Merge remote-tracking branch 'upstream/master' into jdk9

* upstream/master: (184 commits)
  Try to update to gradle 5.0.2 (#4766)
  Post change notifications on JavaFX (#4871)
  fix missing l10n from previous merge
  fix compile error
  Fix right clicking on any entry and selecting "Open folder" results in the NullPointer exception (#4797)
  Bump fontbox from 2.0.14 to 2.0.15 (#4882)
  Bump pdfbox from 2.0.14 to 2.0.15 (#4881)
  Bump xmpbox from 2.0.14 to 2.0.15 (#4883)
  Bump mockito-core from 2.26.0 to 2.27.0 (#4879)
  Bump java-string-similarity from 1.1.0 to 1.2.1 (#4878)
  Fix JabRef dying silently without enough inotify instances (#4875)
  #4795 disable menu item if database not connected (#4828)
  Remove deprecated awt apple extension (#4860)
  Fix IllegalArgumentException when ranking entries (#4779)
  Bump junit-vintage-engine from 5.4.1 to 5.4.2 (#4866)
  Bump junit-platform-launcher from 1.4.1 to 1.4.2 (#4865)
  Bump junit-jupiter from 5.4.1 to 5.4.2 (#4867)
  Add author normalizer for medline import (#4863)
  Fixed group creation with default settings (#4801)
  removed default constructor of FXDialogService (#4847)
  ...

# Conflicts:
#	build.gradle
#	src/main/java/org/jabref/gui/JabRefFrame.java
#	src/main/java/org/jabref/gui/collab/ChangeDisplayDialog.java
#	src/main/java/org/jabref/gui/collab/EntryChangeViewModel.java

Author: Siedlerchr

.gitignore

@@ -10,6 +10,14 @@ status.md
 # Install4J
 install4j6/
 
+# Snap
+parts/
+stage/
+prime/
+*.snap
+jabref_source.tar.bz2
+snap/.snapcraft/
+
 # Gradle
 # generated when `gradlew --gui` is called
 ui/
@@ -23,18 +31,6 @@ ui/
 jabref.xml
 *.sonargraph
 
-# Snapcraft - JabRef places the files into buildres/snapcraft
-snap/
-
-
-
-
-
-
-
-
-
-
 # Created by https://www.gitignore.io/api/gradle,java,jabref,intellij,eclipse,netbeans,windows,linux,macos,node,snapcraft
 
 ### Eclipse ###

.mailmap

@@ -142,4 +142,5 @@ Johannes Manner <johannes.manner@web.de>
 Dominik Traczyk <dominik646@gmail.com>
 Cerrianne Santos <cerrianne.santos@gmail.com>
 Stefan Scheffel <st155160@stud.uni-stuttgart.de>
-Stefan Gerzmann <steppery@gmx.de>
+Stefan Gerzmann <steppery@gmx.de>
+Deepak Kumar <deepakkumar24196@gmail.com>

CHANGELOG.md

@@ -11,6 +11,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- We changed the latex command removal for docbook exporter. [#3838](https://github.com/JabRef/jabref/issues/3838)
 - We changed the location of some fields in the entry editor (you might need to reset your preferences for these changes to come into effect)
   - Journal/Year/Month in biblatex mode -> Deprecated (if filled)
   - DOI/URL: General -> Optional
@@ -48,14 +49,24 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We updated updated the Related Articles tab to accept JSON from the new version of the Mr. DLib service
 - We added an option in the preference dialog box that allows user to choose behavior after dragging and dropping files in Entry Editor. [#4356](https://github.com/JabRef/jabref/issues/4356)
 - We added the ability to have an export preference where previously "File"-->"Export"/"Export selected entries" would not save the user's preference[#4495](https://github.com/JabRef/jabref/issues/4495)
+- We optimized the code responsible for connecting to an external database, which should lead to huge improvements in performance.
+- For automatically created groups, added ability to filter groups by entry type. [#4539](https://github.com/JabRef/jabref/issues/4539)
 - We added the ability to add field names from the Preferences Dialog [#4546](https://github.com/JabRef/jabref/issues/4546)
 - We added the ability change the column widths directly in the main table. [#4546](https://github.com/JabRef/jabref/issues/4546)
 - We added the ability to execute default action in dialog by using with <kbd>Ctrl</kbd> + <kbd>Enter</kbd> combination [#4496](https://github.com/JabRef/jabref/issues/4496)
-
-
+- We grouped and reordered the Main Menu (File, Edit, Library, Quality, Tools, and View tabs & icons). [#4666](https://github.com/JabRef/jabref/issues/4666) [#4667](https://github.com/JabRef/jabref/issues/4667) [#4668](https://github.com/JabRef/jabref/issues/4668) [#4669](https://github.com/JabRef/jabref/issues/4669) [#4670](https://github.com/JabRef/jabref/issues/4670) [#4671](https://github.com/JabRef/jabref/issues/4671) [#4672](https://github.com/JabRef/jabref/issues/4672) [#4673](https://github.com/JabRef/jabref/issues/4673)
+- We added additional modifiers (capitalize, titlecase and sentencecase) to the Bibtex key generator. [#1506](https://github.com/JabRef/jabref/issues/1506)
+- We grouped the toolbar icons and changed the Open Library and Copy icons. [#4584](https://github.com/JabRef/jabref/issues/4584) 
+- We added a browse button next to the path text field for aux-based groups. [#4586](https://github.com/JabRef/jabref/issues/4586)
+- We changed the title of Group Dialog to "Add subgroup" from "Edit group" when we select Add subgroup option.
+- We enable import button only if entries are selected. [#4755](https://github.com/JabRef/jabref/issues/4755)
+- We made modifications to improve contrast of UI elements. [#4583](https://github.com/JabRef/jabref/issues/4583)
+- We added an option in the settings to set the default action in JabRef when right clicking on any entry in any database and selecting "Open folder". [#4763](https://github.com/JabRef/jabref/issues/4763)
+- The Medline fetcher now normalizes the author names according to the BibTeX-Standard [#4345](https://github.com/JabRef/jabref/issues/4345)
 
 
 ### Fixed
+- We fixed an issue where JabRef died silently for the user without enough inotify instances [#4874](https://github.com/JabRef/jabref/issues/4847)
 - We fixed an issue where corresponding groups are sometimes not highlighted when clicking on entries [#3112](https://github.com/JabRef/jabref/issues/3112)
 - We fixed an issue where custom exports could not be selected in the 'Export (selected) entries' dialog [#4013](https://github.com/JabRef/jabref/issues/4013)
 - Italic text is now rendered correctly. https://github.com/JabRef/jabref/issues/3356
@@ -67,6 +78,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where selecting a group messed up the focus of the main table / entry editor. https://github.com/JabRef/jabref/issues/3367
 - We fixed an issue where composite author names were sorted incorrectly. https://github.com/JabRef/jabref/issues/2828
 - We fixed an issue where commands followed by `-` didn't work. [#3805](https://github.com/JabRef/jabref/issues/3805)
+- We fixed an issue where a non-existing aux file in a group made it impossible to open the library. [#4735](https://github.com/JabRef/jabref/issues/4735)
 - We fixed an issue where some journal names were wrongly marked as abbreviated. [#4115](https://github.com/JabRef/jabref/issues/4115)
 - We fixed an issue where the custom file column were sorted incorrectly. https://github.com/JabRef/jabref/issues/3119
 - We fixed an issues where the entry losses focus when a field is edited and at the same time used for sorting. https://github.com/JabRef/jabref/issues/3373
@@ -80,6 +92,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the default icon of a group was not colored correctly.
 - We fixed an issue where the first field in entry editor was not focused when adding a new entry. [#4024](https://github.com/JabRef/jabref/issues/4024)
 - We reworked the "Edit file" dialog to make it resizeable and improved the workflow for adding and editing files https://github.com/JabRef/jabref/issues/2970
+- We fixed an issue where custom name formatters were no longer found correctly. [#3531](https://github.com/JabRef/jabref/issues/3531)
 - We fixed an issue where the month was not shown in the preview https://github.com/JabRef/jabref/issues/3239.
 - Rewritten logic to detect a second jabref instance. [#4023](https://github.com/JabRef/jabref/issues/4023)
 - We fixed an issue where the "Convert to BibTeX-Cleanup" moved the content of the `file` field to the `pdf` field [#4120](https://github.com/JabRef/jabref/issues/4120)
@@ -93,21 +106,27 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where only one PDF file could be imported [#4422](https://github.com/JabRef/jabref/issues/4422)
 - We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
 - We fixed an issue where an older dialog appears when downloading full texts from the quality menu. [#4489](https://github.com/JabRef/jabref/issues/4489)
-
-
+- We fixed an issue where right clicking on any entry in any database and selecting "Open folder" results in the NullPointer exception. [#4763](https://github.com/JabRef/jabref/issues/4763)
+- We fixed an issue where option 'open terminal here' with custom command was passing wrong argument. [#4802](https://github.com/JabRef/jabref/issues/4802)
+- We fixed an issue where ranking an entry would generate an IllegalArgumentException. [#4754](https://github.com/JabRef/jabref/issues/4754)
+- We fixed an issue where special characters where removed from non label key generation pattern parts [#4767](https://github.com/JabRef/jabref/issues/4767)
+- We fixed an issue where the RIS import would overwite the article date with the value of the acessed date [#4816](https://github.com/JabRef/jabref/issues/4816)
 
 
 
 ### Removed
 - The feature to "mark entries" was removed and merged with the groups functionality.  For migration, a group is created for every value of the `__markedentry` field and the entry is added to this group.
 - The number column was removed.
+- We removed the global search feature.
 - We removed the coloring of cells in the maintable according to whether the field is optional/required.
+- We removed the feature to find and resolve duplicate BibTeX keys (as this use case is already covered by the integrity check).
 - We removed a few commands from the right-click menu that are not needed often and thus don't need to be placed that prominently:
   - Print entry preview: available through entry preview
   - All commands related to marking: marking is not yet reimplemented
   - Set/clear/append/rename fields: available through Edit menu
   - Manage keywords: available through Edit menu
   - Copy linked files to folder: available through File menu
+  - Add/move/remove from group: removed completely (functionality still available through group interface)
 - We removed the option to change the column widths in the preferences dialog. [#4546](https://github.com/JabRef/jabref/issues/4546)
 
 
@@ -136,7 +155,6 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 
 
-
 
 
 ## Older versions

build.gradle

@@ -15,21 +15,19 @@ buildscript {
 }
 
 plugins {
-    id 'com.gradle.build-scan' version '1.16'
-    id 'com.install4j.gradle' version '7.0.9'
-    id 'com.github.johnrengelman.shadow' version '4.0.2'
+    id 'com.gradle.build-scan' version '2.0.2'
+    id 'com.install4j.gradle' version '7.0.10'
+    id 'com.github.johnrengelman.shadow' version '5.0.0'
     id "com.simonharrer.modernizer" version '1.6.0-1'
     id 'me.champeau.gradle.jmh' version '0.4.8'
-    id 'net.ltgt.errorprone' version '0.6.1'
+    id 'net.ltgt.errorprone' version '0.7.1'
+    id 'com.github.ben-manes.versions' version '0.21.0'
     id 'com.zyxist.chainsaw' version '0.3.1'
-    id 'com.github.ben-manes.versions' version '0.20.0'
 }
 
 // use the gradle build scan feature: https://scans.gradle.com/get-started
-buildScan {
-    licenseAgreementUrl = 'https://gradle.com/terms-of-service'
-    licenseAgree = 'yes'
-}
+buildScan { termsOfServiceUrl = 'https://gradle.com/terms-of-service'; termsOfServiceAgree = 'yes' }
+
 
 apply plugin: 'java'
 apply plugin: 'application'
@@ -111,50 +109,49 @@ dependencies {
     compile 'com.jgoodies:jgoodies-common:1.8.1'
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
 
-    compile 'org.apache.pdfbox:pdfbox:2.0.13'
-    compile 'org.apache.pdfbox:fontbox:2.0.13'
-    compile 'org.apache.pdfbox:xmpbox:2.0.13'
+    compile 'org.apache.pdfbox:pdfbox:2.0.15'
+    compile 'org.apache.pdfbox:fontbox:2.0.15'
+    compile 'org.apache.pdfbox:xmpbox:2.0.15'
 
     compile group: 'org.apache.tika', name: 'tika-core', version: '1.20'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    compile 'org.bouncycastle:bcprov-jdk15on:1.60'
+    compile 'org.bouncycastle:bcprov-jdk15on:1.61'
 
     compile 'commons-cli:commons-cli:1.4'
 
-    // TODO: LibreOffice has a split package, temporarily removed
-    libreoffice "org.libreoffice:juh:5.4.2"
-    libreoffice "org.libreoffice:jurt:5.4.2"
-    libreoffice "org.libreoffice:ridl:5.4.2"
-    libreoffice "org.libreoffice:unoil:5.4.2"
+    compile "org.libreoffice:juh:6.2.2"
+    compile "org.libreoffice:jurt:6.2.2"
+    compile "org.libreoffice:ridl:6.2.2"
+    compile "org.libreoffice:unoil:6.2.2"
 
     compile 'io.github.java-diff-utils:java-diff-utils:4.0'
-    compile 'info.debatty:java-string-similarity:1.1.0'
+    compile 'info.debatty:java-string-similarity:1.2.1'
 
     antlr3 'org.antlr:antlr:3.5.2'
     compile 'org.antlr:antlr-runtime:3.5.2'
 
     antlr4 'org.antlr:antlr4:4.7.2'
     compile 'org.antlr:antlr4-runtime:4.7.2'
 
-    compile 'mysql:mysql-connector-java:8.0.14'
+    compile 'mysql:mysql-connector-java:8.0.15'
 
     compile 'org.postgresql:postgresql:42.2.5'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:27.0.1-jre'
+    compile 'com.google.guava:guava:27.1-jre'
 
     compile group: 'javax.annotation', name: 'javax.annotation-api', version: '1.3.2'
 
     // JavaFX stuff
+    compile 'de.jensd:fontawesomefx-commons:8.15'
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
-    compile 'de.jensd:fontawesomefx-commons:9.1.2'
-    compile 'de.saxsys:mvvmfx-validation:1.7.0'
-    compile 'de.saxsys:mvvmfx:1.7.0'
+    compile 'de.saxsys:mvvmfx-validation:1.8.0'
+    compile 'de.saxsys:mvvmfx:1.8.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
     compile 'org.fxmisc.flowless:flowless:0.6.1'
-    compile 'org.fxmisc.richtext:richtextfx:0.9.2'
+    compile 'org.fxmisc.richtext:richtextfx:0.9.3'
    //compile 'com.sibvisions.external.jvxfx:dndtabpane:0.1'
     compile 'javax.inject:javax.inject:1'
     compile 'com.jfoenix:jfoenix:9.0.8'
@@ -166,44 +163,41 @@ dependencies {
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
     // >1.8.0-beta is required for java 9 compatibility
-    compile 'org.slf4j:slf4j-api:1.8.0-beta2'
-    compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.11.1'
-    compile 'org.apache.logging.log4j:log4j-jcl:2.11.1'
-    compile 'org.apache.logging.log4j:log4j-api:2.11.1'
-    compile 'org.apache.logging.log4j:log4j-core:2.11.1'
+    compile 'org.slf4j:slf4j-api:1.8.0-beta4'
+    compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.11.2'
+    compile 'org.apache.logging.log4j:log4j-jcl:2.11.2'
+    compile 'org.apache.logging.log4j:log4j-api:2.11.2'
+    compile 'org.apache.logging.log4j:log4j-core:2.11.2'
 
     compile 'de.undercouch:citeproc-java:1.0.1'
 
     // JAX-B is considered JavaEE API and is no longer part of JavaSE (JDK 9)
     compile group: 'javax.xml.bind', name: 'jaxb-api', version: '2.3.0'
     compile group: 'com.sun.xml.bind', name: 'jaxb-core', version: '2.3.0'
+    compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'
 
     errorprone 'com.google.errorprone:error_prone_core:2.3.2'
 
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.0'
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.0'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.1'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
 
-    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.3.2'
-    testCompile 'org.junit.jupiter:junit-jupiter-params:5.3.2'
-    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.3.2'
-    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.3.2'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.3.2'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.4.2'
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.2'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.4.2'
 
-    testCompile 'org.junit-pioneer:junit-pioneer:0.3.0'
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
-    testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.1'
-    testCompile 'org.mockito:mockito-core:2.23.4'
-    testCompile 'com.github.tomakehurst:wiremock:2.20.0'
-    testCompile 'org.assertj:assertj-swing-junit:3.8.0'
+    testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
+    testCompile 'org.mockito:mockito-core:2.27.0'
+    testCompile 'com.github.tomakehurst:wiremock:2.22.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
-    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.9.3'
-    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.9.3'
+    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.10.2'
+    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.10.2'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.16'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.19'
 }
 
 jacoco {
@@ -214,9 +208,6 @@ dependencyUpdates {
     outputFormatter = "json"
 }
 
-//We have to use this as long as junit-pioneer has no official release
-dependencyUpdates.revision = 'integration'
-
 // We have some dependencies which cannot be updated due to various reasons.
 dependencyUpdates.resolutionStrategy = {
     componentSelection { rules ->
@@ -225,11 +216,6 @@ dependencyUpdates.resolutionStrategy = {
                 selection.reject("Ignore SNAPSHOT releases")
             }
         }
-        rules.withModule("com.gradle.build-scan:com.gradle.build-scan.gradle.plugin") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /2.*/) {
-                selection.reject("Cannot be upgraded to version 2 until we upgrade to gradle 5")
-            }
-        }
         rules.withModule("org.controlsfx:controlsfx") { ComponentSelection selection ->
             if (selection.candidate.version ==~ /9.*/) { // Reject version 9 or higher
                 selection.reject("Cannot be updated to 9.*.* until Jabref works with Java 9")
@@ -351,11 +337,14 @@ task generateSearchGrammarSource(type: JavaExec) {
 compileJava {
     options.encoding = 'UTF-8'
     options.compilerArgs << "-Xlint:none"
+    //ignore annotation processor from log4j2
+    options.compilerArgs += '-proc:none'
 }
 compileJava.dependsOn "generateSource"
 
 compileTestJava {
     options.encoding = 'UTF-8'
+    options.compilerArgs += '-proc:none'
 }
 
 javadoc {

gradle/wrapper/gradle-wrapper.jar

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.10.2-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-5.3.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradle/wrapper/gradle-wrapper.properties

@@ -4,7 +4,7 @@ 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=${SNAP}/meta/gui/JabRef-icon-256.png
+Icon=${SNAP}/meta/gui/jabref.png
 Exec=jabref %U
 Keywords=bibtex;biblatex;latex;bibliography
 Categories=Office;

lib/AppleJavaExtensions.jar

@@ -0,0 +1,41 @@
+name: jabref
+version: "git"
+version-script: cat build.gradle | grep "^version =" | cut -d'"' -f2
+#icon: snap/gui/jabref.png
+summary: Bibliography manager
+description: JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format.
+
+grade: devel
+confinement: strict
+
+architectures:
+  - build-on: amd64
+  - build-on: i386
+
+apps:
+  jabref:
+    command: desktop-launch java -jar $SNAP/jar/JabRef-$SNAP_VERSION.jar
+    environment:
+      _JAVA_OPTIONS: "-Duser.home=$SNAP_USER_DATA"
+    plugs:
+      - desktop
+      - desktop-legacy
+      - wayland
+      - unity7
+      - home
+      - opengl
+      - network-bind
+      - removable-media
+
+parts:
+  jabref:
+    plugin: gradle
+    source: .
+    source-type: git
+    stage-packages:
+      - openjdk-8-jre
+      - openjfx
+      - x11-utils
+    gradle-options: [snapJar, -xtest]
+    gradle-output-dir: 'build/releases'
+    after: [desktop-gtk2]