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

* upstream/master: (31 commits)
  Source tab entry duplication (#3360)
  Use CITE_COMMENT not only for external latex editors but also for cop… (#3351)
  Updating with new translations (#3348)
  Upgrade error-prone (#3350)
  Jabref_pt_BR partially updated (#3349)
  Used late initialization for context menus (#3340)
  Fix NPE when calling with bib file as cmd argument (#3343)
  update mockito-core from 2.10.0 -> 2.11.0 (#3338)
  Remove underscore in Localized messages (#3336)
  Localisation: French: new entries translated (#3337)
  Refactoring: Lazy init of all editor tabs (#3333)
  Initializing EntryEditor Tabs on focus (#3331)
  Fix #3292: annotations are now automatically refreshed (#3325)
  Change integrity message for names depending on database mode (#3330)
  Fix location bundle with fast access (#3327)
  Small code cleanup
  Fix "path not found" exception
  Small fix in drag and drop handler of linked files (#3328)
  Fix NPE in MainTable (#3318)
  Increase relative size of abstract field in editor (#3320)
  ...

Author: Siedlerchr

CHANGELOG.md

@@ -17,16 +17,25 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - 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)
+- In the annotation tab, PDF files are now monitored for new or changed annotation. A manual reload is no longer necessary. [#3292](https://github.com/JabRef/jabref/issues/3292)
+- We increased the relative size of the "abstract" field in the entry editor. [Feature request in the forum](http://discourse.jabref.org/t/entry-preview-in-version-4/827)
 - 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)
+- We increased performance and decreased the memory footprint of the entry editor drastically. [#3331](https://github.com/JabRef/jabref/pull/3331)
+- Late initialization of the context menus in the entry editor. This improves performance and memory footprint further [#3340](https://github.com/JabRef/jabref/pull/3340)
 
 
 ### 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)
+ - We fixed an issue where JabRef would not show the translated content at some points, although there existed a translation
+ - We fixed an issue where editing in the source tab would override content of other entries [#3352](https://github.com/JabRef/jabref/issues/3352#issue-268580818)
 ### Removed
 
 

build.gradle

@@ -9,7 +9,7 @@ plugins {
     id "de.sebastianboegl.shadow.transformer.log4j" version "2.1.1"
     id "com.simonharrer.modernizer" version '1.5.0-1'
     id 'me.champeau.gradle.jmh' version '0.4.3'
-    id 'net.ltgt.errorprone' version '0.0.11'
+    id 'net.ltgt.errorprone' version '0.0.13'
 }
 
 // use the gradle build scan feature: https://scans.gradle.com/get-started
@@ -104,11 +104,13 @@ dependencies {
     compile 'de.codecentric.centerdevice:javafxsvg:1.2.1'
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
     compile 'de.saxsys:mvvmfx-validation:1.7.0'
-    compile 'org.controlsfx:controlsfx:8.40.14'
     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'
 
@@ -122,13 +124,13 @@ 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'
+    testCompile 'org.mockito:mockito-core:2.11.0'
     testCompile 'com.github.tomakehurst:wiremock:2.8.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
@@ -353,7 +355,7 @@ task media(type: com.install4j.gradle.Install4jTask, dependsOn: "releaseJar") {
 checkstyle {
     // do not use other packages for checkstyle, excluding gen(erated) sources
     checkstyleMain.source = "src/main/java"
-    toolVersion = '8.0'
+    toolVersion = '8.3'
 }
 
 checkstyleMain.shouldRunAfter test

gradle/wrapper/gradle-wrapper.jar

@@ -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

gradle/wrapper/gradle-wrapper.properties

@@ -4,11 +4,11 @@
 import java.util.Optional;
 import java.util.UUID;
 
-import org.jabref.collab.FileUpdateMonitor;
 import org.jabref.gui.GlobalFocusListener;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.gui.util.DefaultTaskExecutor;
+import org.jabref.gui.util.FileUpdateMonitor;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.importer.ImportFormatReader;
 import org.jabref.logic.journals.JournalAbbreviationLoader;

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

@@ -66,7 +66,9 @@ private static void start(String[] args) {
 
         Globals.prefs = preferences;
         Globals.startBackgroundTasks();
-        Localization.setLanguage(preferences.get(JabRefPreferences.LANGUAGE));
+
+        // Note that the language was already set during the initialization of the preferences and it is safe to
+        // call the next function.
         Globals.prefs.setLanguageDependentDefaultValues();
 
         // Perform Migrations

src/main/java/org/jabref/JabRefMain.java

@@ -519,7 +519,7 @@ private void regenerateBibtexKeys(List<ParserResult> loaded) {
                             database, entry, Globals.prefs.getBibtexKeyPatternPreferences());
                 }
             } else {
-                LOGGER.info(Localization.lang("No meta data present in BIB_file. Cannot regenerate BibTeX keys"));
+                LOGGER.info(Localization.lang("No meta data present in BIB file. Cannot regenerate BibTeX keys"));
             }
         }
     }

src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -103,7 +103,7 @@ public ChangeDisplayDialog(JFrame owner, final BasePanel panel,
             if (anyDisabled) {
                 panel.markBaseChanged();
             }
-            panel.setUpdatedExternally(false);
+            panel.markExternalChangesAsResolved();
             dispose();
             okPressed = true;
         });

src/main/java/org/jabref/collab/ChangeDisplayDialog.java

@@ -49,6 +49,7 @@ public class ChangeScanner implements Runnable {
 
     private static final double MATCH_THRESHOLD = 0.4;
     private final File file;
+    private final Path tempFile;
     private final BibDatabase databaseInMemory;
     private final MetaData metadataInMemory;
 
@@ -67,20 +68,20 @@ public class ChangeScanner implements Runnable {
 
     //  NamedCompound edit = new NamedCompound("Merged external changes")
 
-    public ChangeScanner(JabRefFrame frame, BasePanel bp, File file) {
+    public ChangeScanner(JabRefFrame frame, BasePanel bp, File file, Path tempFile) {
         this.panel = bp;
         this.frame = frame;
         this.databaseInMemory = bp.getDatabase();
         this.metadataInMemory = bp.getBibDatabaseContext().getMetaData();
         this.file = file;
+        this.tempFile = tempFile;
     }
 
     @Override
     public void run() {
         try {
 
             // Parse the temporary file.
-            Path tempFile = Globals.getFileUpdateMonitor().getTempFile(panel.fileMonitorHandle());
             ImportFormatPreferences importFormatPreferences = Globals.prefs.getImportFormatPreferences();
             ParserResult result = OpenDatabase.loadDatabase(tempFile.toFile(), importFormatPreferences);
             databaseInTemp = result.getDatabase();
@@ -153,7 +154,7 @@ private void storeTempDatabase() {
                 Defaults defaults = new Defaults(Globals.prefs.getDefaultBibDatabaseMode());
                 BibDatabaseWriter<SaveSession> databaseWriter = new BibtexDatabaseWriter<>(FileSaveSession::new);
                 SaveSession ss = databaseWriter.saveDatabase(new BibDatabaseContext(databaseInTemp, metadataInTemp, defaults), prefs);
-                ss.commit(Globals.getFileUpdateMonitor().getTempFile(panel.fileMonitorHandle()));
+                ss.commit(tempFile);
             } catch (SaveException ex) {
                 LOGGER.warn("Problem updating tmp file after accepting external changes", ex);
             }