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

* upstream/master: (188 commits)
  Show file description only if not empty
  Add file description to gui and fix sync bug (#3210)
  Don't highlight odd rows in file list editor (#3223)
  Fix assertion by removing typo (#3220)
  Update assertion to change of online reference (#3221)
  Put in null return
  Reformatted code, renamed method, added try/catch
  Add tests for removal changes
  Improve telemetry (#3218)
  Real test linking real other entry (#3214)
  Check for explicit group at different location
  Update java-string-similarity from 0.24 -> 1.0.0
  Only remove ExplicitGroups from entries, but not keyword-based groups
  Localization: French: Translation of a new string (#3212)
  Fix null return
  Changed from Path to Optional<Path>
  Fix #2775: Hyphens in last names are properly parsed (#3209)
  Followup to Issue #3167 (#3202)
  Remove unused import in GroupTreeNode
  Move getEntriesInGroup to GroupTreeNode
  ...

.mailmap

@@ -121,3 +121,8 @@ Anita Armbruster <armbruan@gmail.com>
 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>
+Andrew Levit <dreyskiy@gmail.com>
+

AUTHORS

@@ -12,7 +12,9 @@ Alexsandro Lauber
 Ali Ayan
 Ambrogio Oliva
 Andreas Amann
+Andreas Buhr
 Andreas Rudert
+Andrew Levit
 Anh Nghia Tran
 Anita Armbruster
 Antonio Ribeiro
@@ -56,6 +58,7 @@ Felix Langner
 Felix Wilke
 Fernando Santagata
 Florian Straßer
+Foivos Christoulakis
 Francois Charette
 Frank Steimle
 Fred
@@ -89,6 +92,7 @@ Jörg Zieren
 Jørgen Kvalsvik
 Jürgen Lange
 Kai Mindermann
+Karsten Hiekmann
 Koji Yokota
 Kolja Brix
 Krunoslav Zubrinic
@@ -121,7 +125,6 @@ Michel Baylac
 Mike Smoot
 Moritz Ringler
 Morten Alver
-mpele
 Mélanie Tremblay
 Nadeem Mahmood
 Nathan Dunn
@@ -140,6 +143,7 @@ Paul Martin
 payload
 Peter Ansell
 Philip Johnson
+Predrag Milanovic
 Raik Nagel
 Renato Massao
 Robert Jäschke

CHANGELOG.md

@@ -8,22 +8,45 @@ 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
 
-- If fetched article is already in database, then the entry merge dialog is shown.
-- An error message is now displayed if you try to create a group containing the keyword separator or if there is already a group with the same name. [#3075](https://github.com/JabRef/jabref/issues/3075) and [#1495](https://github.com/JabRef/jabref/issues/1495)
+- 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)
 
 ### Fixed
 
-- We fixed an issue where the fetcher for the Astrophysics Data System (ADS) added some non-bibtex data to the entry returned from the search [#3035](https://github.com/JabRef/jabref/issues/3035)
-- We fixed an issue where assigning an entry via drag and drop to a group caused JabRef to stop/freeze completely [#3036](https://github.com/JabRef/jabref/issues/3036)
-- We fixed the shortcut <kbd>Ctrl</kbd>+<kbd>F</kbd> for the search field.
-- We fixed an issue where the preferences could not be imported without a restart of JabRef [#3064](https://github.com/JabRef/jabref/issues/3064)
-- We fixed an issue where <kbd>DEL</kbd>, <kbd>Ctrl</kbd>+<kbd>C</kbd>, <kbd>Ctrl</kbd>+<kbd>V</kbd> and <kbd>Ctrl</kbd>+<kbd>A</kbd> in the search field triggered corresponding actions in the main table [#3067](https://github.com/JabRef/jabref/issues/3067)
-
+- 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)
 ### Removed
+- We removed support for LatexEditor, as it is not under active development. [#3199](https://github.com/JabRef/jabref/issues/3199)
 
 
 
@@ -74,6 +97,34 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 
 
+## [4.0-beta3] – 2017-08-16
+
+### Changed
+- We made the font size in the entry editor and group panel customizable by "Menu and label font size". [#3034](https://github.com/JabRef/jabref/issues/3034)
+- If fetched article is already in database, then the entry merge dialog is shown.
+- An error message is now displayed if you try to create a group containing the keyword separator or if there is already a group with the same name. [#3075](https://github.com/JabRef/jabref/issues/3075) and [#1495](https://github.com/JabRef/jabref/issues/1495)
+- The FileAnnotationsTab was re-implemented in JavaFx. [#3082](https://github.com/JabRef/jabref/pull/3082)
+- Integrity warnings are now directly displayed in the entry editor.
+- We added the functionality to have `regex` as modifier. [#457](https://github.com/JabRef/jabref/issues/457)
+
+### Fixed
+
+- We fixed an issue where the fetcher for the Astrophysics Data System (ADS) added some non-bibtex data to the entry returned from the search [#3035](https://github.com/JabRef/jabref/issues/3035)
+- We improved the auto completion so that minor changes are not added as suggestions. [#2998](https://github.com/JabRef/jabref/issues/2998)
+- We readded the undo mechanism for changes in the entry editor [#2973](https://github.com/JabRef/jabref/issues/2973)
+- We fixed an issue where assigning an entry via drag and drop to a group caused JabRef to stop/freeze completely [#3036](https://github.com/JabRef/jabref/issues/3036)
+- We fixed the shortcut <kbd>Ctrl</kbd>+<kbd>F</kbd> for the search field.
+- We fixed an issue where `title_case` and `capitalize` modifiers did not work with shorttitle.
+- We fixed an issue where the preferences could not be imported without a restart of JabRef [#3064](https://github.com/JabRef/jabref/issues/3064)
+- We fixed an issue where <kbd>DEL</kbd>, <kbd>Ctrl</kbd>+<kbd>C</kbd>, <kbd>Ctrl</kbd>+<kbd>V</kbd> and <kbd>Ctrl</kbd>+<kbd>A</kbd> in the search field triggered corresponding actions in the main table [#3067](https://github.com/JabRef/jabref/issues/3067)
+- We fixed an issue where JabRef freezed when editing an assigned file in the `General`-Tab [#2930, comment](https://github.com/JabRef/jabref/issues/2930#issuecomment-311050976)
+- We fixed an issue where a file could not be assigned to an existing entry via the entry context menu action `Attach file` [#3080](https://github.com/JabRef/jabref/issues/3080)
+- We fixed an issue where entry editor was not focused after opening up. [#3052](https://github.com/JabRef/jabref/issues/3052)
+- We fixed an issue where changes in the source tab were not stored when selecting a new entry. [#3086](https://github.com/JabRef/jabref/issues/3086)
+- We fixed an issue where the other tab was not updated when fields where changed in the source tab. [#3063](https://github.com/JabRef/jabref/issues/3063)
+- We fixed an issue where the source tab was not updated after fetching data by DOI. [#3103](https://github.com/JabRef/jabref/issues/3103)
+- We fixed an issue where the move to group operation did not remove the entry from other groups [#3101](https://github.com/JabRef/jabref/issues/3101)
+- We fixed an issue where the main table was not updated when grouping changes [#1903](https://github.com/JabRef/jabref/issues/1903)
 
 ## [4.0-beta2] – 2017-07-18
 
@@ -905,7 +956,8 @@ 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-beta2...HEAD
+[unreleased]: https://github.com/JabRef/jabref/compare/v4.0-beta3...HEAD
+[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
 [3.8.2]: https://github.com/JabRef/jabref/compare/v3.8.1...v3.8.2

build.gradle

@@ -32,7 +32,7 @@ apply from: 'xjc.gradle'
 
 group = "org.jabref"
 version = "4.0-dev"
-project.ext.threeDotVersion = "4.0.1.1"
+project.ext.threeDotVersion = "4.0.2.1"
 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'
 
@@ -82,6 +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:1.0.0'
 
     antlr3 'org.antlr:antlr:3.5.2'
     compile 'org.antlr:antlr-runtime:3.5.2'
@@ -90,35 +91,31 @@ 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'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:22.0'
+    compile 'com.google.guava:guava:23.0'
 
     // 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:8.40.13'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
-
     compile 'org.fxmisc.flowless:flowless:0.5.2'
-    compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
     compile 'org.fxmisc.richtext:richtextfx:0.7-M5'
 
-    compile 'commons-logging:commons-logging:1.2'
-
     compile 'org.jsoup:jsoup:1.10.3'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
-    compile 'info.debatty:java-string-similarity:0.24'
 
-    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.xmlunit:xmlunit-core:2.4.0'
-    compile 'org.xmlunit:xmlunit-matchers:2.4.0'
+    compile 'commons-logging:commons-logging:1.2'
+    compile 'org.apache.logging.log4j:log4j-jcl:2.9.0'
+    compile 'org.apache.logging.log4j:log4j-api:2.9.0'
+    compile 'org.apache.logging.log4j:log4j-core:2.9.0'
 
     // 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'
@@ -131,11 +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:2.7.0'
-    testCompile 'org.assertj:assertj-swing-junit:3.7.0'
+    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:2.5.0'
+    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
 }
@@ -153,6 +151,8 @@ sourceSets {
 }
 
 processResources {
+    filteringCharset = 'UTF-8'
+
     filesMatching("build.properties") {
         expand(version: project.version,
                 "year": String.valueOf(Calendar.getInstance().get(Calendar.YEAR)),
@@ -161,7 +161,6 @@ processResources {
                 "azureInstrumentationKey": System.getenv('AzureInstrumentationKey'))
         filteringCharset = 'UTF-8'
     }
-    filteringCharset = 'UTF-8'
 
     filesMatching("resource/**/meta.xml") {
         expand version: project.version
@@ -368,19 +367,23 @@ task release(dependsOn: ["media", "releaseJar"]) {
 task releaseJar(dependsOn: "shadowJar") {
     group = 'JabRef - Release'
     description "Creates a Jar release."
-
     doLast {
         copy {
             from("$buildDir/libs/JabRef-${project.version}-fat.jar")
             into("$buildDir/releases")
-
             rename { String fileName ->
                 fileName.replace('-fat', '')
             }
         }
+        // set executable with read permissions (first true) and for all (false)
+        file("$buildDir/releases/JabRef-${project.version}.jar").setExecutable(true, false);
     }
 }
 
+task snapJar(dependsOn: "releaseJar", type: Delete) {
+    delete fileTree(dir: "$buildDir/releases/", exclude: "JabRef-${project.version}.jar")
+}
+
 jmh {
     warmupIterations = 5
     iterations = 10

buildres/snapcraft/jabref.desktop

@@ -0,0 +1,12 @@
+[Desktop Entry]
+Name=JabRef
+GenericName=BibTeX Editor
+Comment=JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format.
+Type=Application
+Terminal=false
+Icon=${SNAP}/meta/gui/JabRef-icon-256.png
+Exec=jabref %U
+Keywords=bibtex;biblatex;latex;bibliography
+Categories=Office;
+StartupWMClass=org-jabref-JabRefMain
+MimeType=text/x-bibtex;

config/README.md

@@ -2,12 +2,13 @@
 
 1. Press <kbd>Ctrl</kbd> + <kbd>Alt</kbd> + <kbd>S</kbd>
 2. Go to "Editor > Code Style"
-3. Click "Manage..." (right of "Scheme:")
-4. Click "Import..."
-5. Choose `IntelliJ Code Style.xml`
-6. Press "OK"
+3. Click the gear (right of "Scheme: ...")
+4. Click "Import Scheme >"
+5. Choose `IntelliJ IDEA code style XML`
+6. Select the file `config\IntelliJ Code Style.xml`
 7. Press "OK"
-8. Press "Close"
-9. Press "OK"
+8. Press "OK"
+9. Press "Close"
+10. Press "OK"
 
 * Please let `.editorconfig` override the settings of IntelliJ