/android/browserlocation.py

@@ -105,7 +105,7 @@ class BrowserLocationAnalyzer(general.AndroidComponentAnalyzer):
                     blackboard = Case.getCurrentCase().getServices().getBlackboard()
                     blackboard.indexArtifact(artifact)
                 except Blackboard.BlackboardException as ex:
-                    self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + artifact.getArtifactTypeName(), ex)
+                    self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + str(artifact.getArtifactTypeName()), ex)
                     self._logger.log(Level.SEVERE, traceback.format_exc())
                     MessageNotifyUtil.Notify.error("Failed to index GPS trackpoint artifact for keyword search.", artifact.getDisplayName())
 

InternalPythonModules/android/cachelocation.py

@@ -138,7 +138,7 @@ class CacheLocationAnalyzer(general.AndroidComponentAnalyzer):
                     blackboard = Case.getCurrentCase().getServices().getBlackboard()
                     blackboard.indexArtifact(artifact)
                 except Blackboard.BlackboardException as ex:
-                    self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + artifact.getArtifactID(), ex)
+                    self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + str(artifact.getArtifactID()), ex)
                     self._logger.log(Level.SEVERE, traceback.format_exc())
                     MessageNotifyUtil.Notify.error("Failed to index GPS trackpoint artifact for keyword search.", artifact.getDisplayName())
 

InternalPythonModules/android/calllog.py

@@ -157,7 +157,7 @@ class CallLogAnalyzer(general.AndroidComponentAnalyzer):
                                 blackboard = Case.getCurrentCase().getServices().getBlackboard()
                                 blackboard.indexArtifact(artifact)
                             except Blackboard.BlackboardException as ex:
-                                self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + artifact.getArtifactID(), ex)
+                                self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + str(artifact.getArtifactID()), ex)
                                 self._logger.log(Level.SEVERE, traceback.format_exc())
                                 MessageNotifyUtil.Notify.error("Failed to index call log artifact for keyword search.", artifact.getDisplayName())
 

InternalPythonModules/android/contact.py

@@ -164,7 +164,7 @@ class ContactAnalyzer(general.AndroidComponentAnalyzer):
                     blackboard = Case.getCurrentCase().getServices().getBlackboard()
                     blackboard.indexArtifact(artifact)
                 except Blackboard.BlackboardException as ex:
-                    self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + artifact.getArtifactID(), ex)
+                    self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + str(artifact.getArtifactID()), ex)
                     self._logger.log(Level.SEVERE, traceback.format_exc())
                     MessageNotifyUtil.Notify.error("Failed to index contact artifact for keyword search.", artifact.getDisplayName())
 

InternalPythonModules/android/googlemaplocation.py

@@ -115,7 +115,7 @@ class GoogleMapLocationAnalyzer(general.AndroidComponentAnalyzer):
                     blackboard = Case.getCurrentCase().getServices().getBlackboard()
                     blackboard.indexArtifact(artifact)
                 except Blackboard.BlackboardException as ex:
-                    self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + artifact.getArtifactID(), ex)
+                    self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + str(artifact.getArtifactID()), ex)
                     self._logger.log(Level.SEVERE, traceback.format_exc())
                     MessageNotifyUtil.Notify.error("Failed to index GPS route artifact for keyword search.", artifact.getDisplayName())
 

InternalPythonModules/android/tangomessage.py

@@ -116,7 +116,7 @@ class TangoMessageAnalyzer(general.AndroidComponentAnalyzer):
                     blackboard = Case.getCurrentCase().getServices().getBlackboard()
                     blackboard.indexArtifact(artifact)
                 except Blackboard.BlackboardException as ex:
-                    self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + artifact.getArtifactID(), ex)
+                    self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + str(artifact.getArtifactID()), ex)
                     self._logger.log(Level.SEVERE, traceback.format_exc())
                     MessageNotifyUtil.Notify.error("Failed to index Tango message artifact for keyword search.", artifact.getDisplayName())
 

InternalPythonModules/android/textmessage.py

@@ -130,7 +130,7 @@ class TextMessageAnalyzer(general.AndroidComponentAnalyzer):
                     blackboard = Case.getCurrentCase().getServices().getBlackboard()
                     blackboard.indexArtifact(artifact)
                 except Blackboard.BlackboardException as ex:
-                    self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + artifact.getArtifactID(), ex)
+                    self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + str(artifact.getArtifactID()), ex)
                     self._logger.log(Level.SEVERE, traceback.format_exc())
                     MessageNotifyUtil.Notify.error("Failed to index text message artifact for keyword search.", artifact.getDisplayName())
 

InternalPythonModules/android/wwfmessage.py

@@ -125,7 +125,7 @@ class WWFMessageAnalyzer(general.AndroidComponentAnalyzer):
                     blackboard = Case.getCurrentCase().getServices().getBlackboard()
                     blackboard.indexArtifact(artifact)
                 except Blackboard.BlackboardException as ex:
-                    self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + artifact.getArtifactID(), ex)
+                    self._logger.log(Level.SEVERE, "Unable to index blackboard artifact " + str(artifact.getArtifactID()), ex)
                     self._logger.log(Level.SEVERE, traceback.format_exc())
                     MessageNotifyUtil.Notify.error("Failed to index WWF message artifact for keyword search.", artifact.getDisplayName())
 

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

@@ -43,7 +43,6 @@ abstract class AdHocSearchPanel extends javax.swing.JPanel {
     private final String keywordSearchErrorDialogHeader = org.openide.util.NbBundle.getMessage(this.getClass(), "AbstractKeywordSearchPerformer.search.dialogErrorHeader");
     protected int filesIndexed;
     private final Map<Long, String> dataSourceMap = new HashMap<>();
-    private final List<String> toolTipList = new ArrayList<>();
     private List<DataSource> dataSources = new ArrayList<>();
     private final DefaultListModel<String> dataSourceListModel = new DefaultListModel<>();
 
@@ -153,14 +152,12 @@ abstract class AdHocSearchPanel extends javax.swing.JPanel {
      */
     synchronized List<String> getDataSourceArray() {
         List<String> dsList = new ArrayList<>();
-        toolTipList.clear();
         Collections.sort(this.dataSources, (DataSource ds1, DataSource ds2) -> ds1.getName().compareTo(ds2.getName()));
         for (DataSource ds : dataSources) {
             String dsName = ds.getName();
             File dataSourceFullName = new File(dsName);
             String displayName = dataSourceFullName.getName();
             dataSourceMap.put(ds.getId(), displayName);
-            toolTipList.add(dsName);
             dsList.add(displayName);
         }
         return dsList;
@@ -175,22 +172,13 @@ abstract class AdHocSearchPanel extends javax.swing.JPanel {
     }
 
     /**
-     * Get dataSourceMap with object id and data source display name. Add the
+     * Get dataSourceMap with object id and data source display name.
-     * data source full name to toolTipList
      *
      * @return The list of data source name
      */
     Map<Long, String> getDataSourceMap() {
         return dataSourceMap;
     }
-
-    /**
-     * Get a list of tooltip text for data source
-     * @return A list of tool tips 
-     */
-    List<String> getDataSourceToolTipList() {
-        return toolTipList;
-    }
     
     /**
      * Get a list of DataSourceListModel

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

@@ -18,11 +18,11 @@
  */
 package org.sleuthkit.autopsy.keywordsearch;
 
-import java.awt.*;
+import java.awt.Component;
+import java.awt.Cursor;
+import java.awt.EventQueue;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseMotionListener;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.util.ArrayList;
@@ -32,7 +32,6 @@ import java.util.List;
 import java.util.Set;
 import java.util.logging.Level;
 import javax.swing.JCheckBox;
-import javax.swing.JList;
 import javax.swing.JTable;
 import javax.swing.ListSelectionModel;
 import javax.swing.event.ListSelectionEvent;
@@ -73,22 +72,6 @@ class DropdownListSearchPanel extends AdHocSearchPanel {
         dataSourceList.addListSelectionListener((ListSelectionEvent evt) -> {
             firePropertyChange(Bundle.DropdownSingleTermSearchPanel_selected(), null, null);
         });
-        dataSourceList.addMouseMotionListener(new MouseMotionListener() {
-
-            @Override
-            public void mouseDragged(MouseEvent evt) {
-                //Unused by now
-            }
-
-            @Override
-            public void mouseMoved(MouseEvent evt) {
-                JList<String> dsList = (JList<String>) evt.getSource();
-                int index = dsList.locationToIndex(evt.getPoint());
-                if (index > -1) {
-                    dsList.setToolTipText(getDataSourceToolTipList().get(index));
-                }
-            }
-        });
     }
 
     static synchronized DropdownListSearchPanel getDefault() {
@@ -683,11 +666,21 @@ class DropdownListSearchPanel extends AdHocSearchPanel {
      * Set the dataSourceList enabled if the dataSourceCheckBox is selected
      */
     private void setComponentsEnabled() {
-        boolean enabled = this.dataSourceCheckBox.isSelected();
+        
-        this.dataSourceList.setEnabled(enabled);
+        if (getDataSourceListModel().size() > 1) {
-        if (enabled) {
+            this.dataSourceCheckBox.setEnabled(true);
-            this.dataSourceList.setSelectionInterval(0, this.dataSourceList.getModel().getSize()-1);
+            
+            boolean enabled = this.dataSourceCheckBox.isSelected();
+            this.dataSourceList.setEnabled(enabled);
+            if (enabled) {
+                this.dataSourceList.setSelectionInterval(0, this.dataSourceList.getModel().getSize()-1);
+            } else {
+                this.dataSourceList.setSelectedIndices(new int[0]);
+            }
         } else {
+            this.dataSourceCheckBox.setEnabled(false);
+            this.dataSourceCheckBox.setSelected(false);
+            this.dataSourceList.setEnabled(false);
             this.dataSourceList.setSelectedIndices(new int[0]);
         }
     }

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

@@ -23,8 +23,6 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusEvent;
 import java.awt.event.FocusListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseMotionListener;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.util.ArrayList;
@@ -32,7 +30,6 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 import java.util.logging.Level;
-import javax.swing.JList;
 import javax.swing.JMenuItem;
 import javax.swing.event.ListSelectionEvent;
 import org.openide.util.NbBundle;
@@ -88,22 +85,6 @@ public class DropdownSingleTermSearchPanel extends AdHocSearchPanel {
         this.dataSourceList.addListSelectionListener((ListSelectionEvent evt) -> {
             firePropertyChange(Bundle.DropdownSingleTermSearchPanel_selected(), null, null);
         });
-        this.dataSourceList.addMouseMotionListener(new MouseMotionListener() {
-
-            @Override
-            public void mouseDragged(MouseEvent evt) {
-                //Unused by now
-            }
-
-            @Override
-            public void mouseMoved(MouseEvent evt) {
-                JList<String> DsList = (JList<String>) evt.getSource();
-                int index = DsList.locationToIndex(evt.getPoint());
-                if (index > -1) {
-                    DsList.setToolTipText(getDataSourceToolTipList().get(index));
-                }
-            }
-        });
     }
 
     /**
@@ -390,18 +371,26 @@ public class DropdownSingleTermSearchPanel extends AdHocSearchPanel {
         }
         setComponentsEnabled();
         firePropertyChange(Bundle.DropdownSingleTermSearchPanel_selected(), null, null);
-        
     }
     
     /**
      * Set the dataSourceList enabled if the dataSourceCheckBox is selected
      */
     private void setComponentsEnabled() {
-        boolean enabled = this.dataSourceCheckBox.isSelected();
+        if (getDataSourceListModel().size() > 1) {
-        this.dataSourceList.setEnabled(enabled);
+            this.dataSourceCheckBox.setEnabled(true);
-        if (enabled) {
+            
-            this.dataSourceList.setSelectionInterval(0, this.dataSourceList.getModel().getSize()-1);
+            boolean enabled = this.dataSourceCheckBox.isSelected();
+            this.dataSourceList.setEnabled(enabled);
+            if (enabled) {
+                this.dataSourceList.setSelectionInterval(0, this.dataSourceList.getModel().getSize()-1);
+            } else {
+                this.dataSourceList.setSelectedIndices(new int[0]);
+            }
         } else {
+            this.dataSourceCheckBox.setEnabled(false);
+            this.dataSourceCheckBox.setSelected(false);
+            this.dataSourceList.setEnabled(false);
             this.dataSourceList.setSelectedIndices(new int[0]);
         }
     }

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

@@ -28,7 +28,6 @@ import org.openide.util.NbBundle;
 import org.openide.util.NbBundle.Messages;
 import org.sleuthkit.autopsy.casemodule.Case;
 import org.sleuthkit.autopsy.casemodule.NoCurrentCaseException;
-import org.sleuthkit.autopsy.core.UserPreferences;
 import org.sleuthkit.autopsy.coreutils.Logger;
 import org.sleuthkit.autopsy.coreutils.MessageNotifyUtil;
 import org.sleuthkit.autopsy.ingest.FileIngestModule;
@@ -92,6 +91,7 @@ public final class KeywordSearchIngestModule implements FileIngestModule {
     private boolean startedSearching = false;
     private List<ContentTextExtractor> textExtractors;
     private StringsTextExtractor stringExtractor;
+    private TextFileExtractor txtFileExtractor;
     private final KeywordSearchJobSettings settings;
     private boolean initialized = false;
     private long jobId;
@@ -244,6 +244,8 @@ public final class KeywordSearchIngestModule implements FileIngestModule {
         stringExtractor.setScripts(KeywordSearchSettings.getStringExtractScripts());
         stringExtractor.setOptions(KeywordSearchSettings.getStringExtractOptions());
 
+        txtFileExtractor = new TextFileExtractor();
+
         textExtractors = new ArrayList<>();
         //order matters, more specific extractors first
         textExtractors.add(new HtmlTextExtractor());
@@ -343,7 +345,7 @@ public final class KeywordSearchIngestModule implements FileIngestModule {
         textExtractors.clear();
         textExtractors = null;
         stringExtractor = null;
-
+        txtFileExtractor = null;
         initialized = false;
     }
 
@@ -568,6 +570,17 @@ public final class KeywordSearchIngestModule implements FileIngestModule {
                 putIngestStatus(jobId, aFile.getId(), IngestStatus.SKIPPED_ERROR_TEXTEXTRACT);
             }
 
+            if ((wasTextAdded == false) && (aFile.getNameExtension().equalsIgnoreCase("txt"))) {
+                try {
+                    if (Ingester.getDefault().indexText(txtFileExtractor, aFile, context)) {
+                        putIngestStatus(jobId, aFile.getId(), IngestStatus.TEXT_INGESTED);
+                        wasTextAdded = true;
+                    }
+                } catch (IngesterException ex) {
+                    logger.log(Level.WARNING, "Unable to index as unicode", ex);
+                }
+            }
+
             // if it wasn't supported or had an error, default to strings
             if (wasTextAdded == false) {
                 extractStringsAndIndex(aFile);

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

@@ -1,15 +1,15 @@
 /*
  * Autopsy Forensic Browser
- * 
+ *
  * Copyright 2012-2014 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.
@@ -237,8 +237,19 @@ class SearchEngineURLQueryAnalyzer extends Extract {
         try { //try to decode the url
             String decoded = URLDecoder.decode(x, "UTF-8"); //NON-NLS
             return decoded;
-        } catch (UnsupportedEncodingException uee) { //if it fails, return the encoded string
+        } catch (UnsupportedEncodingException exception) { //if it fails, return the encoded string
-            logger.log(Level.FINE, "Error during URL decoding ", uee); //NON-NLS
+            logger.log(Level.FINE, "Error during URL decoding, returning undecoded value:"
+                    + "\n\tURL: " + url
+                    + "\n\tUndecoded value: " + x
+                    + "\n\tEngine name: " + eng.getEngineName()
+                    + "\n\tEngine domain: " + eng.getDomainSubstring(), exception); //NON-NLS
+            return x;
+        } catch (IllegalArgumentException exception) { //if it fails, return the encoded string
+            logger.log(Level.SEVERE, "Illegal argument passed to URL decoding, returning undecoded value:"
+                    + "\n\tURL: " + url
+                    + "\n\tUndecoded value: " + x
+                    + "\n\tEngine name: " + eng.getEngineName()
+                    + "\n\tEngine domain: " + eng.getDomainSubstring(), exception); //NON-NLS)
             return x;
         }
     }

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

@@ -86,11 +86,12 @@ class Util {
 
     public static String getBaseDomain(String url) {
         String host = null;
+        
         //strip protocol
-        String cleanUrl = url.replaceFirst("/.*:\\/\\//", "");
+        String cleanUrl = url.replaceFirst(".*:\\/\\/", "");
 
         //strip after slashes
-        String dirToks[] = cleanUrl.split("/\\//");
+        String dirToks[] = cleanUrl.split("\\/");
         if (dirToks.length > 0) {
             host = dirToks[0];
         } else {
@@ -141,7 +142,6 @@ class Util {
         if (result == null || result.trim().isEmpty()) {
             return getBaseDomain(value);
         }
-
         return result;
     }