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

* upstream/master: (113 commits)
  Open statistics dialog from correct thread (#3272)
  Fix for issue 2811: bibtexkey generator does not use crossref information (#3248)
  Fix for issue 3143: Import entry from clipboard in different formats (#3243)
  French translation correction (#3262)
  Wait to ask to collect anonymous statistics in JabRefExecutorService to allow jvm to terminate (#3266)
  Directory pattern bracketed expressions (#3238)
  Show development information
  Release v4.0
  add another author to mailmap
  moved changelog entry to the right category
  update new AUTHORS info
  Update log4j from 2.9.0 -> 2.9.1
  fix dblp fetcher
  Add missing Turkish translation
  Add "-console" parameter for Windows launcher (#3242)
  Path check converted to if statement
  Changelog updated
  Fixed renaming files which are not in main directory.
  Only use last name for auto completion in search bar. Fixes koppor#253
  Implemented issue #3229 (#3233)
  ...

.mailmap

@@ -1,3 +1,4 @@
+
 # Generate AUTHORS: scripts/generate-authors.sh
 
 # Tip for finding duplicates (besides scanning the output of AUTHORS for name
@@ -122,3 +123,12 @@ Fabian Bauer <125m125@users.noreply.github.com>
 Jong-Ho Shinn <jhshinn@kaist.edu>
 Nadeem Mahmood <mahmoodn@purdue.edu>
 Foivos Christoulakis <halx4@users.noreply.github.com>
+Predrag Milanovic <pmilanovic@gmail.com>
+Karsten Hiekmann <sammann-fnordbedarf-de@users.noreply.github.com>
+Karsten Hiekmann <h.k.hiekmann@nanooq.org>
+Andrew Levit <dreyskiy@gmail.com>
+Berk Gureken <berkgureken@gmail.com>
+Abhishek Rai <abhisheksavitarai@gmail.com>
+Abhishek Rai <betheunique@users.noreply.github.com>
+Stéphane Curet <stephane.curet@orange.fr>
+Erdem Derebasoglu <erdemderebasoglu@hotmail.com>

AUTHORS

@@ -1,6 +1,7 @@
 # This file lists all individuals having contributed content to the repository.
 # For how it is generated, see `scripts/generate-authors.sh`.
 Aaron Chen
+Abhishek Rai
 Adam Rehn
 Admir Obralija
 Adrian Daerr
@@ -14,11 +15,14 @@ Ambrogio Oliva
 Andreas Amann
 Andreas Buhr
 Andreas Rudert
+Andrew Levit
 Anh Nghia Tran
 Anita Armbruster
 Antonio Ribeiro
 Arno Blouin
 Behrouz Javanmardi
+Benjamin Köhler
+Berk Gureken
 Bernd Kalbfuss
 Bernhard Tempel
 Brian Quistorff
@@ -46,6 +50,7 @@ Eduard Braun
 Eduardo Greco
 Egon Willighagen
 Ellen Reitmayr
+Erdem Derebasoglu
 Erik Putrycz
 Ervin Kolenovic
 Fabian Bauer
@@ -91,6 +96,7 @@ Jörg Zieren
 Jørgen Kvalsvik
 Jürgen Lange
 Kai Mindermann
+Karsten Hiekmann
 Koji Yokota
 Kolja Brix
 Krunoslav Zubrinic
@@ -123,7 +129,6 @@ Michel Baylac
 Mike Smoot
 Moritz Ringler
 Morten Alver
-mpele
 Mélanie Tremblay
 Nadeem Mahmood
 Nathan Dunn
@@ -142,6 +147,7 @@ Paul Martin
 payload
 Peter Ansell
 Philip Johnson
+Predrag Milanovic
 Raik Nagel
 Renato Massao
 Robert Jäschke
@@ -168,6 +174,7 @@ Stefan Robert
 Stefano Gariazzo
 Stephan Lau
 Stephan Rave
+Stéphane Curet
 Sven Jäger
 The Gitter Badger
 Thiago Toledo

CHANGELOG.md

@@ -12,20 +12,15 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
-
-- We turned the validation feature in the entry editor off by default, because of a bug in the library we have been using [#3145](https://github.com/JabRef/jabref/issues/3145)
-- Added 'Filter All' and 'Filter None' buttons with corresponding functionality to Quality Check tool.
-- We increased the size of the keywords and file text areas in the entry editor
-- When the entry that is currently shown in the entry editor is deleted externally, the editor is now closed automatically [#2946](https://github.com/JabRef/jabref/issues/2946)
+- 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 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)
 
 ### Fixed
- - We re-added the "Normalize to BibTeX name format" context menu item [#3136](https://github.com/JabRef/jabref/issues/3136)
- - We fixed a memory leak in the source tab of the entry editor [#3113](https://github.com/JabRef/jabref/issues/3113)
- - We fixed a [java bug](https://bugs.openjdk.java.net/browse/JDK-8185792) where linux users could not enter accented characters in the entry editor and the search bar [#3028](https://github.com/JabRef/jabref/issues/3028)
- - We fixed a regression introduced in v4.0-beta2: A file can be dropped to the entry preview to attach it to the entry [koppor#245](https://github.com/koppor/jabref/issues/245)
- - We fixed an issue in the "Replace String" dialog (<kbd>Ctrl</kbd>+<kbd>R</kbd> where search and replace did not work for the `bibtexkey` field. [#3132](https://github.com/JabRef/jabref/issues/3132)
--  We fixed an issue in the entry editor where adding a term to a new protected terms list freezed JabRef completely. [#3157](https://github.com/JabRef/jabref/issues/3157)
--  We fixed an issue in the "Manage protected terms" dialog where an 'Open file' dialog instead of a 'Save file' dialog was shown when creating a new list. [#3157](https://github.com/JabRef/jabref/issues/3157)
+ - 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)
+
 ### Removed
 
 
@@ -73,9 +68,49 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 
 
+## [4.0] - 2017-10-04
 
+### Changed
 
+- We add a textArea to see versionInfo in the About JabRef Dialog.[#2942](https://github.com/JabRef/jabref/issues/2942)
+- We turned the validation feature in the entry editor off by default, because of a bug in the library we have been using [#3145](https://github.com/JabRef/jabref/issues/3145)
+- Added 'Filter All' and 'Filter None' buttons with corresponding functionality to Quality Check tool.
+- We increased the size of the keywords and file text areas in the entry editor
+- When the entry that is currently shown in the entry editor is deleted externally, the editor is now closed automatically [#2946](https://github.com/JabRef/jabref/issues/2946)
+- We added reordering of file and link entries in the `General`-Tab [3165, comment](https://github.com/JabRef/jabref/issues/3165#issuecomment-326269715)
+- We added autcompletion for the `crossref` field on basis of the BibTeX-key. To accept such an autcompleted key as new entry-link, you have to press <kbd>Enter</kbd> two times, otherwise the field data is not stored in the library file.[koppor#257](https://github.com/koppor/jabref/issues/257)
+- We added drag and drop support for adding files directly in the `General`-Tab. The dragged files are currently only linked from their existing directory. For more advanced features use the `Add files` dialog. [#koppor#244](https://github.com/koppor/jabref/issues/244)
+- We added the file description filed back to the list of files in the `General`-Tab [#2930, comment](https://github.com/JabRef/jabref/issues/2930#issuecomment-328328172)
+- Added an error dialog if the file is open in another process and cannot be renamed. [#3229]
+- On Windows, the `JabRef.exe` executable can now be used to start JabRef from the command line. By default, no output is shown unless the new "-console" option is specified. 
 
+### Fixed
+
+- We re-added the "Normalize to BibTeX name format" context menu item [#3136](https://github.com/JabRef/jabref/issues/3136)
+- We fixed a memory leak in the source tab of the entry editor [#3113](https://github.com/JabRef/jabref/issues/3113)
+- We fixed a [java bug](https://bugs.openjdk.java.net/browse/JDK-8185792) where linux users could not enter accented characters in the entry editor and the search bar [#3028](https://github.com/JabRef/jabref/issues/3028)
+- We fixed a regression introduced in v4.0-beta2: A file can be dropped to the entry preview to attach it to the entry [koppor#245](https://github.com/koppor/jabref/issues/245)
+- We fixed an issue in the "Replace String" dialog (<kbd>Ctrl</kbd>+<kbd>R</kbd> where search and replace did not work for the `bibtexkey` field. [#3132](https://github.com/JabRef/jabref/issues/3132)
+- We fixed an issue in the entry editor where adding a term to a new protected terms list freezed JabRef completely. [#3157](https://github.com/JabRef/jabref/issues/3157)
+- We fixed an issue in the "Manage protected terms" dialog where an 'Open file' dialog instead of a 'Save file' dialog was shown when creating a new list. [#3157](https://github.com/JabRef/jabref/issues/3157)
+- We fixed an issue where unparseable dates of the FileAnnotations caused the FileAnnotationsTab to crash.
+- We fixed an issue where a new protected terms list was not available immediately after its addition. [#3161](https://github.com/JabRef/jabref/issues/3161)
+- We fixed an issue where an online file link could not be removed from an entry [#3165](https://github.com/JabRef/jabref/issues/3165)
+- We fixed an issue where an online file link did not open the browser and created an error [#3165](https://github.com/JabRef/jabref/issues/3165)
+- We fixed an issue where the arrow keys in the search bar did not work as expected [#3081](https://github.com/JabRef/jabref/issues/3081)
+- We fixed wrong hotkey being displayed at "automatically file links" in the entry editor
+- We fixed an issue where metadata syncing with local and shared database were unstable. It will also fix syncing groups and sub-groups in database. [#2284](https://github.com/JabRef/jabref/issues/2284)
+- We fixed an issue where renaming a linked file would fail silently if a file with the same name existed.  Added support for overriding existing file at user discretion. [#3172] (https://github.com/JabRef/jabref/issues/3172)
+- We fixed an issue where the "Remove group and subgroups" operation did not remove group information from entries in the group [#3190](https://github.com/JabRef/jabref/issues/3190)
+- We fixed an issue where it was possible to leave the entry editor with an imbalance of braces. [#3167](https://github.com/JabRef/jabref/issues/3167)
+- Renaming files now truncates the filename to not exceed the limit of 255 chars [#2622](https://github.com/JabRef/jabref/issues/2622)
+- We improved the handling of hyphens in names. [#2775](https://github.com/JabRef/jabref/issues/2775)
+- We fixed an issue where an entered file description was not written to the bib-file [#3208](https://github.com/JabRef/jabref/issues/3208)
+- We improved the auto completion in the search bar. [koppor#253](https://github.com/koppor/jabref/issues/253)
+- We fixed renaming files which are not in the main directory. [#3230](https://github.com/JabRef/jabref/issues/3230)
+
+### Removed
+- We removed support for LatexEditor, as it is not under active development. [#3199](https://github.com/JabRef/jabref/issues/3199)
 
 
 ## [4.0-beta3] – 2017-08-16
@@ -937,7 +972,8 @@ Since much functionality has changed during development, a release of this versi
 
 The changelog of 2.11 and versions before is maintained as [text file](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG) in the [v2.11.1 tag](https://github.com/JabRef/jabref/tree/v2.11.1).
 
-[unreleased]: https://github.com/JabRef/jabref/compare/v4.0-beta3...HEAD
+[Unreleased]: https://github.com/JabRef/jabref/compare/v4.0...HEAD
+[4.0]: https://github.com/JabRef/jabref/compare/v4.0-beta3...v4.0
 [4.0-beta3]: https://github.com/JabRef/jabref/compare/v4.0-beta2...v4.0-beta3
 [4.0-beta2]: https://github.com/JabRef/jabref/compare/v4.0-beta...v4.0-beta2
 [4.0-beta]: https://github.com/JabRef/jabref/compare/v3.8.2...v4.0-beta

build.gradle

@@ -31,8 +31,8 @@ apply from: 'localization.gradle'
 apply from: 'xjc.gradle'
 
 group = "org.jabref"
-version = "4.0-dev"
-project.ext.threeDotVersion = "4.0.2.1"
+version = "4.1-dev"
+project.ext.threeDotVersion = "4.0.3.1"
 project.ext.install4jDir = hasProperty("install4jDir") ? getProperty("install4jDir") : (OperatingSystem.current().isWindows() ? 'C:/Program Files/install4j6' : 'install4j6')
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
@@ -72,7 +72,7 @@ dependencies {
     compile 'org.apache.pdfbox:jempbox:1.8.13'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    compile 'org.bouncycastle:bcprov-jdk15on:1.57'
+    compile 'org.bouncycastle:bcprov-jdk15on:1.58'
 
     compile 'commons-cli:commons-cli:1.4'
 
@@ -82,7 +82,7 @@ dependencies {
     compile 'org.openoffice:unoil:4.1.2'
 
     compile 'com.github.bkromhout:java-diff-utils:2.1.1'
-    compile 'info.debatty:java-string-similarity:0.24'
+    compile 'info.debatty:java-string-similarity:1.0.0'
 
     antlr3 'org.antlr:antlr:3.5.2'
     compile 'org.antlr:antlr-runtime:3.5.2'
@@ -91,7 +91,7 @@ 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:5.1.42'
+    compile 'mysql:mysql-connector-java:5.1.43'
 
     compile 'com.impossibl.pgjdbc-ng:pgjdbc-ng:0.7.1'
 
@@ -104,7 +104,7 @@ dependencies {
     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:8.40.13'
+    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'
@@ -113,9 +113,9 @@ dependencies {
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
     compile 'commons-logging:commons-logging:1.2'
-    compile 'org.apache.logging.log4j:log4j-jcl:2.8.2'
-    compile 'org.apache.logging.log4j:log4j-api:2.8.2'
-    compile 'org.apache.logging.log4j:log4j-core:2.8.2'
+    compile 'org.apache.logging.log4j:log4j-jcl:2.9.1'
+    compile 'org.apache.logging.log4j:log4j-api:2.9.1'
+    compile 'org.apache.logging.log4j:log4j-core:2.9.1'
 
     // need to use snapshots as the stable version is from 2013 and doesn't support v1.0.1 CitationStyles
     compile 'org.citationstyles:styles:1.0.1-SNAPSHOT'
@@ -128,12 +128,12 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '1.0.+'
 
     testCompile 'junit:junit:4.12'
-    testCompile 'org.mockito:mockito-core:2.8.47'
-    testCompile 'com.github.tomakehurst:wiremock:2.7.1'
+    testCompile 'org.mockito:mockito-core:2.10.0'
+    testCompile 'com.github.tomakehurst:wiremock:2.8.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
-    testCompile 'org.xmlunit:xmlunit-core:2.4.0'
-    testCompile 'org.xmlunit:xmlunit-matchers:2.4.0'
+    testCompile 'org.xmlunit:xmlunit-core:2.5.0'
+    testCompile 'org.xmlunit:xmlunit-matchers:2.5.0'
     testCompile 'com.tngtech.archunit:archunit-junit:0.4.0'
     testCompile 'org.slf4j:slf4j-jcl:1.7.25' // required by ArchUnit to enable logging over jcl
 }

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,5 @@
-#Mon Aug 14 21:03:12 CEST 2017
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.2-bin.zip

scripts/syncLang.py

@@ -11,6 +11,7 @@
 
 RES_DIR = "src/main/resources/l10n"
 STATUS_FILE = "status.md"
+URL_BASE = "https://github.com/JabRef/jabref/tree/master/src/main/resources/l10n/"
 
 
 def get_current_branch():
@@ -413,12 +414,13 @@ def write_properties(property_files):
             num_keys_translated = num_keys - num_keys_missing_value
             percent_translated = int((num_keys_translated / float(num_keys)) * 100) if num_keys != 0 else 0
 
-            markdown.append("| {file} | {num_keys} | {num_keys_translated} | {num_keys_missing} | {percent_translated} |\n"
-                .format(file=get_filename(filepath=file), num_keys=num_keys, num_keys_translated=num_keys_translated, num_keys_missing=num_keys_missing_value, percent_translated=percent_translated))
+            markdown.append("| [{file}]({url_base}{file}) | {num_keys} | {num_keys_translated} | {num_keys_missing} | {percent_translated} |\n"
+         .format(url_base=URL_BASE, file=os.path.basename(file), num_keys=num_keys, num_keys_translated=num_keys_translated, num_keys_missing=num_keys_missing_value, percent_translated=percent_translated))
 
     markdown = []
     date = datetime.datetime.now().strftime("%Y-%m-%d %H:%M")
-    markdown.append("### Localization files status ({date} - Branch `{branch}` `{hash}`)\n".format(date=date, branch=get_current_branch(), hash=get_current_hash_short()))
+    markdown.append("### Localization files status ({date} - Branch `{branch}` `{hash}`)\n\n".format(date=date, branch=get_current_branch(), hash=get_current_hash_short()))
+    markdown.append("Note: To get the current status from your local repository, run `python ./scripts/syncLang.py markdown`\n")
 
     write_properties(property_files=get_all_jabref_properties())
     write_properties(property_files=get_all_menu_properties())

src/main/java/org/jabref/FallbackExceptionHandler.java

@@ -1,24 +1,21 @@
 package org.jabref;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.Marker;
-import org.apache.logging.log4j.MarkerManager;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 
 /**
  * Catch and log any unhandled exceptions.
  */
 public class FallbackExceptionHandler implements Thread.UncaughtExceptionHandler {
 
-    private static final Marker UncaughtException_MARKER = MarkerManager.getMarker("UncaughtException");
+    private static final Log LOGGER = LogFactory.getLog(FallbackExceptionHandler.class);
 
     public static void installExceptionHandler() {
         Thread.setDefaultUncaughtExceptionHandler(new FallbackExceptionHandler());
     }
 
     @Override
     public void uncaughtException(Thread thread, Throwable exception) {
-        Logger logger = LogManager.getLogger(FallbackExceptionHandler.class);
-        logger.error(UncaughtException_MARKER, "Uncaught exception Occurred in " + thread, exception);
+        LOGGER.error("Uncaught exception occurred in " + thread, exception);
     }
 }

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

@@ -75,8 +75,10 @@ private static void start(String[] args) {
         PreferencesMigrations.upgradeSortOrder();
         PreferencesMigrations.upgradeFaultyEncodingStrings();
         PreferencesMigrations.upgradeLabelPatternToBibtexKeyPattern();
+        PreferencesMigrations.upgradeImportFileAndDirePatterns();
         PreferencesMigrations.upgradeStoredCustomEntryTypes();
         PreferencesMigrations.upgradeKeyBindingsToJavaFX();
+        PreferencesMigrations.addCrossRefRelatedFieldsForAutoComplete();
 
         // Update handling of special fields based on preferences
         InternalBibtexFields