Merge remote-tracking branch 'upstream/maintable-beta' into jdk9

* upstream/maintable-beta: (46 commits) update gradle to 4.7 (#4049) Add missing translation for "HTML to Unicode" (#4046) New Crowdin translations (#4042) Use all-text-fields magic also in BibTeX cleanup. (#4039) Switch to org.postgresql (#4031) Fix freeze when importing (#4037) Use JavaFX-native SVGPath for logo in About dialog (#4035) Remove reflection hack to set WM_CLASS (#4034) Fix initial freeze when downloading files Inline comment Move color related method Extract dialog service to field Extract dialog service to field Remove unused class Show tooltip for icon-based columns Remove commented-out code Convert static methods to instance members (and fix spelling) Fix formatting Fix formatting Remove unused argument ... # Conflicts: # build.gradle # gradle/wrapper/gradle-wrapper.properties # src/main/java/org/jabref/gui/GUIGlobals.java # src/main/java/org/jabref/gui/SidePaneComponent.java # src/main/java/org/jabref/gui/groups/GroupModeViewModel.java # src/main/java/org/jabref/gui/groups/GroupSidePane.java # src/main/java/org/jabref/gui/help/AboutDialogView.java # src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java # src/main/java/org/jabref/logic/shared/PostgreSQLProcessor.java # src/main/resources/l10n/JabRef_en.properties
JabRef · May 22, 2018 · 9980c74 · 9980c74
2 parents bcfde56 + 8cbe028
commit 9980c74
Show file tree

Hide file tree

Showing 75 changed files with 851 additions and 1,404 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,11 +13,16 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ### Changed
 - We added a text file export for 'Find Unlinked Files'. [#3341](https://github.com/JabRef/jabref/issues/3341)
 - We added a fetcher based on RFC-IDs. [#3971](https://github.com/JabRef/jabref/issues/3971)
+- We changed the implementation of the `[shorttitle]` key pattern. It now removes small words like `a`, `an`, `on`, `the` etc. Refer to the help page for a complete overview. [Feature request in the forum](http://discourse.jabref.org/t/jabref-differences-in-shorttitle-between-versions-3-8-1-and-4-not-discounting-the-a-an-of-in-titles/1147)
+- We streamlined the defaults for a [cleanup of entries](http://help.jabref.org/en/CleanupEntries) in the case of BibTeX.
 
 ### Fixed
-We fixed an issue where the export to clipboard functionality could not be invoked [#3994](https://github.com/JabRef/jabref/issues/3994)
-We fixed an issue with the migration of invalid Look and Feels [#3995, comment](https://github.com/JabRef/jabref/issues/3995#issuecomment-385649448)
-We fixed an issue where JabRef would no longer start, when the option "Override default font settings" was activated [#3986](https://github.com/JabRef/jabref/issues/3986)
+We fixed an issue where the export to clipboard functionality could not be invoked. [#3994](https://github.com/JabRef/jabref/issues/3994)
+We fixed an issue with the migration of invalid Look and Feels. [#3995, comment](https://github.com/JabRef/jabref/issues/3995#issuecomment-385649448)
+We fixed an issue where JabRef would no longer start, when the option "Override default font settings" was activated. [#3986](https://github.com/JabRef/jabref/issues/3986)
+We fixed an issue where JabRef removed whitespace from the Title-fetcher which resulting in no entries being found. [#4014](https://github.com/JabRef/jabref/issues/4014)
+We fixed an issue where fetched entries from the ACM fetcher could not be imported. [#4018](https://github.com/JabRef/jabref/issues/4018)
+
 ### Removed
 We removed the GTK Look and Feel from the Options, as it leads to freezes in JabRef on MacOSX and Linux [#3995](https://github.com/JabRef/jabref/issues/3995)
 The GTK Look and Feel is now replaced with the "Nimbus" style as default.

diff --git a/build.gradle b/build.gradle
@@ -121,7 +121,7 @@ dependencies {
     // VersionEye states that 6.0.5 is the most recent version, but http://dev.mysql.com/downloads/connector/j/ shows that as "Development Release"
     compile 'mysql:mysql-connector-java:5.1.46'
 
-    compile 'com.impossibl.pgjdbc-ng:pgjdbc-ng:0.7.1'
+    compile 'org.postgresql:postgresql:42.2.2'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
@@ -130,8 +130,6 @@ dependencies {
     compile group: 'javax.annotation', name: 'javax.annotation-api', version: '1.3.2'
 
     // JavaFX stuff
-    // TODO: has an internal dependency exporting org.w3c.dom, temporarily removed
-    //compile 'de.codecentric.centerdevice:javafxsvg:1.3.0'
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
     compile 'de.jensd:fontawesomefx-commons:9.1.2'
     compile 'de.saxsys:mvvmfx-validation:1.7.0'
@@ -163,19 +161,18 @@ dependencies {
     // JAX-B is considered JavaEE API and is no longer part of JavaSE (JDK 9)
     compile group: 'javax.xml.bind', name: 'jaxb-api', version: '2.3.0'
     compile group: 'com.sun.xml.bind', name: 'jaxb-core', version: '2.3.0'
-
-
-    // TODO: recognized as 'latex2unicode.2.12', which is an invalid module name, temporarily removed
+
+// TODO: recognized as 'latex2unicode.2.12', which is an invalid module name, temporarily removed
 //    compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'
 
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '1.0.10'
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '1.0.10'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.1.1'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.1.1'
 
-    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.2.0-RC1'
-    testCompile 'org.junit.jupiter:junit-jupiter-params:5.2.0-RC1'
-    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.2.0-RC1'
-    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.2.0-RC1'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.2.0-RC1'
+    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.2.0'
+    testCompile 'org.junit.jupiter:junit-jupiter-params:5.2.0'
+    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.2.0'
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.2.0'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.2.0'
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.0'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.0'
     testCompile 'org.mockito:mockito-core:2.18.3'
@@ -184,11 +181,11 @@ dependencies {
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.0'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.0'
-    testCompile 'com.tngtech.archunit:archunit-junit:0.6.0-java9-SNAPSHOT'
+    testCompile 'com.tngtech.archunit:archunit-junit:0.8.0'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.9'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.10'
 }
 
 jacoco {

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-4.7-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.6-all.zip
diff --git a/src/main/java/org/jabref/JabRefExecutorService.java b/src/main/java/org/jabref/JabRefExecutorService.java
@@ -140,7 +140,7 @@ public void shutdownEverything() {
         this.lowPriorityExecutorService.shutdownNow();
         // kill the remote thread
         stopRemoteThread();
-        // timer doesn't need to be canceled as it is run in daemon mode, which ensures that it is stopped if the application is shut down
+        timer.cancel();
     }
 
     private class NamedRunnable implements Runnable {

diff --git a/src/main/java/org/jabref/JabRefMain.java b/src/main/java/org/jabref/JabRefMain.java
@@ -66,11 +66,9 @@ private static void ensureCorrectJavaVersion() {
 
         if (java9Fail || versionFail) {
             StringBuilder versionError = new StringBuilder(
-                    Localization.lang("Your current Java version (%0) is not supported. Please install version %1 or higher.",
-                            checker.getJavaVersion(),
-                            buildInfo.getMinRequiredJavaVersion()
-                    )
-            );
+                                                           Localization.lang("Your current Java version (%0) is not supported. Please install version %1 or higher.",
+                                                                             checker.getJavaVersion(),
+                                                                             buildInfo.getMinRequiredJavaVersion()));
 
             versionError.append("\n");
             versionError.append(Localization.lang("Your Java Runtime Environment is located at %0.", checker.getJavaInstallationDirectory()));
@@ -93,7 +91,7 @@ private static void ensureCorrectJavaVersion() {
     @Override
     public void start(Stage mainStage) throws Exception {
         FallbackExceptionHandler.installExceptionHandler();
-      
+
         ensureCorrectJavaVersion();
 
         // Init preferences
@@ -121,7 +119,7 @@ public void start(Stage mainStage) throws Exception {
 
         // Update handling of special fields based on preferences
         InternalBibtexFields
-                .updateSpecialFields(Globals.prefs.getBoolean(JabRefPreferences.SERIALIZESPECIALFIELDS));
+                            .updateSpecialFields(Globals.prefs.getBoolean(JabRefPreferences.SERIALIZESPECIALFIELDS));
         // Update name of the time stamp field based on preferences
         InternalBibtexFields.updateTimeStampField(Globals.prefs.getTimestampPreferences().getTimestampField());
         // Update which fields should be treated as numeric, based on preferences:
@@ -132,9 +130,9 @@ public void start(Stage mainStage) throws Exception {
 
         /* Build list of Import and Export formats */
         Globals.IMPORT_FORMAT_READER.resetImportFormats(Globals.prefs.getImportFormatPreferences(),
-                Globals.prefs.getXMPPreferences(), Globals.getFileUpdateMonitor());
+                                                        Globals.prefs.getXMPPreferences(), Globals.getFileUpdateMonitor());
         EntryTypes.loadCustomEntryTypes(preferences.loadCustomEntryTypes(BibDatabaseMode.BIBTEX),
-                preferences.loadCustomEntryTypes(BibDatabaseMode.BIBLATEX));
+                                        preferences.loadCustomEntryTypes(BibDatabaseMode.BIBLATEX));
         Globals.exportFactory = Globals.prefs.getExporterFactory(Globals.journalAbbreviationLoader);
 
         // Initialize protected terms loader
@@ -151,9 +149,11 @@ public void start(Stage mainStage) throws Exception {
                     // We have successfully sent our command line options through the socket to another JabRef instance.
                     // So we assume it's all taken care of, and quit.
                     LOGGER.info(Localization.lang("Arguments passed on to running JabRef instance. Shutting down."));
+                    Globals.stopBackgroundTasks();
                     Globals.shutdownThreadPools();
                     // needed to tell JavaFx to stop
                     Platform.exit();
+                    System.exit(0);
                     return;
                 }
             }
@@ -170,12 +170,20 @@ public void start(Stage mainStage) throws Exception {
 
         // See if we should shut down now
         if (argumentProcessor.shouldShutDown()) {
+            Globals.stopBackgroundTasks();
             Globals.shutdownThreadPools();
             Platform.exit();
+            System.exit(0);
             return;
         }
 
         // If not, start GUI
         new JabRefGUI(mainStage, argumentProcessor.getParserResults(), argumentProcessor.isBlank());
     }
+
+    @Override
+    public void stop() {
+        Platform.exit();
+        System.exit(0);
+    }
 }
diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
@@ -464,7 +464,7 @@ public void update() {
         actions.put(Actions.COPY_CITATION_TEXT, (BaseAction) () -> copyCitationToClipboard(CitationStyleOutputFormat.TEXT));
 
         // The action for copying the BibTeX keys as hyperlinks to the urls of the selected entries
-        actions.put(Actions.COPY_KEY_AND_LINK, new CopyBibTeXKeyAndLinkAction(mainTable));
+        actions.put(Actions.COPY_KEY_AND_LINK, new CopyBibTeXKeyAndLinkAction(mainTable, Globals.clipboardManager));
 
         actions.put(Actions.MERGE_DATABASE, new AppendDatabaseAction(frame, this));
 

diff --git a/src/main/java/org/jabref/gui/EntryTypeDialog.java b/src/main/java/org/jabref/gui/EntryTypeDialog.java
@@ -72,6 +72,7 @@ public EntryTypeDialog(JabRefFrame frame) {
         setTitle(Localization.lang("Select entry type"));
 
         addWindowListener(new WindowAdapter() {
+
             @Override
             public void windowClosing(WindowEvent e) {
                 cancelAction.actionPerformed(null);
@@ -245,7 +246,6 @@ static class TypeButton extends JButton implements Comparable<TypeButton> {
 
         private final EntryType type;
 
-
         TypeButton(String label, EntryType type) {
             super(label);
             this.type = type;
@@ -262,6 +262,7 @@ public EntryType getType() {
     }
 
     class CancelAction extends AbstractAction {
+
         public CancelAction() {
             super("Cancel");
         }
@@ -274,6 +275,7 @@ public void actionPerformed(ActionEvent e) {
     }
 
     private class FetcherWorker extends SwingWorker<Optional<BibEntry>, Void> {
+
         private boolean fetcherException = false;
         private String fetcherExceptionMessage = "";
         private IdBasedFetcher fetcher = null;
@@ -287,10 +289,9 @@ protected Optional<BibEntry> doInBackground() throws Exception {
                 generateButton.setText(Localization.lang("Searching..."));
             });
 
-            Globals.prefs.put(JabRefPreferences.ID_ENTRY_GENERATOR,String.valueOf(comboBox.getSelectedItem()));
-            searchID = idTextField.getText().trim();
-            searchID = searchID.replaceAll(" ", "");
+            Globals.prefs.put(JabRefPreferences.ID_ENTRY_GENERATOR, String.valueOf(comboBox.getSelectedItem()));
             fetcher = WebFetchers.getIdBasedFetchers(Globals.prefs.getImportFormatPreferences()).get(comboBox.getSelectedIndex());
+            searchID = idTextField.getText();
             if (!searchID.isEmpty()) {
                 try {
                     bibEntry = fetcher.performSearchById(searchID);
@@ -310,7 +311,7 @@ protected void done() {
                 if (result.isPresent()) {
                     final BibEntry bibEntry = result.get();
                     if ((DuplicateCheck.containsDuplicate(frame.getCurrentBasePanel().getDatabase(), bibEntry, frame.getCurrentBasePanel().getBibDatabaseContext().getMode()).isPresent())) {
-                		//If there are duplicates starts ImportInspectionDialog
+                        //If there are duplicates starts ImportInspectionDialog
                         final BasePanel panel = frame.getCurrentBasePanel();
 
                         ImportInspectionDialog diag = new ImportInspectionDialog(frame, panel, Localization.lang("Import"), false);
@@ -319,7 +320,7 @@ protected void done() {
                         diag.setVisible(true);
                         diag.toFront();
                     } else {
-                		// Regenerate CiteKey of imported BibEntry
+                        // Regenerate CiteKey of imported BibEntry
                         new BibtexKeyGenerator(frame.getCurrentBasePanel().getBibDatabaseContext(), Globals.prefs.getBibtexKeyPatternPreferences()).generateAndSetKey(bibEntry);
                         // Update Timestamps
                         if (Globals.prefs.getTimestampPreferences().includeCreatedTimestamp()) {

diff --git a/src/main/java/org/jabref/gui/GUIGlobals.java b/src/main/java/org/jabref/gui/GUIGlobals.java
@@ -2,12 +2,10 @@
 
 import java.awt.Color;
 import java.awt.Font;
-import java.awt.Toolkit;
 
 import org.jabref.Globals;
 import org.jabref.gui.keyboard.EmacsKeyBindings;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.util.OS;
 import org.jabref.preferences.JabRefPreferences;
 
 import org.slf4j.Logger;
@@ -61,20 +59,6 @@ public static void init() {
 
         GUIGlobals.currentFont = new Font(Globals.prefs.get(JabRefPreferences.FONT_FAMILY),
                 Globals.prefs.getInt(JabRefPreferences.FONT_STYLE), Globals.prefs.getInt(JabRefPreferences.FONT_SIZE));
-
-        // Set WM_CLASS using reflection for certain Un*x window managers
-        if (!OS.WINDOWS && !OS.OS_X) {
-            try {
-                // TODO: reflective access, should be removed (Java 9)
-                Toolkit xToolkit = Toolkit.getDefaultToolkit();
-                java.lang.reflect.Field awtAppClassNameField = xToolkit.getClass().getDeclaredField("awtAppClassName");
-                awtAppClassNameField.setAccessible(true);
-                awtAppClassNameField.set(xToolkit, "org-jabref-JabRefMain");
-            } catch (Exception e) {
-                // ignore any error since this code only works for certain toolkits
-            }
-        }
-
     }
 
     public static void setFont(int size) {

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -63,11 +63,11 @@
 import org.jabref.gui.actions.CopyFilesAction;
 import org.jabref.gui.actions.CustomizeEntryAction;
 import org.jabref.gui.actions.CustomizeKeyBindingAction;
+import org.jabref.gui.actions.DatabasePropertiesAction;
 import org.jabref.gui.actions.EditExternalFileTypesAction;
 import org.jabref.gui.actions.ErrorConsoleAction;
 import org.jabref.gui.actions.FindUnlinkedFilesAction;
 import org.jabref.gui.actions.IntegrityCheckAction;
-import org.jabref.gui.actions.LibraryPropertiesAction;
 import org.jabref.gui.actions.LookupIdentifierAction;
 import org.jabref.gui.actions.ManageCustomExportsAction;
 import org.jabref.gui.actions.ManageCustomImportsAction;
@@ -725,10 +725,10 @@ private MenuBar createMenu() {
 
                 factory.createSubMenu(StandardActions.IMPORT_EXPORT,
                         factory.createMenuItem(StandardActions.MERGE_DATABASE, new OldDatabaseCommandWrapper(Actions.MERGE_DATABASE, this, Globals.stateManager)), // TODO: merge with import
-                        factory.createMenuItem(StandardActions.IMPORT_INTO_CURRENT_LIBRARY, new ImportCommand(this, true)),
-                        factory.createMenuItem(StandardActions.IMPORT_INTO_NEW_LIBRARY, new ImportCommand(this, false)),
-                        factory.createMenuItem(StandardActions.EXPORT_ALL, new ExportCommand(this, false)),
-                        factory.createMenuItem(StandardActions.EXPORT_SELECTED, new ExportCommand(this, true)),
+                        factory.createMenuItem(StandardActions.IMPORT_INTO_CURRENT_LIBRARY, new ImportCommand(this, false)),
+                        factory.createMenuItem(StandardActions.IMPORT_INTO_NEW_LIBRARY, new ImportCommand(this, true)),
+                        factory.createMenuItem(StandardActions.EXPORT_ALL, new ExportCommand(this, false, Globals.prefs)),
+                        factory.createMenuItem(StandardActions.EXPORT_SELECTED, new ExportCommand(this, true, Globals.prefs)),
                         factory.createMenuItem(StandardActions.SAVE_SELECTED_AS_PLAIN_BIBTEX, new OldDatabaseCommandWrapper(Actions.SAVE_SELECTED_AS_PLAIN, this, Globals.stateManager))
                 ),
 
@@ -831,7 +831,7 @@ private MenuBar createMenu() {
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.LIBRARY_PROPERTIES, new LibraryPropertiesAction(this)),
+                factory.createMenuItem(StandardActions.LIBRARY_PROPERTIES, new DatabasePropertiesAction(this)),
                 factory.createMenuItem(StandardActions.EDIT_PREAMBLE, new PreambleEditor(this)),
                 factory.createMenuItem(StandardActions.EDIT_STRINGS, new OldDatabaseCommandWrapper(Actions.EDIT_STRINGS, this, Globals.stateManager))
 

diff --git a/src/main/java/org/jabref/gui/PreambleEditor.java b/src/main/java/org/jabref/gui/PreambleEditor.java
@@ -29,23 +29,23 @@ public void execute() {
         DialogPane pane = new DialogPane();
 
         editor.setText(frame.getCurrentBasePanel()
-                .getDatabase()
-                .getPreamble()
-                .orElse(""));
+                            .getDatabase()
+                            .getPreamble()
+                            .orElse(""));
         pane.setContent(editor);
 
         Optional<ButtonType> pressedButton = frame.getDialogService().showCustomDialogAndWait(Localization.lang("Edit Preamble"), pane, ButtonType.APPLY, ButtonType.CANCEL);
 
         if (pressedButton.isPresent() && pressedButton.get().equals(ButtonType.APPLY)) {
-            String toSet = editor.getText();
+            String newPreamble = editor.getText();
 
             // We check if the field has changed, since we don't want to mark the
             // base as changed unless we have a real change.
-            if (!database.getPreamble().orElse("").equals(toSet)) {
+            if (!database.getPreamble().orElse("").equals(newPreamble)) {
 
                 panel.getUndoManager().addEdit(
-                        new UndoablePreambleChange(database, database.getPreamble().orElse(null), toSet));
-                database.setPreamble(toSet);
+                        new UndoablePreambleChange(database, database.getPreamble().orElse(null), newPreamble));
+                database.setPreamble(newPreamble);
 
                 panel.markBaseChanged();
             }