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

* upstream/master: (61 commits) 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) 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) Remove deprecated awt apple extension (#4860) Fix IllegalArgumentException when ranking entries (#4779) Bump junit-vintage-engine from 5.4.1 to 5.4.2 (#4866) Bump junit-platform-launcher from 1.4.1 to 1.4.2 (#4865) Bump junit-jupiter from 5.4.1 to 5.4.2 (#4867) Add author normalizer for medline import (#4863) Fixed group creation with default settings (#4801) removed default constructor of FXDialogService (#4847) QuotedStringTokenizer now does not unquote (#4830) Bump juh from 5.4.2 to 6.2.2 (#4851) ...
JabRef · Apr 13, 2019 · 5ded28a · 5ded28a
2 parents 9300128 + 504c0d3
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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
@@ -11,6 +11,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- We changed the latex command removal for docbook exporter. [#3838](https://github.com/JabRef/jabref/issues/3838)
 - We changed the location of some fields in the entry editor (you might need to reset your preferences for these changes to come into effect)
   - Journal/Year/Month in biblatex mode -> Deprecated (if filled)
   - DOI/URL: General -> Optional
@@ -60,8 +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
@@ -73,6 +78,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where selecting a group messed up the focus of the main table / entry editor. https://github.com/JabRef/jabref/issues/3367
 - We fixed an issue where composite author names were sorted incorrectly. https://github.com/JabRef/jabref/issues/2828
 - We fixed an issue where commands followed by `-` didn't work. [#3805](https://github.com/JabRef/jabref/issues/3805)
+- We fixed an issue where a non-existing aux file in a group made it impossible to open the library. [#4735](https://github.com/JabRef/jabref/issues/4735)
 - We fixed an issue where some journal names were wrongly marked as abbreviated. [#4115](https://github.com/JabRef/jabref/issues/4115)
 - We fixed an issue where the custom file column were sorted incorrectly. https://github.com/JabRef/jabref/issues/3119
 - We fixed an issues where the entry losses focus when a field is edited and at the same time used for sorting. https://github.com/JabRef/jabref/issues/3373
@@ -86,6 +92,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the default icon of a group was not colored correctly.
 - We fixed an issue where the first field in entry editor was not focused when adding a new entry. [#4024](https://github.com/JabRef/jabref/issues/4024)
 - We reworked the "Edit file" dialog to make it resizeable and improved the workflow for adding and editing files https://github.com/JabRef/jabref/issues/2970
+- We fixed an issue where custom name formatters were no longer found correctly. [#3531](https://github.com/JabRef/jabref/issues/3531)
 - We fixed an issue where the month was not shown in the preview https://github.com/JabRef/jabref/issues/3239.
 - Rewritten logic to detect a second jabref instance. [#4023](https://github.com/JabRef/jabref/issues/4023)
 - We fixed an issue where the "Convert to BibTeX-Cleanup" moved the content of the `file` field to the `pdf` field [#4120](https://github.com/JabRef/jabref/issues/4120)
@@ -99,14 +106,18 @@ 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.
+- We removed the global search feature.
 - We removed the coloring of cells in the maintable according to whether the field is optional/required.
 - We removed the feature to find and resolve duplicate BibTeX keys (as this use case is already covered by the integrity check).
 - We removed a few commands from the right-click menu that are not needed often and thus don't need to be placed that prominently:
@@ -144,7 +155,6 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 
 
-
 
 
 ## Older versions

diff --git a/build.gradle b/build.gradle
@@ -93,9 +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'
 
@@ -104,13 +104,13 @@ dependencies {
 
     compile 'commons-cli:commons-cli:1.4'
 
-    compile "org.libreoffice:juh:5.4.2"
-    compile "org.libreoffice:jurt:5.4.2"
-    compile "org.libreoffice:ridl:5.4.2"
-    compile "org.libreoffice:unoil:5.4.2"
+    compile "org.libreoffice:juh:6.2.2"
+    compile "org.libreoffice:jurt:6.2.2"
+    compile "org.libreoffice:ridl:6.2.2"
+    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'
@@ -159,23 +159,23 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.1'
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
 
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.4.0'
-    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.0'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.4.0'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.4.2'
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.2'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.4.2'
 
     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:2.25.0'
-    testCompile 'com.github.tomakehurst:wiremock:2.21.0'
+    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'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
-    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.9.3'
-    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.9.3'
+    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.10.2'
+    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.10.2'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.18'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.19'
 }
 
 jacoco {

diff --git a/lib/AppleJavaExtensions.jar b/lib/AppleJavaExtensions.jar
diff --git a/src/main/java/org/jabref/JabRefException.java b/src/main/java/org/jabref/JabRefException.java
@@ -33,7 +33,7 @@ public JabRefException(Throwable cause) {
     @Override
     public String getLocalizedMessage() {
         if (localizedMessage == null) {
-            LOGGER.debug("No localized message exception message defined. Falling back to getMessage().");
+            LOGGER.debug("No localized exception message defined. Falling back to getMessage().");
             return getMessage();
         } else {
             return localizedMessage;

diff --git a/src/main/java/org/jabref/JabRefGUI.java b/src/main/java/org/jabref/JabRefGUI.java
@@ -10,8 +10,6 @@
 import javafx.stage.Stage;
 
 import org.jabref.gui.BasePanel;
-import org.jabref.gui.DialogService;
-import org.jabref.gui.FXDialogService;
 import org.jabref.gui.GUIGlobals;
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.dialogs.BackupUIManager;
@@ -43,14 +41,13 @@ public class JabRefGUI {
     private final boolean isBlank;
     private final List<ParserResult> failed = new ArrayList<>();
     private final List<ParserResult> toOpenTab = new ArrayList<>();
-    private final DialogService dialogService;
 
     private final String focusedFile;
 
     public JabRefGUI(Stage mainStage, List<ParserResult> argsDatabases, boolean isBlank) {
         this.bibDatabases = argsDatabases;
         this.isBlank = isBlank;
-        this.dialogService = new FXDialogService(mainStage);
+        mainFrame = new JabRefFrame(mainStage);
 
         // passed file (we take the first one) should be focused
         focusedFile = argsDatabases.stream()
@@ -60,22 +57,12 @@ public JabRefGUI(Stage mainStage, List<ParserResult> argsDatabases, boolean isBl
                                     .orElse(Globals.prefs.get(JabRefPreferences.LAST_FOCUSED));
 
         openWindow(mainStage);
-        new VersionWorker(Globals.BUILD_INFO.getVersion(), Globals.prefs.getVersionPreferences().getIgnoredVersion(), JabRefGUI.getMainFrame().getDialogService(), Globals.TASK_EXECUTOR)
+        new VersionWorker(Globals.BUILD_INFO.getVersion(), Globals.prefs.getVersionPreferences().getIgnoredVersion(), mainFrame.getDialogService(), Globals.TASK_EXECUTOR)
                 .checkForNewVersionAsync(false);
     }
 
     private void openWindow(Stage mainStage) {
-        // Set antialiasing on everywhere. This only works in JRE >= 1.5.
-        // Or... it doesn't work, period.
-        // TODO test and maybe remove this! I found this commented out with no additional info ( payload@lavabit.com )
-        // Enabled since JabRef 2.11 beta 4
-        System.setProperty("swing.aatext", "true");
-        // Default is "on".
-        // "lcd" instead of "on" because of http://wiki.netbeans.org/FaqFontRendering and http://docs.oracle.com/javase/6/docs/technotes/guides/2d/flags.html#aaFonts
-        System.setProperty("awt.useSystemAAFontSettings", "lcd");
-
-        // look and feel. This MUST be the first thing to do before loading any Swing-specific code!
-        setLookAndFeel();
+        applyFontRenderingTweak();
 
         // If the option is enabled, open the last edited libraries, if any.
         if (!isBlank && Globals.prefs.getBoolean(JabRefPreferences.OPEN_LAST_EDITED)) {
@@ -85,7 +72,7 @@ private void openWindow(Stage mainStage) {
         GUIGlobals.init();
 
         LOGGER.debug("Initializing frame");
-        JabRefGUI.mainFrame = new JabRefFrame(mainStage);
+        mainFrame.init();
 
         // Add all bibDatabases databases to the frame:
         boolean first = false;
@@ -109,7 +96,7 @@ private void openWindow(Stage mainStage) {
                         pr.getDatabase().clearSharedDatabaseID();
 
                         LOGGER.error("Connection error", e);
-                        dialogService.showErrorDialogAndWait(
+                        mainFrame.getDialogService().showErrorDialogAndWait(
                                 Localization.lang("Connection error"),
                                 Localization.lang("A local copy will be opened."),
                                 e);
@@ -120,15 +107,15 @@ private void openWindow(Stage mainStage) {
                     // add them to the list
                     toOpenTab.add(pr);
                 } else {
-                    JabRefGUI.getMainFrame().addParserResult(pr, first);
+                    mainFrame.addParserResult(pr, first);
                     first = false;
                 }
             }
         }
 
         // finally add things to the currently opened tab
         for (ParserResult pr : toOpenTab) {
-            JabRefGUI.getMainFrame().addParserResult(pr, first);
+            mainFrame.addParserResult(pr, first);
             first = false;
         }
 
@@ -168,14 +155,14 @@ private void openWindow(Stage mainStage) {
             String message = Localization.lang("Error opening file '%0'.", pr.getFile().get().getName()) + "\n"
                     + pr.getErrorMessage();
 
-            dialogService.showErrorDialogAndWait(Localization.lang("Error opening file"), message);
+            mainFrame.getDialogService().showErrorDialogAndWait(Localization.lang("Error opening file"), message);
 
         }
 
         // Display warnings, if any
         int tabNumber = 0;
         for (ParserResult pr : bibDatabases) {
-            ParserResultWarningDialog.showParserResultWarningDialog(pr, JabRefGUI.getMainFrame(), tabNumber++);
+            ParserResultWarningDialog.showParserResultWarningDialog(pr, mainFrame, tabNumber++);
         }
 
         // After adding the databases, go through each and see if
@@ -187,9 +174,9 @@ private void openWindow(Stage mainStage) {
         // This is because importToOpen might have been used, which adds to
         // loadedDatabases, but not to getBasePanelCount()
 
-        for (int i = 0; (i < bibDatabases.size()) && (i < JabRefGUI.getMainFrame().getBasePanelCount()); i++) {
+        for (int i = 0; (i < bibDatabases.size()) && (i < mainFrame.getBasePanelCount()); i++) {
             ParserResult pr = bibDatabases.get(i);
-            BasePanel panel = JabRefGUI.getMainFrame().getBasePanelAt(i);
+            BasePanel panel = mainFrame.getBasePanelAt(i);
             OpenDatabaseAction.performPostOpenActions(panel, pr);
         }
 
@@ -219,7 +206,7 @@ private void openLastEditedDatabases() {
             }
 
             if (BackupManager.checkForBackupFile(dbFile.toPath())) {
-                BackupUIManager.showRestoreBackupDialog(dialogService, dbFile.toPath());
+                BackupUIManager.showRestoreBackupDialog(mainFrame.getDialogService(), dbFile.toPath());
             }
 
             ParserResult parsedDatabase = OpenDatabase.loadDatabase(fileName,
@@ -242,9 +229,9 @@ private boolean isLoaded(File fileToOpen) {
         return false;
     }
 
-    private void setLookAndFeel() {
-        // On Linux, Java FX fonts look blurry per default. This can be improved by using a non-default rendering
-        // setting. See https://github.com/woky/javafx-hates-linux
+    private void applyFontRenderingTweak() {
+        // On Linux, Java FX fonts look blurry per default. This can be improved by using a non-default rendering setting.
+        // See https://github.com/woky/javafx-hates-linux
         if (Globals.prefs.getBoolean(JabRefPreferences.FX_FONT_RENDERING_TWEAK)) {
             System.setProperty("prism.text", "t2k");
             System.setProperty("prism.lcdtext", "true");
@@ -254,9 +241,4 @@ private void setLookAndFeel() {
     public static JabRefFrame getMainFrame() {
         return mainFrame;
     }
-
-    // Only used for testing, other than that do NOT set the mainFrame...
-    public static void setMainFrame(JabRefFrame mainFrame) {
-        JabRefGUI.mainFrame = mainFrame;
-    }
 }