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

* upstream/master:
  Update gradle to 4.2.1 (#3322)
  Avoid recreation of the EntryEditor (#3187)
  Fix #3133 telemetry by locking azure to 1.0.9
  German translation for missing properties (#3312)
  Improvement for Java FX font rendering on Linux (#3305)
  Add also conversion for em dash
  Add \textendash to the html conversion table
  Update latex2tunicode from 0.2.1 -> 0.2.2
  Added note about updating controlsfx
  Fix exception/freezing on EntryChangedEvent in Entry Editor (#3299)
  Update libs (#3300)
  update guava from 23.0 -> 23.2
  update mvvmfx-validation from 1.6.0 -> 1.7.0
  Resolves #3255 file open dialog should have "supported formates" filetype
  Fix #3235: remote metadata is updated instead of delete + insert (#3282)
  Change OO paths to Libre Office in preferences (#3287)
  Fix #2471: remove line breaks from abstracts in ADS fetcher (#3285)
  Resolves #3280 Empty String instead of N/A (#3288)

CHANGELOG.md

@@ -15,13 +15,20 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We added bracketed expresion support for file search patterns, import file name patterns and file directory patters, in addition to bibtexkey patterns.
 - We added support for '[entrytype]' bracketed expression.
 - Updated French translation
+- We improved the handling of abstracts in the "Astrophysics Data System" fetcher. [#2471](https://github.com/JabRef/jabref/issues/2471)
 - We added support for pasting entries in different formats [#3143](https://github.com/JabRef/jabref/issues/3143)
 - Crossreferenced entries are now used when a BibTex key is generated for an entry with empty fields. [#2811](https://github.com/JabRef/jabref/issues/2811)
 - We now set the WM_CLASS of the UI to org-jabref-JabRefMain to allow certain Un*x window managers to properly identify its windows
+- We changed the default paths for the OpenOffice/LibreOffice binaries to the default path for LibreOffice
+- We no longer create a new entry editor when selecting a new entry to increase performance. [#3187](https://github.com/JabRef/jabref/pull/3187)
 
 ### Fixed
+ - We fixed the translation of \textendash in the entry preview [#3307](https://github.com/JabRef/jabref/issues/3307)
  - We fixed an issue where JabRef would not terminated after asking to collect anonymous statistics [#2955 comment](https://github.com/JabRef/jabref/issues/2955#issuecomment-334591123)
- - We fixed an issue where JabRef would not shut down when started with the '-n' (No GUI) option.
+ - We fixed an issue where JabRef would not shut down when started with the '-n' (No GUI) option. [#3247](https://github.com/JabRef/jabref/issues/3247)
+ - We improved the way metadata is updated in remote databases. [#3235](https://github.com/JabRef/jabref/issues/3235)
+ - We improved font rendering of the Entry Editor for Linux based systems [#3295](https://github.com/JabRef/jabref/issues/3295)
+ - We fixed an issue where JabRef would freeze when trying to replace the original entry after a merge with new information from identifiers like DOI/ISBN etc. [3294](https://github.com/JabRef/jabref/issues/3294)
 
 ### Removed
 

build.gradle

@@ -91,24 +91,26 @@ dependencies {
     compile 'org.antlr:antlr4-runtime:4.7'
 
     // 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:5.1.43'
+    compile 'mysql:mysql-connector-java:5.1.44'
 
     compile 'com.impossibl.pgjdbc-ng:pgjdbc-ng:0.7.1'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:23.0'
+    compile 'com.google.guava:guava:23.2-jre'
 
     // JavaFX stuff
     compile 'com.airhacks:afterburner.fx:1.7.0'
     compile 'de.codecentric.centerdevice:javafxsvg:1.2.1'
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
-    compile 'de.saxsys:mvvmfx-validation:1.6.0'
-    compile 'org.controlsfx:controlsfx:8.40.14'
+    compile 'de.saxsys:mvvmfx-validation:1.7.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
     compile 'org.fxmisc.flowless:flowless:0.5.2'
     compile 'org.fxmisc.richtext:richtextfx:0.7-M5'
 
+    // Cannot be updated to 9.*.* until Jabref works with Java 9
+    compile 'org.controlsfx:controlsfx:8.40.14'
+
     compile 'org.jsoup:jsoup:1.10.3'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
@@ -122,10 +124,10 @@ dependencies {
     compile 'org.citationstyles:locales:1.0.1-SNAPSHOT'
     compile 'de.undercouch:citeproc-java:1.0.1'
 
-    compile 'com.github.tomtung:latex2unicode_2.12:0.2.1'
+    compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'
 
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '1.0.+'
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '1.0.+'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '1.0.9'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '1.0.9'
 
     testCompile 'junit:junit:4.12'
     testCompile 'org.mockito:mockito-core:2.10.0'

gradle/wrapper/gradle-wrapper.properties

@@ -2,4 +2,4 @@ distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.2-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.2.1-bin.zip

src/main/java/org/jabref/JabRefGUI.java

@@ -272,6 +272,13 @@ private void setLookAndFeel() {
                     LOGGER.warn("Unable to find requested look and feel", e);
                 }
             }
+
+            // 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");
+            }
         } catch (Exception e) {
             LOGGER.warn("Look and feel could not be set", e);
         }

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

@@ -1486,11 +1486,14 @@ public void showEntry(final BibEntry bibEntry) {
      * @return A suitable entry editor.
      */
     public EntryEditor getEntryEditor(BibEntry entry) {
-        String lastTabName = "";
         if (currentEditor != null) {
-            lastTabName = currentEditor.getVisibleTabName();
+            currentEditor.setEntry(entry);
+            return currentEditor;
+        } else {
+            EntryEditor editor = new EntryEditor(this);
+            editor.setEntry(entry);
+            return editor;
         }
-        return new EntryEditor(frame, BasePanel.this, entry, lastTabName);
     }
 
     public EntryEditor getCurrentEditor() {

src/main/java/org/jabref/gui/entryeditor/EntryEditor.java

@@ -114,11 +114,11 @@ public class EntryEditor extends JPanel implements EntryContainer {
     /**
      * A reference to the entry this object works on.
      */
-    private final BibEntry entry;
+    private BibEntry entry;
     /**
      * The currently displayed type
      */
-    private final String displayedBibEntryType;
+    private String displayedBibEntryType;
 
     /**
      * The action concerned with closing the window.
@@ -157,71 +157,57 @@ public class EntryEditor extends JPanel implements EntryContainer {
      * Indicates that we are about to go to the next or previous entry
      */
     private final BooleanProperty movingToDifferentEntry = new SimpleBooleanProperty();
-    private final EntryType entryType;
+    private EntryType entryType;
     private SourceTab sourceTab;
+    private final BorderLayout layout;
+    private TypeLabel typeLabel;
 
-    public EntryEditor(JabRefFrame frame, BasePanel panel, BibEntry entry, String lastTabName) {
-        this.frame = frame;
+    public EntryEditor(BasePanel panel) {
+        this.frame = panel.frame();
         this.panel = panel;
-        this.entry = Objects.requireNonNull(entry);
-        entry.registerListener(this);
-        entryType = EntryTypes.getTypeOrDefault(entry.getType(),
-                this.frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
-
-        displayedBibEntryType = entry.getType();
 
         writeXmp = new WriteXMPEntryEditorAction(panel, this);
 
-        BorderLayout borderLayout = new BorderLayout();
-        setLayout(borderLayout);
-        setupToolBar();
+        layout = new BorderLayout();
+        setLayout(layout);
 
         container = OS.LINUX ? new CustomJFXPanel() : new JFXPanel();
+        // Create type-label
+        typeLabel = new TypeLabel("");
+        setupToolBar();
+        DefaultTaskExecutor.runInJavaFXThread(() ->
+                container.setScene(new Scene(tabbed))
+        );
+        add(container, BorderLayout.CENTER);
 
-        container.addKeyListener(new KeyAdapter() {
+        DefaultTaskExecutor.runInJavaFXThread(() -> {
+                    EasyBind.subscribe(tabbed.getSelectionModel().selectedItemProperty(), tab -> {
+                        EntryEditorTab activeTab = (EntryEditorTab) tab;
+                        if (activeTab != null) {
+                            activeTab.notifyAboutFocus();
+                        }
+                    });
+                });
 
-            @Override
-            public void keyPressed(java.awt.event.KeyEvent e) {
+        setupKeyBindings();
+    }
+
+    public void setEntry(BibEntry entry) {
+        this.entry = Objects.requireNonNull(entry);
+        entry.registerListener(this);
+        entryType = EntryTypes.getTypeOrDefault(entry.getType(),
+                this.frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
+
+        displayedBibEntryType = entry.getType();
 
-                //We need to consume this event here to prevent the propgation of keybinding events back to the JFrame
-                Optional<KeyBinding> keyBinding = Globals.getKeyPrefs().mapToKeyBinding(e);
-                if (keyBinding.isPresent()) {
-                    switch (keyBinding.get()) {
-                        case CUT:
-                        case COPY:
-                        case PASTE:
-                        case CLOSE_ENTRY_EDITOR:
-                        case DELETE_ENTRY:
-                        case SELECT_ALL:
-                        case ENTRY_EDITOR_NEXT_PANEL:
-                        case ENTRY_EDITOR_NEXT_PANEL_2:
-                        case ENTRY_EDITOR_PREVIOUS_PANEL:
-                        case ENTRY_EDITOR_PREVIOUS_PANEL_2:
-                            e.consume();
-                            break;
-                        default:
-                            //do nothing
-                    }
-                }
-            }
-        });
         DefaultTaskExecutor.runInJavaFXThread(() -> {
-            addTabs(lastTabName);
+            addTabs(this.getVisibleTabName());
 
             tabbed.setStyle("-fx-font-size: " + Globals.prefs.getFontSizeFX() + "pt;");
 
-            container.setScene(new Scene(tabbed));
         });
-        add(container, BorderLayout.CENTER);
-
-        EasyBind.subscribe(tabbed.getSelectionModel().selectedItemProperty(), tab -> {
-            EntryEditorTab activeTab = (EntryEditorTab) tab;
-            if (activeTab != null) {
-                activeTab.notifyAboutFocus();
-            }
-        });
-
-        setupKeyBindings();
+        TypedBibEntry typedEntry = new TypedBibEntry(entry, panel.getBibDatabaseContext().getMode());
+        typeLabel.setText(typedEntry.getTypeForDisplay());
     }
 
     @Subscribe
@@ -234,7 +220,7 @@ public synchronized void listen(FieldAddedOrRemovedEvent event) {
 
     @Subscribe
     public synchronized void listen(EntryChangedEvent event) {
-        sourceTab.updateSourcePane();
+        DefaultTaskExecutor.runInJavaFXThread(() -> sourceTab.updateSourcePane());
     }
 
     private void rebuildOtherFieldsTab() {
@@ -288,6 +274,34 @@ private void selectLastUsedTab(String lastTabName) {
      * Set-up key bindings specific for the entry editor.
      */
     private void setupKeyBindings() {
+        container.addKeyListener(new KeyAdapter() {
+
+            @Override
+            public void keyPressed(java.awt.event.KeyEvent e) {
+
+                //We need to consume this event here to prevent the propgation of keybinding events back to the JFrame
+                Optional<KeyBinding> keyBinding = Globals.getKeyPrefs().mapToKeyBinding(e);
+                if (keyBinding.isPresent()) {
+                    switch (keyBinding.get()) {
+                        case CUT:
+                        case COPY:
+                        case PASTE:
+                        case CLOSE_ENTRY_EDITOR:
+                        case DELETE_ENTRY:
+                        case SELECT_ALL:
+                        case ENTRY_EDITOR_NEXT_PANEL:
+                        case ENTRY_EDITOR_NEXT_PANEL_2:
+                        case ENTRY_EDITOR_PREVIOUS_PANEL:
+                        case ENTRY_EDITOR_PREVIOUS_PANEL_2:
+                            e.consume();
+                            break;
+                        default:
+                            //do nothing
+                    }
+                }
+            }
+        });
+
         tabbed.addEventFilter(KeyEvent.KEY_PRESSED, event -> {
             Optional<KeyBinding> keyBinding = Globals.getKeyPrefs().mapToKeyBinding(event);
             if (keyBinding.isPresent()) {
@@ -387,6 +401,7 @@ public BibDatabase getDatabase() {
     }
 
     private void setupToolBar() {
+
         JPanel leftPan = new JPanel();
         leftPan.setLayout(new BorderLayout());
         JToolBar toolBar = new OSXCompatibleToolbar(SwingConstants.VERTICAL);
@@ -426,9 +441,7 @@ private void setupToolBar() {
         closeBut.setMargin(new Insets(8, 0, 8, 0));
         leftPan.add(closeBut, BorderLayout.NORTH);
 
-        // Create type-label
-        TypedBibEntry typedEntry = new TypedBibEntry(entry, panel.getBibDatabaseContext().getMode());
-        leftPan.add(new TypeLabel(typedEntry.getTypeForDisplay()), BorderLayout.CENTER);
+        leftPan.add(typeLabel, BorderLayout.CENTER);
         TypeButton typeButton = new TypeButton();
 
         toolBar.add(typeButton);

src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationViewModel.java

@@ -26,23 +26,16 @@ public FileAnnotationViewModel(FileAnnotation annotation) {
 
     private void setupContentProperties(FileAnnotation annotation) {
         if (annotation.hasLinkedAnnotation()) {
-            this.content.set(toNAifEmpty(annotation.getLinkedFileAnnotation().getContent()));
+            this.content.set(annotation.getLinkedFileAnnotation().getContent());
             String annotationContent = annotation.getContent();
             String illegibleTextMessage = Localization.lang("The marked area does not contain any legible text!");
             this.marking.set(annotationContent.isEmpty() ? illegibleTextMessage : annotationContent);
         } else {
-            this.content.set(toNAifEmpty(annotation.getContent()));
-            this.marking.set("N/A");
+            this.content.set(annotation.getContent());
+            this.marking.set("");
         }
     }
 
-    private static String toNAifEmpty(String content) {
-        if (content.isEmpty()) {
-            return "N/A";
-        }
-        return content;
-    }
-
     public String getAuthor() {
         return author.get();
     }

src/main/java/org/jabref/gui/importer/ImportFileFilter.java

@@ -24,7 +24,9 @@ public static FileChooser.ExtensionFilter convert(Importer format) {
     public static FileChooser.ExtensionFilter convert(String description, Collection<Importer> formats) {
         List<FileExtensions> extensions = formats.stream().map(Importer::getExtensions).collect(Collectors.toList());
         List<String> flatExtensions = extensions.stream().flatMap(extList -> Arrays.stream(extList.getExtensions()))
+                .map(ending -> "*." + ending)
                 .collect(Collectors.toList());
+
         return new FileChooser.ExtensionFilter(description, flatExtensions.toArray(new String[flatExtensions.size()]));
     }
 

src/main/java/org/jabref/gui/importer/ImportFormats.java

@@ -81,6 +81,7 @@ public void actionPerformed(ActionEvent e) {
                 DialogService ds = new FXDialogService();
 
                 FileChooser fs = ds.getConfiguredFileChooser(fileDialogConfiguration);
+                fs.getExtensionFilters().add(0, allImports);
                 fs.setSelectedExtensionFilter(allImports);
                 File f = DefaultTaskExecutor
                         .runInJavaFXThread(() -> fs.showOpenDialog(null));