Merge remote-tracking branch 'upstream/master' into fix4817

* upstream/master:
  Fix right clicking on any entry and selecting "Open folder" results in the NullPointer exception (#4797)
  Bump fontbox from 2.0.14 to 2.0.15 (#4882)
  Bump pdfbox from 2.0.14 to 2.0.15 (#4881)
  Bump xmpbox from 2.0.14 to 2.0.15 (#4883)
  Bump mockito-core from 2.26.0 to 2.27.0 (#4879)
  Bump java-string-similarity from 1.1.0 to 1.2.1 (#4878)
  Fix JabRef dying silently without enough inotify instances (#4875)
  #4795 disable menu item if database not connected (#4828)

Author: Siedlerchr

.mailmap

@@ -142,4 +142,5 @@ Johannes Manner <johannes.manner@web.de>
 Dominik Traczyk <dominik646@gmail.com>
 Cerrianne Santos <cerrianne.santos@gmail.com>
 Stefan Scheffel <st155160@stud.uni-stuttgart.de>
-Stefan Gerzmann <steppery@gmx.de>
+Stefan Gerzmann <steppery@gmx.de>
+Deepak Kumar <deepakkumar24196@gmail.com>

CHANGELOG.md

@@ -61,10 +61,12 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We changed the title of Group Dialog to "Add subgroup" from "Edit group" when we select Add subgroup option.
 - We enable import button only if entries are selected. [#4755](https://github.com/JabRef/jabref/issues/4755)
 - We made modifications to improve contrast of UI elements. [#4583](https://github.com/JabRef/jabref/issues/4583)
+- We added an option in the settings to set the default action in JabRef when right clicking on any entry in any database and selecting "Open folder". [#4763](https://github.com/JabRef/jabref/issues/4763)
 - The Medline fetcher now normalizes the author names according to the BibTeX-Standard [#4345](https://github.com/JabRef/jabref/issues/4345)
 
 
 ### Fixed
+- We fixed an issue where JabRef died silently for the user without enough inotify instances [#4874](https://github.com/JabRef/jabref/issues/4847)
 - We fixed an issue where corresponding groups are sometimes not highlighted when clicking on entries [#3112](https://github.com/JabRef/jabref/issues/3112)
 - We fixed an issue where custom exports could not be selected in the 'Export (selected) entries' dialog [#4013](https://github.com/JabRef/jabref/issues/4013)
 - Italic text is now rendered correctly. https://github.com/JabRef/jabref/issues/3356
@@ -104,13 +106,14 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where only one PDF file could be imported [#4422](https://github.com/JabRef/jabref/issues/4422)
 - We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
 - We fixed an issue where an older dialog appears when downloading full texts from the quality menu. [#4489](https://github.com/JabRef/jabref/issues/4489)
+- We fixed an issue where right clicking on any entry in any database and selecting "Open folder" results in the NullPointer exception. [#4763](https://github.com/JabRef/jabref/issues/4763)
+- We fixed an issue where option 'open terminal here' with custom command was passing wrong argument. [#4802](https://github.com/JabRef/jabref/issues/4802)
 - We fixed an issue where ranking an entry would generate an IllegalArgumentException. [#4754](https://github.com/JabRef/jabref/issues/4754)
 - We fixed an issue where special characters where removed from non label key generation pattern parts [#4767](https://github.com/JabRef/jabref/issues/4767)
 - We fixed an issue where the RIS import would overwite the article date with the value of the acessed date [#4816](https://github.com/JabRef/jabref/issues/4816)
 
 
 
-
 ### Removed
 - The feature to "mark entries" was removed and merged with the groups functionality.  For migration, a group is created for every value of the `__markedentry` field and the entry is added to this group.
 - The number column was removed.

build.gradle

@@ -95,9 +95,9 @@ dependencies {
     compile 'com.jgoodies:jgoodies-common:1.8.1'
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
 
-    compile 'org.apache.pdfbox:pdfbox:2.0.14'
-    compile 'org.apache.pdfbox:fontbox:2.0.14'
-    compile 'org.apache.pdfbox:xmpbox:2.0.14'
+    compile 'org.apache.pdfbox:pdfbox:2.0.15'
+    compile 'org.apache.pdfbox:fontbox:2.0.15'
+    compile 'org.apache.pdfbox:xmpbox:2.0.15'
 
     compile group: 'org.apache.tika', name: 'tika-core', version: '1.20'
 
@@ -112,7 +112,7 @@ dependencies {
     compile "org.libreoffice:unoil:6.2.2"
 
     compile 'io.github.java-diff-utils:java-diff-utils:4.0'
-    compile 'info.debatty:java-string-similarity:1.1.0'
+    compile 'info.debatty:java-string-similarity:1.2.1'
 
     antlr3 'org.antlr:antlr:3.5.2'
     compile 'org.antlr:antlr-runtime:3.5.2'
@@ -167,7 +167,7 @@ dependencies {
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
-    testCompile 'org.mockito:mockito-core:2.26.0'
+    testCompile 'org.mockito:mockito-core:2.27.0'
     testCompile 'com.github.tomakehurst:wiremock:2.22.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'

src/main/java/org/jabref/gui/JabRefFrame.java

@@ -100,7 +100,7 @@
 import org.jabref.gui.metadata.BibtexStringEditorAction;
 import org.jabref.gui.metadata.PreambleEditor;
 import org.jabref.gui.protectedterms.ManageProtectedTermsAction;
-import org.jabref.gui.push.PushToApplicationButton;
+import org.jabref.gui.push.PushToApplicationAction;
 import org.jabref.gui.push.PushToApplications;
 import org.jabref.gui.search.GlobalSearchBar;
 import org.jabref.gui.specialfields.SpecialFieldMenuItemFactory;
@@ -559,7 +559,8 @@ private Node createToolbar() {
         leftSide.setMinWidth(100);
         leftSide.prefWidthProperty().bind(sidePane.widthProperty());
         leftSide.maxWidthProperty().bind(sidePane.widthProperty());
-        PushToApplicationButton pushToExternal = new PushToApplicationButton(this, pushApplications.getApplications());
+
+        PushToApplicationAction pushToApplicationAction = new PushToApplicationAction(this, Globals.stateManager);
         HBox rightSide = new HBox(
                 factory.createIconButton(StandardActions.NEW_ARTICLE, new NewEntryAction(this, BiblatexEntryTypes.ARTICLE, dialogService, Globals.prefs)),
                 factory.createIconButton(StandardActions.DELETE_ENTRY, new OldDatabaseCommandWrapper(Actions.DELETE, this, Globals.stateManager)),
@@ -570,7 +571,7 @@ private Node createToolbar() {
                 factory.createIconButton(StandardActions.COPY, new OldDatabaseCommandWrapper(Actions.COPY, this, Globals.stateManager)),
                 factory.createIconButton(StandardActions.PASTE, new OldDatabaseCommandWrapper(Actions.PASTE, this, Globals.stateManager)),
                 new Separator(Orientation.VERTICAL),
-                factory.createIconButton(pushToExternal.getMenuAction(), pushToExternal),
+                factory.createIconButton(pushToApplicationAction.getActionInformation(), pushToApplicationAction),
                 factory.createIconButton(StandardActions.GENERATE_CITE_KEYS, new OldDatabaseCommandWrapper(Actions.MAKE_KEY, this, Globals.stateManager)),
                 factory.createIconButton(StandardActions.CLEANUP_ENTRIES, new OldDatabaseCommandWrapper(Actions.CLEANUP, this, Globals.stateManager)),
                 new Separator(Orientation.VERTICAL),
@@ -798,7 +799,7 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction(this, prefs))
         );
 
-        PushToApplicationButton pushToExternal = new PushToApplicationButton(this, pushApplications.getApplications());
+        final PushToApplicationAction pushToApplicationAction = new PushToApplicationAction(this, Globals.stateManager);
         tools.getItems().addAll(
                 factory.createMenuItem(StandardActions.NEW_SUB_LIBRARY_FROM_AUX, new NewSubLibraryAction(this)),
                 factory.createMenuItem(StandardActions.FIND_UNLINKED_FILES, new FindUnlinkedFilesAction(this)),
@@ -815,7 +816,7 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.GENERATE_CITE_KEYS, new OldDatabaseCommandWrapper(Actions.MAKE_KEY, this, Globals.stateManager)),
                 factory.createMenuItem(StandardActions.REPLACE_ALL, new OldDatabaseCommandWrapper(Actions.REPLACE_ALL, this, Globals.stateManager)),
                 factory.createMenuItem(StandardActions.SEND_AS_EMAIL, new OldDatabaseCommandWrapper(Actions.SEND_AS_EMAIL, this, Globals.stateManager)),
-                factory.createMenuItem(pushToExternal.getMenuAction(), pushToExternal),
+                factory.createMenuItem(pushToApplicationAction.getActionInformation(), pushToApplicationAction),
 
                 factory.createSubMenu(StandardActions.ABBREVIATE,
                         factory.createMenuItem(StandardActions.ABBREVIATE_ISO, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_ISO, this, Globals.stateManager)),

src/main/java/org/jabref/gui/actions/OldDatabaseCommandWrapper.java

@@ -14,7 +14,10 @@
 
 /**
  * A command that is only executable if a database is open.
+ * Deprecated use instead
+ * @see org.jabref.gui.actions.SimpleCommand
  */
+@Deprecated
 public class OldDatabaseCommandWrapper extends CommandBase {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(OldDatabaseCommandWrapper.class);

src/main/java/org/jabref/gui/desktop/JabRefDesktop.java

@@ -166,7 +166,33 @@ private static void openExternalFilePlatformIndependent(Optional<ExternalFileTyp
      * @throws IOException
      */
     public static void openFolderAndSelectFile(Path fileLink) throws IOException {
-        NATIVE_DESKTOP.openFolderAndSelectFile(fileLink);
+        if (fileLink == null) {
+            return;
+        }
+        boolean usingDefault = Globals.prefs.getBoolean(JabRefPreferences.USE_DEFAULT_FILE_BROWSER_APPLICATION);
+
+        if (usingDefault) {
+            NATIVE_DESKTOP.openFolderAndSelectFile(fileLink);
+        } else {
+            String absolutePath = fileLink.toAbsolutePath().getParent().toString();
+            String command = Globals.prefs.get(JabRefPreferences.FILE_BROWSER_COMMAND);
+            if (!command.isEmpty()) {
+                command = command.replaceAll("\\s+", " "); // normalize white spaces
+
+                // replace the placeholder if used
+                command = command.replace("%DIR", absolutePath);
+                String[] subcommands = command.split(" ");
+
+                LOGGER.info("Executing command \"" + command + "\"...");
+
+                try {
+                    new ProcessBuilder(subcommands).start();
+                } catch (IOException exception) {
+                    LOGGER.error("Open File Browser", exception);
+                    JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Error occured while executing the command \"%0\".", command));
+                }
+            }
+        }
     }
 
     /**
@@ -228,22 +254,19 @@ public static void openConsole(File file) throws IOException {
 
             if (!command.isEmpty()) {
                 command = command.replaceAll("\\s+", " "); // normalize white spaces
-                String[] subcommands = command.split(" ");
+                command = command.replace("%DIR", absolutePath); // replace the placeholder if used
 
-                // replace the placeholder if used
-                String commandLoggingText = command.replace("%DIR", absolutePath);
+                String[] subcommands = command.split(" ");
 
+                LOGGER.info("Executing command \"" + command + "\"...");
                 JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Executing command \"%0\"...", commandLoggingText));
-                LOGGER.info("Executing command \"" + commandLoggingText + "\"...");
 
                 try {
                     new ProcessBuilder(subcommands).start();
                 } catch (IOException exception) {
                     LOGGER.error("Open console", exception);
 
-                    JabRefGUI.getMainFrame().getDialogService().showErrorDialogAndWait(
-                            Localization.lang("Open console") + " - " + Localization.lang("Error",
-                            Localization.lang("Error occured while executing the command \"%0\".", commandLoggingText)));
+                    JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Error occured while executing the command \"%0\".", command));
                 }
             }
         }

src/main/java/org/jabref/gui/desktop/os/Linux.java

@@ -51,18 +51,18 @@ public void openFileWithApplication(String filePath, String application) throws
 
     @Override
     public void openFolderAndSelectFile(Path filePath) throws IOException {
-        String desktopSession = System.getenv("DESKTOP_SESSION").toLowerCase(Locale.ROOT);
+        String desktopSession = System.getenv("DESKTOP_SESSION");
 
-        String cmd;
+        String cmd = "xdg-open " + filePath.toAbsolutePath().getParent().toString(); //default command
 
-        if (desktopSession.contains("gnome")) {
-            cmd = "nautilus" + filePath.toString().replace(" ", "\\ ");
-        } else if (desktopSession.contains("kde")) {
-            cmd = "dolphin --select " + filePath.toString().replace(" ", "\\ ");
-        } else {
-            cmd = "xdg-open " + filePath.toAbsolutePath().getParent().toString();
+        if (desktopSession != null) {
+            desktopSession = desktopSession.toLowerCase(Locale.ROOT);
+            if (desktopSession.contains("gnome")) {
+                cmd = "nautilus" + filePath.toString().replace(" ", "\\ ");
+            } else if (desktopSession.contains("kde")) {
+                cmd = "dolphin --select " + filePath.toString().replace(" ", "\\ ");
+            }
         }
-
         Runtime.getRuntime().exec(cmd);
     }
 
@@ -73,7 +73,6 @@ public void openConsole(String absolutePath) throws IOException {
         BufferedReader reader = new BufferedReader(new InputStreamReader(p.getInputStream()));
 
         String emulatorName = reader.readLine();
-
         if (emulatorName != null) {
             emulatorName = emulatorName.substring(emulatorName.lastIndexOf(File.separator) + 1);
 

src/main/java/org/jabref/gui/preferences/ExternalTab.java

@@ -20,6 +20,7 @@
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.OS;
+import org.jabref.model.strings.StringUtil;
 import org.jabref.preferences.JabRefPreferences;
 
 class ExternalTab implements PrefsTab {
@@ -38,6 +39,12 @@ class ExternalTab implements PrefsTab {
     private final RadioButton sumatraReader;
     private final TextField adobeAcrobatReaderPath;
     private final TextField sumatraReaderPath;
+
+    private final RadioButton defaultFileBrowser;
+    private final RadioButton executeFileBrowser;
+    private final TextField fileBrowserCommand;
+    private final Button fileBrowserButton;
+
     private final GridPane builder = new GridPane();
     private final DialogService dialogService;
     private final FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder().build();
@@ -59,11 +66,20 @@ public ExternalTab(JabRefFrame frame, PreferencesDialog prefsDiag, JabRefPrefere
         sumatraReaderPath = new TextField();
         Button browseSumatraReader = new Button(Localization.lang("Browse"));
 
+        defaultFileBrowser = new RadioButton(Localization.lang("Use default file browser"));
+        executeFileBrowser = new RadioButton(Localization.lang("Execute Command"));
+        fileBrowserCommand = new TextField();
+        fileBrowserButton = new Button(Localization.lang("Browser"));
+
         Label commandDescription = new Label(Localization.lang("Note: Use the placeholder %0 for the location of the opened library file.", "%DIR"));
         defaultConsole.setOnAction(e -> updateExecuteConsoleButtonAndFieldEnabledState());
         executeConsole.setOnAction(e -> updateExecuteConsoleButtonAndFieldEnabledState());
         browseButton.setOnAction(e -> showConsoleChooser());
 
+        fileBrowserButton.disableProperty().bind(executeFileBrowser.selectedProperty().not());
+        fileBrowserCommand.disableProperty().bind(executeFileBrowser.selectedProperty().not());
+        fileBrowserButton.setOnAction(e -> showFileBrowserCommandChooser());
+
         browseAdobeAcrobatReader.setOnAction(e -> showAdobeChooser());
 
         GridPane consoleOptionPanel = new GridPane();
@@ -83,6 +99,17 @@ public ExternalTab(JabRefFrame frame, PreferencesDialog prefsDiag, JabRefPrefere
         adobeAcrobatReader.setToggleGroup(pdfReaderGroup);
         pdfOptionPanel.add(browseAdobeAcrobatReader, 3, 1);
 
+        Label fileBrowserCommandDescription = new Label(Localization.lang("Note: Use the placeholder %0 for the location of the opened library file.", "%DIR"));
+        GridPane fileBrowserOptionPanel = new GridPane();
+        final ToggleGroup fileBrowserGroup = new ToggleGroup();
+        defaultFileBrowser.setToggleGroup(fileBrowserGroup);
+        executeFileBrowser.setToggleGroup(fileBrowserGroup);
+        fileBrowserOptionPanel.add(defaultFileBrowser, 1, 1);
+        fileBrowserOptionPanel.add(executeFileBrowser, 1, 2);
+        fileBrowserOptionPanel.add(fileBrowserCommand, 2, 2);
+        fileBrowserOptionPanel.add(fileBrowserButton, 3, 2);
+        fileBrowserOptionPanel.add(fileBrowserCommandDescription, 2, 3);
+
         if (OS.WINDOWS) {
             browseSumatraReader.setOnAction(e -> showSumatraChooser());
             pdfOptionPanel.add(sumatraReader, 1, 2);
@@ -133,6 +160,12 @@ public ExternalTab(JabRefFrame frame, PreferencesDialog prefsDiag, JabRefPrefere
 
         builder.add(pdfOptionPanel, 1, 13);
 
+        Label openFileBrowser = new Label(Localization.lang("Open File Browser"));
+        openFileBrowser.getStyleClass().add("sectionHeader");
+        builder.add(openFileBrowser,  1, 14);
+
+        builder.add(fileBrowserOptionPanel, 1, 15);
+
     }
 
     @Override
@@ -165,6 +198,10 @@ public void setValues() {
 
         consoleCommand.setText(Globals.prefs.get(JabRefPreferences.CONSOLE_COMMAND));
 
+        defaultFileBrowser.setSelected(Globals.prefs.getBoolean(JabRefPreferences.USE_DEFAULT_FILE_BROWSER_APPLICATION));
+        executeFileBrowser.setSelected(!Globals.prefs.getBoolean(JabRefPreferences.USE_DEFAULT_FILE_BROWSER_APPLICATION));
+        fileBrowserCommand.setText(Globals.prefs.get(JabRefPreferences.FILE_BROWSER_COMMAND));
+
         adobeAcrobatReaderPath.setText(Globals.prefs.get(JabRefPreferences.ADOBE_ACROBAT_COMMAND));
         if (OS.WINDOWS) {
             sumatraReaderPath.setText(Globals.prefs.get(JabRefPreferences.SUMATRA_PDF_COMMAND));
@@ -187,6 +224,13 @@ public void storeSettings() {
         prefs.putBoolean(JabRefPreferences.USE_DEFAULT_CONSOLE_APPLICATION, defaultConsole.isSelected());
         prefs.put(JabRefPreferences.CONSOLE_COMMAND, consoleCommand.getText());
         prefs.put(JabRefPreferences.ADOBE_ACROBAT_COMMAND, adobeAcrobatReaderPath.getText());
+
+        prefs.putBoolean(JabRefPreferences.USE_DEFAULT_FILE_BROWSER_APPLICATION, defaultFileBrowser.isSelected());
+        if (StringUtil.isNotBlank(fileBrowserCommand.getText())) {
+            prefs.put(JabRefPreferences.FILE_BROWSER_COMMAND, fileBrowserCommand.getText());
+        } else {
+            prefs.putBoolean(JabRefPreferences.USE_DEFAULT_FILE_BROWSER_APPLICATION, true); //default if no command specified
+        }
         if (OS.WINDOWS) {
             prefs.put(JabRefPreferences.SUMATRA_PDF_COMMAND, sumatraReaderPath.getText());
         }
@@ -220,6 +264,10 @@ private void showSumatraChooser() {
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> sumatraReaderPath.setText(file.toAbsolutePath().toString()));
     }
 
+    private void showFileBrowserCommandChooser() {
+        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> fileBrowserCommand.setText(file.toAbsolutePath().toString()));
+    }
+
     private void readerSelected() {
         if (adobeAcrobatReader.isSelected()) {
             prefs.put(JabRefPreferences.USE_PDF_READER, adobeAcrobatReaderPath.getText());