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

* upstream/master: Try to update to gradle 5.0.2 (#4766) Post change notifications on JavaFX (#4871) fix missing l10n from previous merge fix compile error 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) # Conflicts: # src/main/resources/l10n/JabRef_en.properties
JabRef · Apr 14, 2019 · 3dfdf20 · 3dfdf20
2 parents 2bb6fe8 + 7a190c9
commit 3dfdf20
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diff --git a/.mailmap b/.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>
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -61,6 +61,7 @@ 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)
 
 
@@ -105,13 +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.

diff --git a/build.gradle b/build.gradle
@@ -15,20 +15,18 @@ buildscript {
 }
 
 plugins {
-    id 'com.gradle.build-scan' version '1.16'
-    id 'com.install4j.gradle' version '7.0.9'
-    id 'com.github.johnrengelman.shadow' version '4.0.2'
+    id 'com.gradle.build-scan' version '2.0.2'
+    id 'com.install4j.gradle' version '7.0.10'
+    id 'com.github.johnrengelman.shadow' version '5.0.0'
     id "com.simonharrer.modernizer" version '1.6.0-1'
     id 'me.champeau.gradle.jmh' version '0.4.8'
-    id 'net.ltgt.errorprone' version '0.6.1'
-    id 'com.github.ben-manes.versions' version '0.20.0'
+    id 'net.ltgt.errorprone' version '0.7.1'
+    id 'com.github.ben-manes.versions' version '0.21.0'
 }
 
 // use the gradle build scan feature: https://scans.gradle.com/get-started
-buildScan {
-    licenseAgreementUrl = 'https://gradle.com/terms-of-service'
-    licenseAgree = 'yes'
-}
+buildScan { termsOfServiceUrl = 'https://gradle.com/terms-of-service'; termsOfServiceAgree = 'yes' }
+
 
 apply plugin: 'java'
 apply plugin: 'application'
@@ -95,9 +93,9 @@ 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'
 
@@ -129,9 +127,10 @@ dependencies {
     compile 'com.google.guava:guava:27.1-jre'
 
     // JavaFX stuff
+    compile 'de.jensd:fontawesomefx-commons:8.15'
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
     compile 'de.saxsys:mvvmfx-validation:1.8.0'
-    compile 'de.saxsys:mvvmfx:1.7.0'
+    compile 'de.saxsys:mvvmfx:1.8.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
     compile 'org.fxmisc.flowless:flowless:0.6.1'
     compile 'org.fxmisc.richtext:richtextfx:0.9.3'
@@ -196,11 +195,6 @@ dependencyUpdates.resolutionStrategy = {
                 selection.reject("Ignore SNAPSHOT releases")
             }
         }
-        rules.withModule("com.gradle.build-scan:com.gradle.build-scan.gradle.plugin") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /2.*/) {
-                selection.reject("Cannot be upgraded to version 2 until we upgrade to gradle 5")
-            }
-        }
         rules.withModule("org.controlsfx:controlsfx") { ComponentSelection selection ->
             if (selection.candidate.version ==~ /9.*/) { // Reject version 9 or higher
                 selection.reject("Cannot be updated to 9.*.* until Jabref works with Java 9")
@@ -322,11 +316,14 @@ task generateSearchGrammarSource(type: JavaExec) {
 compileJava {
     options.encoding = 'UTF-8'
     options.compilerArgs << "-Xlint:none"
+    //ignore annotation processor from log4j2
+    options.compilerArgs += '-proc:none'
 }
 compileJava.dependsOn "generateSource"
 
 compileTestJava {
     options.encoding = 'UTF-8'
+    options.compilerArgs += '-proc:none'
 }
 
 javadoc {

diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.10.2-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-5.3.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
@@ -255,7 +255,7 @@ public void output(String s) {
 
     private void setupActions() {
         SaveDatabaseAction saveAction = new SaveDatabaseAction(this, Globals.prefs);
-        CleanupAction cleanUpAction = new CleanupAction(this, Globals.prefs);
+        CleanupAction cleanUpAction = new CleanupAction(this, Globals.prefs, Globals.TASK_EXECUTOR);
 
         actions.put(Actions.UNDO, undoAction);
         actions.put(Actions.REDO, redoAction);

diff --git a/src/main/java/org/jabref/gui/actions/CleanupAction.java b/src/main/java/org/jabref/gui/actions/CleanupAction.java
@@ -9,6 +9,8 @@
 import org.jabref.gui.cleanup.CleanupDialog;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableFieldChange;
+import org.jabref.gui.util.BackgroundTask;
+import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.cleanup.CleanupPreset;
 import org.jabref.logic.cleanup.CleanupWorker;
 import org.jabref.logic.l10n.Localization;
@@ -20,15 +22,17 @@ public class CleanupAction implements BaseAction {
 
     private final BasePanel panel;
     private final DialogService dialogService;
+    private final TaskExecutor taskExecutor;
 
     private boolean isCanceled;
     private int modifiedEntriesCount;
     private final JabRefPreferences preferences;
 
-    public CleanupAction(BasePanel panel, JabRefPreferences preferences) {
+    public CleanupAction(BasePanel panel, JabRefPreferences preferences, TaskExecutor taskExecutor) {
         this.panel = panel;
         this.preferences = preferences;
         this.dialogService = panel.frame().getDialogService();
+        this.taskExecutor = taskExecutor;
     }
 
     @Override
@@ -58,8 +62,9 @@ public void action() {
 
             preferences.setCleanupPreset(chosenPreset.get());
 
-            this.cleanup(chosenPreset.get());
-            this.showResults();
+            BackgroundTask.wrap(() -> cleanup(chosenPreset.get()))
+                          .onSuccess(result -> showResults())
+                          .executeWith(taskExecutor);
         }
     }
 

diff --git a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java b/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(" ");
 
-                JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Executing command \"%0\"...", commandLoggingText));
-                LOGGER.info("Executing command \"" + commandLoggingText + "\"...");
+                LOGGER.info("Executing command \"" + command + "\"...");
+                JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Executing command \"%0\"...", command));
 
                 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));
                 }
             }
         }

diff --git a/src/main/java/org/jabref/gui/desktop/os/Linux.java b/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);
 

diff --git a/src/main/java/org/jabref/gui/maintable/MainTable.java b/src/main/java/org/jabref/gui/maintable/MainTable.java
@@ -36,6 +36,7 @@
 import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableInsertEntry;
+import org.jabref.gui.util.BindingsHelper;
 import org.jabref.gui.util.CustomLocalDragboard;
 import org.jabref.gui.util.ViewModelTableRowFactory;
 import org.jabref.logic.l10n.Localization;
@@ -108,7 +109,7 @@ public MainTable(MainTableDataModel model, JabRefFrame frame,
         }
         this.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
 
-        this.setItems(model.getEntriesFilteredAndSorted());
+        this.setItems(BindingsHelper.forUI(model.getEntriesFilteredAndSorted()));
         // Enable sorting
         model.getEntriesFilteredAndSorted().comparatorProperty().bind(this.comparatorProperty());
 

diff --git a/src/main/java/org/jabref/gui/preferences/ExternalTab.java b/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());