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

* upstream/master: (108 commits) Fetcher for IACR eprints (#3473) Update internal state of DatabaseChangeMonitor when external changes … (#3503) Fixes #3505: Another try to fix the NPE in the search bar (#3512) Replace ' with ' so that our HTML preview can handle it correctly Added a "Clear text" button in right click menu within the text boxes. (#3475) Add reset to English language after a test New translations JabRef_en.properties (German) Remove ampersand in non-menu localizations New translations JabRef_en.properties (German) New translations Menu_en.properties (German) New translations Menu_en.properties (German) New translations JabRef_en.properties (Vietnamese) New translations JabRef_en.properties (Italian) New translations Menu_en.properties (Italian) New translations JabRef_en.properties (Indonesian) New translations Menu_en.properties (Indonesian) New translations JabRef_en.properties (Greek) New translations Menu_en.properties (Greek) New translations Menu_en.properties (Japanese) New translations JabRef_en.properties (German) ... # Conflicts: # build.gradle
JabRef · Dec 13, 2017 · 74151de · 74151de
2 parents fac2c3d + c2d0070
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diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md
@@ -2,9 +2,13 @@
 Feature requests,  questions and general feedback is now handled at http://discourse.jabref.org 
 Thanks! --> 
 
+- [ ] I have tested the latest master version from http://builds.jabref.org/master/ and the problem persists
+
+
 JabRef version <!-- version as shown in the about box --> on <!-- Windows 10|Ubuntu 14.04|Mac OS X 10.8|... -->
 <!-- Hint: If you use a development version (available at http://builds.jabref.org/master/), ensure that you use the latest one. -->
 
+
 Steps to reproduce:
 
 1. ...

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,5 +1,8 @@
 <!-- describe the changes you have made here: what, why, ... -->
 
+
+----
+
 - [ ] Change in CHANGELOG.md described
 - [ ] Tests created for changes
 - [ ] Screenshots added (for bigger UI changes)

diff --git a/.travis.yml b/.travis.yml
@@ -19,11 +19,13 @@ env:
     - TEST_SUITE=databaseTest
     - TEST_SUITE=guiTest
     - TEST_SUITE=checkstyle
+    - TEST_SUITE=codecov
 
 matrix:
     fast_finish: true
     allow_failures:
       - env: TEST_SUITE=fetcherTest
+      - env: TEST_SUITE=codecov
 
 # JavaFX localization tests need a running X environment
 before_install:
@@ -40,19 +42,19 @@ before_script:
 script:
   # --scan enables the Gradle build scan, which can be used to investigate the time each action consumes
   # For more information see https://gradle.com/scans/get-started
-  - if [ "$TEST_SUITE" != "guiTest" ] && [ "$TEST_SUITE" != "checkstyle" ]; then ./gradlew $TEST_SUITE $OPTIONS --scan; fi
+  - if [ "$TEST_SUITE" != "guiTest" ] && [ "$TEST_SUITE" != "checkstyle" ] && [ "$TEST_SUITE" != "codecov" ]; then ./gradlew $TEST_SUITE $OPTIONS --scan; fi
   - if [ "$TEST_SUITE" == "checkstyle" ]; then ./gradlew checkstyleMain checkstyleTest checkstyleJmh; fi
   - if [ "$TEST_SUITE" == "guiTest" ]; then ./buildres/gui-tests.sh; fi
-
-after_success:
-  # enable codecov report
-  - ./gradlew jacocoTestReport
-  - bash <(curl -s https://codecov.io/bash)
+  - if [ "$TEST_SUITE" == "codecov" ]; then ./gradlew jacocoJunit5TestReport; bash <(curl -s https://codecov.io/bash); fi
 
 after_failure:
   # show test results if build fails
   - $TRAVIS_BUILD_DIR/scripts/after-failure.sh
 
+branches:
+  only: 
+    - master
+
 # cache gradle dependencies
 # https://docs.travis-ci.com/user/languages/java#Caching
 before_cache:

diff --git a/AUTHORS b/AUTHORS
@@ -182,6 +182,7 @@ Thomas Arildsen
 Thomas Ilsche
 Thorsten Dahlheimer
 Tim van Rossum
+Tim Würtele
 Tobias Boceck
 Tobias Denkinger
 Tobias Diez

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -23,17 +23,23 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - 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
+- File annotation tab now removes newlines and hyphens before newlines from content and displays an empty String instead of N/A if no contents are found. [#3280](https://github.com/JabRef/jabref/issues/3280)
 - We moved the groups field from the "Other fields" tab to "General" (you may have to reset your editor preferences under Options > Set up general fields)
 - 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 added the possibility to copy linked files from entries to a single output folder [#2539](https://github.com/JabRef/jabref/pull/2593)
 - 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)
 - Integrity check "Abbreviation Detection" detects abbreviated names for journals and booktitles based on the internal list instead of only looking for "." signs. Fixes [#3144](https://github.com/JabRef/jabref/issues/3144).
 - We added a dialog to show that JabRef is working on checking integrity. [#3358](https://github.com/JabRef/jabref/issues/3358)
+- When you click the PDF icon in the file list of the entry editor, then the file is opened. [#3491](https://github.com/JabRef/jabref/issues/3491)
 - We added an option to mass append to fields via the Quality -> set/clear/append/rename fields dialog. [#2721](https://github.com/JabRef/jabref/issues/2721)
+- We added a check on startup to ensure JabRef is run with an adequate Java version. [3310](https://github.com/JabRef/jabref/issues/3310)
+- In the preference, all installed java Look and Feels are now listed and selectable
+- We added an ID fetcher for [IACR eprints](https://eprint.iacr.org/). [#3473](https://github.com/JabRef/jabref/pull/3473)
+- We added a clear option to the right-click menu of the text field in the entry editor. [koppor#198](https://github.com/koppor/jabref/issues/198)
 
 ### Fixed
- - We fixed the translation of \textendash in the entry preview [#3307](https://github.com/JabRef/jabref/issues/3307)
+ - We fixed the translation of \textendash and \textquotesingle 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. [#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)
@@ -42,10 +48,21 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
  - We no longer allow to add a field multiple times in customized entry types and thereby fix an issue in the entry editor that resulted from having a field multiple times. [#3046](https://github.com/JabRef/jabref/issues/3046)
  - 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)
+ - We fixed an issue where file links created under windows could not be opened on Linux/OSX [#3311](https://github.com/JabRef/jabref/issues/3311)
  - We fixed several issues with the automatic linking of files in the entry editor where files were not found or not correctly saved in the bibtex source [#3346](https://github.com/JabRef/jabref/issues/3346)
  - We fixed an issue where fetching entries from crossref that had no titles caused an error [#3376](https://github.com/JabRef/jabref/issues/3376)
  - We fixed an issue where the same Java Look and Feel would be listed more than once in the Preferences. [#3391](https://github.com/JabRef/jabref/issues/3391)
  - We fixed an issue where errors in citation styles triggered an exception when opening the preferences dialog [#3389](https://github.com/JabRef/jabref/issues/3389)
+ - We fixed an issue where entries were displayed twice after insertion into a shared database. [#3164](https://github.com/JabRef/jabref/issues/3164)
+ - We fixed an issue where special fields (such as `printed`) could not be cleared when syncing special fields via the keywords [#3432](https://github.com/JabRef/jabref/issues/3432)
+ - We fixed an issue where the tooltip of the global search bar showed html tags instead of formatting the text [#3381](https://github.com/JabRef/jabref/issues/3381)
+ - We fixed an issue where timestamps were not updated for changed entries [#2810](https://github.com/JabRef/jabref/issues/2810)
+ - We fixed an issue where trying to fetch data from Medline/PubMed resulted in an error [#3463](https://github.com/JabRef/jabref/issues/3463)
+ - We fixed an issue where double clicking on an entry in the integrity check dialog resulted in an exception [#3485](https://github.com/JabRef/jabref/issues/3485)
+ - We fixed an issue where the entry type could sometimes not be changed when the entry editor was open [#3435](https://github.com/JabRef/jabref/issues/3435)
+ - We fixed an issue where dropping a pdf on the entry table and renaming it triggered an exception [#3490](https://github.com/JabRef/jabref/issues/3490)
+ - We fixed an issue where integrating external changes to a bib file caused instability [#3498](https://github.com/JabRef/jabref/issues/3498)
+ - We fixed an issue where fetched entries from the ACM fetcher could not be imported [#3500](https://github.com/JabRef/jabref/issues/3500)
 
  ### Removed
 

diff --git a/build.gradle b/build.gradle
@@ -2,14 +2,28 @@ import org.gradle.internal.os.OperatingSystem
 
 // to update the gradle wrapper, execute ./gradlew wrapper --gradle-version 4.0
 
+buildscript {
+    repositories {
+        mavenLocal()
+        jcenter()
+        maven {
+            url 'https://oss.sonatype.org/content/groups/public'
+        }
+    }
+    dependencies {
+        classpath 'org.junit.platform:junit-platform-gradle-plugin:1.0.2'
+    }
+}
+
 plugins {
-    id 'com.gradle.build-scan' version '1.9'
-    id 'com.install4j.gradle' version '6.1.5'
+    id 'com.gradle.build-scan' version '1.10.3'
+    id 'com.install4j.gradle' version '7.0.3'
     id 'com.github.johnrengelman.shadow' version '2.0.1'
     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 '0.0.13'
+    id 'com.github.ben-manes.versions' version '0.17.0'
 }
 
 // use the gradle build scan feature: https://scans.gradle.com/get-started
@@ -25,6 +39,7 @@ apply plugin: 'jacoco'
 apply plugin: 'install4j'
 apply plugin: 'me.champeau.gradle.jmh'
 apply plugin: 'checkstyle'
+apply plugin: 'org.junit.platform.gradle.plugin'
 
 apply from: 'eclipse.gradle'
 apply from: 'localization.gradle'
@@ -38,6 +53,10 @@ sourceCompatibility = 1.8
 targetCompatibility = 1.8
 mainClassName = "org.jabref.JabRefMain"
 
+// These are the Java version requirements we will check on each start of JabRef
+ext.minRequiredJavaVersion = "1.8.0_144"
+ext.allowJava9 = false
+
 install4j {
     installDir = file(project.ext.install4jDir)
 }
@@ -62,10 +81,6 @@ dependencies {
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
     compile 'com.jgoodies:jgoodies-looks:2.7.0'
 
-    // Later versions cannot be used. Tested until 1.6.5-1.
-    // See https://github.com/JabRef/jabref/issues/271 for details.
-    compile 'org.swinglabs.swingx:swingx-core:1.6.4'
-
     // update to 2.0.x is not possible - see https://github.com/JabRef/jabref/pull/1096#issuecomment-208857517
     compile 'org.apache.pdfbox:pdfbox:1.8.13'
     compile 'org.apache.pdfbox:fontbox:1.8.13'
@@ -82,7 +97,7 @@ 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'
+    compile 'info.debatty:java-string-similarity:1.0.1'
 
     antlr3 'org.antlr:antlr:3.5.2'
     compile 'org.antlr:antlr-runtime:3.5.2'
@@ -97,7 +112,7 @@ dependencies {
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:23.3-jre'
+    compile 'com.google.guava:guava:23.5-jre'
 
     // JavaFX stuff
     compile 'com.airhacks:afterburner.fx:1.7.0'
@@ -111,14 +126,13 @@ dependencies {
     // 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 'org.jsoup:jsoup:1.11.2'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
     compile 'commons-logging:commons-logging:1.2'
-    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'
+    compile 'org.apache.logging.log4j:log4j-jcl:2.10.0'
+    compile 'org.apache.logging.log4j:log4j-api:2.10.0'
+    compile 'org.apache.logging.log4j:log4j-core:2.10.0'
 
     // 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'
@@ -137,13 +151,20 @@ dependencies {
     compile "org.bitbucket.cowwoc:diff-match-patch:1.1"
 
     testCompile 'junit:junit:4.12'
-    testCompile 'org.mockito:mockito-core:2.11.0'
-    testCompile 'com.github.tomakehurst:wiremock:2.10.1'
+    testCompile 'org.junit.jupiter:junit-jupiter-api:5.0.2'
+    testCompile 'org.junit.jupiter:junit-jupiter-params:5.0.2'
+    testRuntime 'org.junit.jupiter:junit-jupiter-engine:5.0.2'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.0.2'
+    testRuntime 'org.junit.vintage:junit-vintage-engine:4.12.1'
+    testRuntime 'org.apache.logging.log4j:log4j-core:2.9.1'
+    testRuntime 'org.apache.logging.log4j:log4j-jul:2.9.1'
+    testCompile 'org.mockito:mockito-core:2.12.0'
+    testCompile 'com.github.tomakehurst:wiremock:2.12.0'
     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.xmlunit:xmlunit-core:2.5.1'
+    testCompile 'org.xmlunit:xmlunit-matchers:2.5.1'
+    testCompile 'com.tngtech.archunit:archunit-junit:0.5.0'
     testCompile 'org.slf4j:slf4j-jcl:1.7.25' // required by ArchUnit to enable logging over jcl
 }
 
@@ -167,7 +188,11 @@ processResources {
                 "year": String.valueOf(Calendar.getInstance().get(Calendar.YEAR)),
                 "authors": new File('AUTHORS').readLines().findAll { !it.startsWith("#") }.join(", "),
                 "developers": new File('DEVELOPERS').readLines().findAll { !it.startsWith("#") }.join(", "),
-                "azureInstrumentationKey": System.getenv('AzureInstrumentationKey'))
+                "azureInstrumentationKey": System.getenv('AzureInstrumentationKey'),
+                "minRequiredJavaVersion": minRequiredJavaVersion,
+                "allowJava9": allowJava9
+
+        )
         filteringCharset = 'UTF-8'
     }
 
@@ -244,33 +269,31 @@ javadoc {
     }
 }
 
-test {
-    useJUnit {
-        excludeCategories 'org.jabref.testutils.category.DatabaseTests'
-        excludeCategories 'org.jabref.testutils.category.FetcherTests'
-        excludeCategories 'org.jabref.testutils.category.GUITests'
-    }
-    testLogging {
-        events "failed"
-        exceptionFormat "full"
+junitPlatform {
+    filters {
+        tags {
+            exclude 'DatabaseTest', 'org.jabref.testutils.category.FetcherTest', 'org.jabref.testutils.category.GUITest'
+        }
     }
+
+    logManager 'org.apache.logging.log4j.jul.LogManager'
 }
 
 task databaseTest(type: Test) {
     useJUnit {
-        includeCategories 'org.jabref.testutils.category.DatabaseTests'
+        includeCategories 'org.jabref.testutils.category.DatabaseTest'
     }
 }
 
 task fetcherTest(type: Test) {
     useJUnit {
-        includeCategories 'org.jabref.testutils.category.FetcherTests'
+        includeCategories 'org.jabref.testutils.category.FetcherTest'
     }
 }
 
 task guiTest(type: Test) {
     useJUnit {
-        includeCategories 'org.jabref.testutils.category.GUITests'
+        includeCategories 'org.jabref.testutils.category.GUITest'
     }
 }
 
@@ -289,7 +312,8 @@ tasks.withType(Test) {
 }
 
 task jacocoMerge(type: JacocoMerge) {
-    executionData test, databaseTest
+    executionData file("$buildDir/jacoco/junitPlatformTest.exec"), file("$buildDir/jacoco/databaseTest.exec"), file("$buildDir/jacoco/fetcherTest.exec")
+    dependsOn junitPlatformTest, databaseTest, fetcherTest
 }
 
 jacocoTestReport {
@@ -302,6 +326,27 @@ jacocoTestReport {
     }
 }
 
+afterEvaluate {
+    def junitPlatformTest = tasks.junitPlatformTest
+
+    jacoco {
+        applyTo(junitPlatformTest)
+    }
+
+    task jacocoJunit5TestReport(type: JacocoReport) {
+        executionData jacocoMerge.destinationFile
+        dependsOn jacocoMerge
+        sourceSets sourceSets.main
+        sourceDirectories = files(sourceSets.main.allSource.srcDirs)
+        classDirectories = files(sourceSets.main.output)
+
+        reports {
+            xml.enabled true
+            html.enabled true
+        }
+    }
+}
+
 shadowJar {
     classifier 'fat'
 }

diff --git a/circle.yml b/circle.yml
@@ -35,6 +35,7 @@ deployment:
       - ./gradlew -Pinstall4jDir="install4j7" clean release --stacktrace
       # upload at all circumstances
       - scripts/upload-to-builds.jabref.org.sh
+      - ./gradlew dependencyUpdates -Drevision=release -DoutputFormatter=json -DoutputDir=build/releases
   development:
      # match all branches; this is executed, if "release" is not matched - see https://circleci.com/docs/configuration/
     branch: /.*/

diff --git a/crowdin.yml b/crowdin.yml
@@ -0,0 +1,13 @@
+files:
+  - source: /src/main/resources/l10n/Menu_en.properties
+    translation: /src/main/resources/l10n/Menu_%two_letters_code%.properties
+    languages_mapping:
+      two_letters_code:
+        pt-BR: pt_BR
+        id: in
+  - source: /src/main/resources/l10n/JabRef_en.properties
+    translation: /src/main/resources/l10n/JabRef_%two_letters_code%.properties
+    languages_mapping:
+      two_letters_code:
+        pt-BR: pt_BR
+        id: in
diff --git a/external-libraries.txt b/external-libraries.txt
@@ -235,11 +235,6 @@ Project: OpenOffice.org
 URL:     http://www.openoffice.org/api/SDK
 License: Apache-2.0
 
-Id:      org.swinglabs.swingx:swingx-core
-Project: SwingX
-URL:     https://swingx.java.net/
-License: LGPL-3.0
-
 Id:      org.xmlunit:xmlunit-core
 Project: XMLUnit
 URL:     http://www.xmlunit.org/

diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -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-4.3.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.4-bin.zip
diff --git a/jabref.install4j b/jabref.install4j
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<install4j version="7.0.1" transformSequenceNumber="7">
+<install4j version="7.0.3" transformSequenceNumber="7">
   <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="">
+  <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="1.8" allowBetaVM="false" jdkMode="runtimeJre" jdkName="">
     <languages skipLanguageSelection="true" languageSelectionInPrincipalLanguage="false">
       <principalLanguage id="en" customLocalizationFile="" />
       <additionalLanguages>
@@ -31,6 +31,7 @@
       </additionalLanguages>
     </languages>
     <searchSequence>
+      <envVar name="PATH" />
       <registry />
       <envVar name="JAVA_HOME" />
       <envVar name="JDK_HOME" />