[WIP] Show PDF-Comments in JabRef

build.gradle

@@ -108,6 +108,7 @@ dependencies {
     compile 'commons-logging:commons-logging:1.2'
 
     compile 'org.apache.commons:commons-lang3:3.4'
+    compile 'org.apache.commons:commons-collections4:4.0'
 
     compile 'org.jsoup:jsoup:1.9.2'
     compile 'com.mashape.unirest:unirest-java:1.4.9'

src/main/java/net/sf/jabref/gui/BasePanel.java

@@ -105,6 +105,7 @@
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.logic.layout.Layout;
 import net.sf.jabref.logic.layout.LayoutHelper;
+import net.sf.jabref.logic.pdf.FileAnnotationCache;
 import net.sf.jabref.logic.search.SearchQuery;
 import net.sf.jabref.logic.util.FileExtensions;
 import net.sf.jabref.logic.util.UpdateField;
@@ -156,6 +157,7 @@ public class BasePanel extends JPanel implements ClipboardOwner, FileUpdateListe
     private final MainTableDataModel tableModel;
 
     private final CitationStyleCache citationStyleCache;
+    private final FileAnnotationCache annotationCache;
 
     // To contain instantiated entry editors. This is to save time
     // As most enums, this must not be null
@@ -224,6 +226,7 @@ public BasePanel(JabRefFrame frame, BibDatabaseContext bibDatabaseContext) {
         this.tableModel = new MainTableDataModel(getBibDatabaseContext());
 
         citationStyleCache = new CitationStyleCache(bibDatabaseContext);
+        annotationCache = new FileAnnotationCache(bibDatabaseContext);
 
         setupMainPanel();
 
@@ -2415,6 +2418,10 @@ public CitationStyleCache getCitationStyleCache() {
         return citationStyleCache;
     }
 
+    public FileAnnotationCache getAnnotationCache() {
+        return annotationCache;
+    }
+
     public PreviewPanel getPreviewPanel() {
         if (selectionListener == null) {
             // only occurs if this is called while instantiating this BasePanel

src/main/java/net/sf/jabref/gui/IconTheme.java

@@ -81,9 +81,11 @@ public enum JabRefIcon {
         PASTE("\uf192") /*css: content-paste*/,
         CUT("\uf190") /*css: content-cut*/,
         COPY("\uf18f") /*css: content-copy */,
+        COMMENT("\uF188") /*css: comment*/,
         REDO("\uf44e") /*css: redo*/,
         UNDO("\uf54c") /*css: undo*/,
         MARK_ENTRIES("\uf0c0") /*css: bookmark */,
+        MARKER("\uF524") /*css: marker */,
         UNMARK_ENTRIES("\uf0c3") /*css: bookmark-outline */,
         REFRESH("\uf450") /*css: refresh */,
         DELETE_ENTRY("\uf1c0") /*css: delete */,

src/main/java/net/sf/jabref/gui/desktop/os/DefaultDesktop.java

@@ -4,6 +4,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Paths;
+import java.util.List;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -32,6 +33,11 @@ public void openConsole(String absolutePath) throws IOException {
         LOGGER.error("This feature is not supported by your Operating System.");
     }
 
+    @Override
+    public void openPdfWithParameters(String filePath, List<String> parameters) throws IOException {
+        //TODO imlement default
+    }
+
     @Override
     public String detectProgramPath(String programName, String directoryName) {
         return programName;

src/main/java/net/sf/jabref/gui/desktop/os/Linux.java

@@ -5,10 +5,16 @@
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.nio.file.Paths;
+import java.util.List;
 import java.util.Optional;
+import java.util.StringJoiner;
 
 import net.sf.jabref.gui.externalfiletype.ExternalFileType;
 import net.sf.jabref.gui.externalfiletype.ExternalFileTypes;
+import net.sf.jabref.preferences.JabRefPreferences;
+
+import static net.sf.jabref.preferences.JabRefPreferences.ADOBE_ACROBAT_COMMAND;
+import static net.sf.jabref.preferences.JabRefPreferences.USE_PDF_READER;
 
 public class Linux implements NativeDesktop {
     @Override
@@ -81,6 +87,23 @@ public void openConsole(String absolutePath) throws IOException {
         }
     }
 
+    @Override
+    public void openPdfWithParameters(String filePath, List<String> parameters) throws IOException {
+
+        String application;
+        if(JabRefPreferences.getInstance().get(USE_PDF_READER).equals(JabRefPreferences.getInstance().get(ADOBE_ACROBAT_COMMAND))){
+            application = "acroread";
+
+            StringJoiner sj = new StringJoiner(" ");
+            sj.add(application);
+            parameters.forEach((param) -> sj.add(param));
+
+            openFileWithApplication(filePath, sj.toString());
+        } else {
+            openFile( filePath, "PDF");
+        }
+    }
+
     @Override
     public String detectProgramPath(String programName, String directoryName) {
         return programName;

src/main/java/net/sf/jabref/gui/desktop/os/NativeDesktop.java

@@ -1,6 +1,7 @@
 package net.sf.jabref.gui.desktop.os;
 
 import java.io.IOException;
+import java.util.List;
 
 public interface NativeDesktop {
     void openFile(String filePath, String fileType) throws IOException;
@@ -18,5 +19,13 @@ public interface NativeDesktop {
 
     void openConsole(String absolutePath) throws IOException;
 
+    /**
+     * This method opens a pdf using the giving the parameters to the executing pdf reader
+     * @param filePath absolute path to the pdf file to be opened
+     * @param parameters console parameters depending on the pdf reader
+     * @throws IOException
+     */
+    void openPdfWithParameters(String filePath, List<String> parameters) throws  IOException;
+
     String detectProgramPath(String programName, String directoryName);
 }

src/main/java/net/sf/jabref/gui/desktop/os/OSX.java

@@ -3,6 +3,7 @@
 import java.awt.Desktop;
 import java.io.File;
 import java.io.IOException;
+import java.util.List;
 import java.util.Optional;
 
 import net.sf.jabref.gui.externalfiletype.ExternalFileType;
@@ -40,6 +41,11 @@ public void openConsole(String absolutePath) throws IOException {
         Runtime.getRuntime().exec("open -a Terminal " + absolutePath, null, new File(absolutePath));
     }
 
+    @Override
+    public void openPdfWithParameters(String filePath, List<String> parameters) throws IOException {
+        //TODO implement
+    }
+
     @Override
     public String detectProgramPath(String programName, String directoryName) {
         return programName;

src/main/java/net/sf/jabref/gui/desktop/os/Windows.java

@@ -3,10 +3,16 @@
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Paths;
+import java.util.List;
 import java.util.Optional;
 
 import net.sf.jabref.gui.externalfiletype.ExternalFileType;
 import net.sf.jabref.gui.externalfiletype.ExternalFileTypes;
+import net.sf.jabref.preferences.JabRefPreferences;
+
+import static net.sf.jabref.preferences.JabRefPreferences.ADOBE_ACROBAT_COMMAND;
+import static net.sf.jabref.preferences.JabRefPreferences.SUMATRA_PDF_COMMAND;
+import static net.sf.jabref.preferences.JabRefPreferences.USE_PDF_READER;
 
 public class Windows implements NativeDesktop {
     private static String DEFAULT_EXECUTABLE_EXTENSION = ".exe";
@@ -52,4 +58,20 @@ public void openConsole(String absolutePath) throws IOException {
         process.directory(new File(absolutePath));
         process.start();
     }
+
+    @Override
+    public void openPdfWithParameters(String filePath, List<String> parameters) throws IOException {
+        String pdfReaderPath = JabRefPreferences.getInstance().get(USE_PDF_READER);
+        if (pdfReaderPath.equals(SUMATRA_PDF_COMMAND) || pdfReaderPath.equals(ADOBE_ACROBAT_COMMAND)) {
+            String[] command = new String[parameters.size() + 2];
+            command[0] = "\"" + Paths.get(pdfReaderPath).toString() + "\"";
+            for (int i = 1; i < command.length - 1; i++) {
+                command[i] = "\"" + parameters.get(i - 1) + "\"";
+            }
+            command[command.length - 1] = "\"" + filePath + "\"";
+            new ProcessBuilder(command).start();
+        } else {
+            openFile(filePath, "PDF");
+        }
+    }
 }

src/main/java/net/sf/jabref/gui/entryeditor/EntryEditor.java

@@ -158,6 +158,8 @@ public class EntryEditor extends JPanel implements EntryContainer {
 
     private final BasePanel panel;
 
+    private FileAnnotationTab fileAnnotationTab;
+
     private boolean updateSource = true; // This can be set to false to stop the source
     private boolean movingToDifferentEntry; // Indicates that we are about to go to the next or previous entry
     private boolean validEntry = true;
@@ -226,7 +228,6 @@ public EntryEditor(JabRefFrame frame, BasePanel panel, BibEntry entry) {
     private void setupFieldPanels() {
         tabbed.removeAll();
         tabs.clear();
-
         EntryType type = EntryTypes.getTypeOrDefault(entry.getType(),
                 this.frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
 
@@ -310,6 +311,7 @@ private void setupFieldPanels() {
         addGeneralTabs();
         // source tab
         addSourceTab();
+        addPdfTab();
     }
 
     private void addGeneralTabs() {
@@ -332,7 +334,7 @@ private void addSourceTab() {
         tabbed.addTab(panelName, IconTheme.JabRefIcon.SOURCE.getSmallIcon(), srcPanel, toolTip);
         tabs.add(srcPanel);
         sourceIndex = tabs.size() - 1; // Set the sourceIndex variable.
-        srcPanel.setFocusCycleRoot(true);
+        srcPanel.setFocusCycleRoot(false);
     }
 
     private void addOtherTab(List<String> otherFields) {
@@ -371,6 +373,22 @@ private void addOptionalTab(EntryType type) {
         tabs.add(optionalPanel);
     }
 
+    /**
+     * Add a tab for displaying comments from a PDF
+     */
+    private void addPdfTab() {
+        tabbed.remove(fileAnnotationTab);
+        tabs.remove(fileAnnotationTab);
+        Optional<String> field = entry.getField(FieldName.FILE);
+        if (field.isPresent()) {
+            fileAnnotationTab = new FileAnnotationTab(this, panel, tabbed);
+            tabbed.addTab(Localization.lang("File annotations"), IconTheme.JabRefIcon.COMMENT.getSmallIcon(), fileAnnotationTab,
+                    Localization.lang("Show file annotations"));
+            tabs.add(fileAnnotationTab);
+        }
+
+    }
+
     public String getDisplayedBibEntryType() {
         return displayedBibEntryType;
     }
@@ -469,7 +487,6 @@ public void rebuildPanels() {
         // Remove change listener, because the rebuilding causes meaningless
         // events and trouble:
         tabbed.removeChangeListener(tabListener);
-
         setupFieldPanels();
         // Add the change listener again:
         tabbed.addChangeListener(tabListener);
@@ -651,9 +668,10 @@ public void requestFocus() {
 
     private void activateVisible() {
         Object activeTab = tabs.get(tabbed.getSelectedIndex());
-
         if (activeTab instanceof EntryEditorTab) {
             ((EntryEditorTab) activeTab).activate();
+        } else if (activeTab instanceof FileAnnotationTab) {
+            ((FileAnnotationTab)activeTab).requestFocus();
         } else {
             source.requestFocus();
         }
@@ -765,6 +783,7 @@ public synchronized void switchTo(BibEntry switchEntry) {
         validateAllFields();
         updateSource();
         panel.newEntryShowing(switchEntry);
+        addPdfTab();
 
     }
 
@@ -922,6 +941,7 @@ public void validateAllFields() {
             if (tab instanceof EntryEditorTab) {
                 ((EntryEditorTab) tab).validateAllFields();
             }
+
         }
     }
 
@@ -1032,6 +1052,13 @@ public void stateChanged(ChangeEvent event) {
             // or more of the same fields as this one:
             SwingUtilities.invokeLater(() -> {
                 Object activeTab = tabs.get(tabbed.getSelectedIndex());
+                if (activeTab instanceof FileAnnotationTab && !((FileAnnotationTab) activeTab).isInitialized()) {
+                    //Initialize by getting notes from cache if they are cached
+                    FileAnnotationTab.initializeTab((FileAnnotationTab) activeTab,
+                            panel.getAnnotationCache().getFromCache(Optional.of(entry)));
+                    panel.getAnnotationCache().addToCache(entry, ((FileAnnotationTab) activeTab).getAllNotes());
+                }
+
                 if (activeTab instanceof EntryEditorTab) {
                     ((EntryEditorTab) activeTab).updateAll();
                     activateVisible();
@@ -1040,6 +1067,7 @@ public void stateChanged(ChangeEvent event) {
         }
     }
 
+
     class DeleteAction extends AbstractAction {
         public DeleteAction() {
             super(Localization.lang("Delete"), IconTheme.JabRefIcon.DELETE_ENTRY.getIcon());

src/main/java/net/sf/jabref/gui/entryeditor/EntryEditorTabbedPane.java

@@ -0,0 +1,18 @@
+package net.sf.jabref.gui.entryeditor;
+
+import javax.swing.JTabbedPane;
+
+public class EntryEditorTabbedPane extends JTabbedPane {
+
+    private FileAnnotationTab pdfTab;
+
+    public EntryEditorTabbedPane() {
+        super();
+    }
+
+    public void hidePdfTab(FileAnnotationTab pdfTab){
+        this.pdfTab = pdfTab;
+        this.remove(pdfTab);
+    }
+
+}