Merge remote-tracking branch 'upstream/master'

* upstream/master: (32 commits)
  Extend architecture tests to javafx and javafx.collections (#2719)
  Entry editor goes JavaFX (#2754)
  Fix tests
  Implement feedback
  Update Install4J from 6.1.4 to 6.1.5
  Show development information
  Release v4.0-beta
  Fix tests
  Changed the Normalizer from NFKC to NFC to allow superscripts to be converted into unicode
  Update AUTHORS
  Return month in JabRef format
  Extract setDate to new method
  Fix RisImporter
  Fix test output
  Remove year from RepecNepImporterTest as this case does not seem to appear in the wild
  Add test case for month format behavior
  Rename getBibtexFormat to getJabRefFormat as this string is something special for JabRef
  Use BibEntry#parseMonth at BibTeXConverter
  Use BibEntry#setMonth at RisImporter
  Change month on MSXMLimport to numeric
  ...

.mailmap

@@ -4,6 +4,9 @@
 # duplicates that aren't also email duplicates): scan the output of:
 #   git log --format='%aE - %aN' | sort --unique --ignore-case
 #
+# One can find out the real name by using the GitHub API.
+# E.g., https://api.github.com/users/sauliusg/events/public
+#
 # For explanation on this file format: man git-shortlog
 Ruy Minoru Ito Takata <ruy.takata@gmail.com>
 Ruy Minoru Ito Takata <ruy.takata@gmail.com> <21537850814@serpro-1557637.(none)>
@@ -109,3 +112,8 @@ Arno Blouin <blouin.arno@gmail.com>
 Jeff Miller <miller@psy.otago.ac.nz>
 Alain Vaucher <avaucher@users.noreply.github.com>
 Daniel Mair <mairdl.dev@gmail.com> <mairdl.dev@googlemail.com>
+Sven Jäger <svenjaeger@gmx.de>
+Tim van Rossum <trvanrossum@gmail.com>
+Saulius Gražulis <grazulis@ibt.lt>
+Rolf Starre <rolf.starre@gmail.com> <RolfStarre@users.noreply.github.com>
+Owen Huang <ohuang12@users.noreply.github.com>

AUTHORS

@@ -40,6 +40,7 @@ David Weitzman
 Dennis Tschechlov
 Dominik Waßenhoven
 Douglas Nassif Roma Junior
+Eduard Braun
 Eduardo Greco
 Egon Willighagen
 Ellen Reitmayr
@@ -129,13 +130,15 @@ Olaf Lenz
 Oliver Beckmann
 Oliver Kopp
 Oscar Gustafsson
+Owen Huang
 Paul Martin
 payload
 Peter Ansell
 Philip Johnson
 Raik Nagel
 Renato Massao
 Robert Jäschke
+Rolf Starre
 Rudolf Seemann
 Ruy Minoru Ito Takata
 Ryo Igarashi
@@ -144,6 +147,7 @@ Saivert
 Samin Muhammad Ridwanul Karim
 Sascha Hunold
 Sascha Zeller
+Saulius Gražulis
 Saverio Mori
 Scott Townsend
 Seb Wills
@@ -157,10 +161,12 @@ Stefan Robert
 Stefano Gariazzo
 Stephan Lau
 Stephan Rave
+Sven Jäger
 The Gitter Badger
 Thiago Toledo
 Thomas Arildsen
 Thorsten Dahlheimer
+Tim van Rossum
 Tobias Boceck
 Tobias Denkinger
 Tobias Diez
@@ -173,6 +179,7 @@ Uwe Kuehn
 Vincent W. Yang
 Waluyo Adi Siswanto
 Ward Poelmans
+Wenbo Yang
 wuw
 Yang Zongze
 Yara Grassi Gouffon

CHANGELOG.md

@@ -8,9 +8,57 @@ Here, the categories "Changed" for added and changed functionality,
 
 We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#NUM`.
 
-
 ## [Unreleased]
 
+### Changed
+
+### Fixed
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+### Removed
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+## [4.0-beta] – 2017-04-17
+
 ### Changed
 - JabRef has a new logo! The logo was designed by "[AikTheOne](https://99designs.de/profiles/theonestudio)" - who was the winner of a design contest at 99designs.com
 - Partly switched to a new UI technology ([JavaFX]).
@@ -36,14 +84,14 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
   - All file dialogs now use the native file selector of the OS. [#1711](https://github.com/JabRef/jabref/issues/1711)
 - We added a few properties to a group:
     - Icon (with customizable color) that is shown in the groups panel (implements a [feature request in the forum](http://discourse.jabref.org/t/assign-colors-to-groups/321)).
-    - Description text that is shown on mouse hover (implements old feature requests [489](https://sourceforge.net/p/jabref/feature-requests/489/) and [818](https://sourceforge.net/p/jabref/feature-requests/818/)
-- We introduced "automatic groups" that automatically create subgroups based on a certain criteria (e.g., a subgroup for every author or keyword) and supports hierarchies. Implements [91](https://sourceforge.net/p/jabref/feature-requests/91/), [398](https://sourceforge.net/p/jabref/feature-requests/398/) and [#1173](https://github.com/JabRef/jabref/issues/1173) and [#628](https://github.com/JabRef/jabref/issues/628).
+    - Description text that is shown on mouse hover (implements old feature requests [489](https://sourceforge.net/p/jabref/feature-requests/489/) and [818](https://sourceforge.net/p/jabref/feature-requests/818/))
+- We introduced "automatic groups" that automatically create subgroups based on a certain criteria (e.g., a subgroup for every author or keyword) and supports hierarchies. Implements [91](https://sourceforge.net/p/jabref/feature-requests/91/), [398](https://sourceforge.net/p/jabref/feature-requests/398/), [#1173](https://github.com/JabRef/jabref/issues/1173) and [#628](https://github.com/JabRef/jabref/issues/628).
 - We added a document viewer which allows you to have a glance at your PDF documents directly from within JabRef.
 - Using "Look up document identifier" in the quality menu, it is possible to look up DOIs, ArXiv ids and other identifiers for multiple entries.
 - Comments in PDF files can now be displayed inside JabRef in a separate tab
 - We separated the `Move file` and `Rename Pdfs` logic and context menu entries in the `General`-Tab for the Field `file` to improve the semantics
 - We integrated support for the [paper recommender system Mr.DLib](http://help.jabref.org/en/EntryEditor#related-articles-tab) in a new tab in the entry editor.
-- We renamed "database" to "library" to have a real distinction to SQL and NoSQL databases. [#2095](https://github.com/JabRef/jabref/issues/2095)
+- We renamed "database" to "library" to have a real distinction to SQL databases ("shared database") and `bib` files ("library"). [#2095](https://github.com/JabRef/jabref/issues/2095)
 - We improved the UI customization possibilities:
     - It is now possible to customize the colors and the size of the icons (implements a [feature request in the forum](http://discourse.jabref.org/t/menu-and-buttons-with-a-dark-theme/405)).
     - Resizing the menu and label sizes has been improved.
@@ -54,7 +102,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Add tab which shows the MathSciNet review website if the `MRNumber` field is present.
 - A scrollbar was added to the cleanup panel, as a result of issue [#2501](https://github.com/JabRef/jabref/issues/2501)
 - Several scrollbars were added to the preference dialog which show up when content is too large [#2559](https://github.com/JabRef/jabref/issues/2559)
-- We fixed and improved the auto detection of the []OpenOffice and LibreOffice connection](http://help.jabref.org/en/OpenOfficeIntegration)
+- We fixed and improved the auto detection of the [OpenOffice and LibreOffice connection](http://help.jabref.org/en/OpenOfficeIntegration)
 - We added an option to copy the title of BibTeX entries to the clipboard through `Edit -> Copy title` (implements [#210](https://github.com/koppor/jabref/issues/210))
 - The `Move linked files to default file directory`-Cleanup operation respects the `File directory pattern` setting
 - We removed the ordinals-to-superscript formatter from the recommendations for biblatex save actions [#2596](https://github.com/JabRef/jabref/issues/2596)
@@ -102,51 +150,6 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
  - OpenOffice text formatting now handles nested tags properly [#2483](https://github.com/JabRef/jabref/issues/#2483)
  - The group selection is no longer lost when switching tabs [#1104](https://github.com/JabRef/jabref/issues/1104)
 
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 ## [3.8.2] – 2017-01-29
 
@@ -492,7 +495,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Main table now accepts pasted DOIs and tries to retrieve the entry
 - Added support for several Biblatex-fields through drop-down lists with valid alternatives
 - Added integrity checker for an odd number of unescaped '#'
-- Implemented [feature request 384](https://sourceforge.net/p/jabref/features/384): The merge entries dialog now show all text and colored differences between the fields
+- Implemented [feature request #384](https://sourceforge.net/p/jabref/features/384): The merge entries dialog now show all text and colored differences between the fields
 - Implemented [#1233](https://github.com/JabRef/jabref/issues/1233): Group side pane now takes up all the remaining space
 - Added integrity check detecting HTML-encoded characters
 - Added missing help files
@@ -843,7 +846,8 @@ 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/v3.8.2...HEAD
+[unreleased]: https://github.com/JabRef/jabref/compare/v4.0-beta...HEAD
+[4.0-beta]: https://github.com/JabRef/jabref/compare/v3.8.2...v4.0-beta
 [3.8.2]: https://github.com/JabRef/jabref/compare/v3.8.1...v3.8.2
 [3.8.1]: https://github.com/JabRef/jabref/compare/v3.8...v3.8.1
 [3.8]: https://github.com/JabRef/jabref/compare/v3.7...v3.8

README.md

@@ -24,9 +24,9 @@ JabRef also lets you easily link to PDF or web sources for your reference entrie
 JabRef can import from and export to several formats, and you can customize export filters.
 JabRef can be run as a command line application to convert from any import format to any export format.
 
-* Homepage: https://www.jabref.org
-* Development page: https://github.com/JabRef/jabref
-* Open HUB page: https://www.openhub.net/p/jabref
+* Homepage: <https://www.jabref.org>
+* Development page: <https://github.com/JabRef/jabref>
+* Open HUB page: <https://www.openhub.net/p/jabref>
 
 ### Bug Reports, Suggestions, Other Feedback
 
@@ -47,6 +47,11 @@ For details see [CONTRIBUTING](CONTRIBUTING.md).
 ### Requirements
 
 JabRef runs on any system equipped with the Java Virtual Machine (1.8 or newer), which can be downloaded at no cost from [Oracle](http://www.oracle.com/technetwork/java/javase/downloads/index.html).
+From JabRef 4.0 onwards, [JavaFX] support has to be available.
+
+### Installing and Running, Linux:
+
+Please see our [Installation Guide](http://help.jabref.org/en/Installation).
 
 ### Installing and Running, Mac OS X:
 
@@ -109,4 +114,5 @@ See [external libraries](external-libraries.txt) for details.
   [BibTeX]: https://www.ctan.org/pkg/bibtex
   [Biblatex]: https://www.ctan.org/pkg/biblatex
   [install4j]: https://www.ej-technologies.com/products/install4j/overview.html
-  [JabRef]: http://www.jabref.org
+  [JabRef]: https://www.jabref.org
+  [JavaFX]: https://en.wikipedia.org/wiki/JavaFX

build.gradle

@@ -15,7 +15,7 @@ buildscript {
 
 plugins {
     id 'com.gradle.build-scan' version '1.3'
-    id "com.install4j.gradle" version "6.1.3"
+    id "com.install4j.gradle" version "6.1.5"
     id 'com.github.johnrengelman.shadow' version '1.2.4'
     id "com.simonharrer.modernizer" version "1.4.0-1"
     id 'me.champeau.gradle.jmh' version '0.3.1'
@@ -43,7 +43,7 @@ apply from: 'xjc.gradle'
 
 group = "org.jabref"
 version = "4.0.0-dev"
-project.ext.threeDotVersion = "4.0.0.0"
+project.ext.threeDotVersion = "4.0.0.1"
 project.ext.install4jDir = hasProperty("install4jDir") ? getProperty("install4jDir") : (OperatingSystem.current().isWindows() ? 'C:/Program Files/install4j6' : 'install4j6')
 sourceCompatibility = 1.8
 targetCompatibility = 1.8

jabref.install4j

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<install4j version="6.1.4" transformSequenceNumber="5">
+<install4j version="6.1.5" transformSequenceNumber="5">
   <directoryPresets config="build/releases/${compiler:buildFileName}" />
   <application name="JabRef" distributionSourceDir="" applicationId="0034-7691-1464-4754" mediaDir="build/install4j" mediaFilePattern="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:sys.version}" compression="6" lzmaCompression="false" pack200Compression="false" excludeSignedFromPacking="true" commonExternalFiles="false" createMd5Sums="true" shrinkRuntime="true" shortName="JabRef" publisher="JabRef Community" publisherWeb="https://www.jabref.org/" version="DEV" allPathsRelative="true" backupOnSave="false" autoSave="true" convertDotsToUnderscores="true" macSignature="????" macVolumeId="780dfea2d33a0244" javaMinVersion="1.8" javaMaxVersion="" allowBetaVM="false" jdkMode="runtimeJre" jdkName="">
     <languages skipLanguageSelection="true" languageSelectionInPrincipalLanguage="false">

scripts/prepare-install4j.sh

@@ -7,11 +7,11 @@ fi
 
 # ensure that tar archive of install4j exists
 cd ~/downloads
-wget --quiet -nc http://download-keycdn.ej-technologies.com/install4j/install4j_unix_6_1_4.tar.gz
+wget --quiet -nc http://download-keycdn.ej-technologies.com/install4j/install4j_unix_6_1_5.tar.gz
 
 # extract tar archive of install4j into the source directory of JabRef
 cd ~/jabref
-tar -xzf ~/downloads/install4j_unix_6_1_4.tar.gz
+tar -xzf ~/downloads/install4j_unix_6_1_5.tar.gz
 
 # fetch JREs
 if [ ! -d ~/.install4j6/jres/ ]; then

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

@@ -53,7 +53,7 @@ public static void main(String[] args) throws IOException, InterruptedException
 
                     @Override
                     public void run() {
-                        Optional<DOI> origDOI = entry.getField(FieldName.DOI).flatMap(DOI::build);
+                        Optional<DOI> origDOI = entry.getField(FieldName.DOI).flatMap(DOI::parse);
                         if (origDOI.isPresent()) {
                             dois.incrementAndGet();
                             try {

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

@@ -136,6 +136,7 @@
 import org.jabref.model.entry.event.EntryEventSource;
 import org.jabref.model.entry.specialfields.SpecialField;
 import org.jabref.model.entry.specialfields.SpecialFieldValue;
+import org.jabref.model.util.FileHelper;
 import org.jabref.preferences.JabRefPreferences;
 import org.jabref.preferences.PreviewPreferences;
 import org.jabref.shared.DBMSSynchronizer;
@@ -522,11 +523,11 @@ public void update() {
         actions.put(Actions.OPEN_EXTERNAL_FILE, (BaseAction) () -> openExternalFile());
 
         actions.put(Actions.OPEN_FOLDER, (BaseAction) () -> JabRefExecutorService.INSTANCE.execute(() -> {
-            final List<File> files = FileUtil.getListOfLinkedFiles(mainTable.getSelectedEntries(),
+            final List<Path> files = FileUtil.getListOfLinkedFiles(mainTable.getSelectedEntries(),
                     bibDatabaseContext.getFileDirectories(Globals.prefs.getFileDirectoryPreferences()));
-            for (final File f : files) {
+            for (final Path f : files) {
                 try {
-                    JabRefDesktop.openFolderAndSelectFile(f.getAbsolutePath());
+                    JabRefDesktop.openFolderAndSelectFile(f.toAbsolutePath());
                 } catch (IOException e) {
                     LOGGER.info("Could not open folder", e);
                 }
@@ -1447,11 +1448,6 @@ public void showEntry(final BibEntry be) {
                 // setting showing to null, and recursively calling this method.
                 newEntryShowing(null);
                 showEntry(be);
-            } else {
-                // The correct entry is already being shown. Make sure the editor
-                // is updated.
-                ((EntryEditor) splitPane.getBottomComponent()).updateAllFields();
-
             }
             return;
 
@@ -1594,7 +1590,6 @@ public void ensureNotShowingBottomPanel(BibEntry entry) {
     public void updateEntryEditorIfShowing() {
         if (mode == BasePanelMode.SHOWING_EDITOR) {
             if (currentEditor.getDisplayedBibEntryType().equals(currentEditor.getEntry().getType())) {
-                currentEditor.updateAllFields();
                 currentEditor.updateSource();
             } else {
                 // The entry has changed type, so we must get a new editor.
@@ -2119,7 +2114,7 @@ public Optional<String> searchAndOpen() {
                 final List<File> res = result.get(entry);
                 if (!res.isEmpty()) {
                     final String filepath = res.get(0).getPath();
-                    final Optional<String> extension = FileUtil.getFileExtension(filepath);
+                    final Optional<String> extension = FileHelper.getFileExtension(filepath);
                     if (extension.isPresent()) {
                         Optional<ExternalFileType> type = ExternalFileTypes.getInstance()
                                 .getExternalFileTypeByExt(extension.get());