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

* upstream/master: (130 commits) Update gradle from 4.7 to 4.8 (#4102) Add gradle task downloadDependencies and use it at CircleCI (#4091) Set minimum java to 171 (#4095) Also use https in the CHANGELOG itself Add missing CHANGELOG entry Fix localiazation test Use official TempFolder extension for JUnit 5 tests Remove menu* from crowdin.yml (#4094) Merge recent changes to exporter/importer Add missing CHANGELOG entry New translations JabRef_en.properties (Vietnamese) New translations JabRef_en.properties (Dutch) New translations JabRef_en.properties (French) New translations JabRef_en.properties (German) New translations JabRef_en.properties (Greek) New translations JabRef_en.properties (Indonesian) New translations JabRef_en.properties (Italian) New translations JabRef_en.properties (Japanese) New translations JabRef_en.properties (Danish) New translations JabRef_en.properties (Norwegian) ... # Conflicts: # src/main/java/org/jabref/gui/BasePanel.java # src/main/java/org/jabref/gui/PreviewPanel.java # src/main/java/org/jabref/gui/openoffice/StyleSelectDialog.java
JabRef · Jun 5, 2018 · a8c3a67 · a8c3a67
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,52 +11,46 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
-- We added a text file export for 'Find Unlinked Files'. [#3341](https://github.com/JabRef/jabref/issues/3341)
-- We added a fetcher based on RFC-IDs. [#3971](https://github.com/JabRef/jabref/issues/3971)
+- We changed the minimum required version of Java to 1.8.0_171, as this is the latest release for which the automatic Java update works.  [4093](https://github.com/JabRef/jabref/issues/4093)
+- The special fields like `Printed` and `Read status` now show gray icons when the row is hovered.
+- We added a button in the tab header which allows you to close the database with one click. https://github.com/JabRef/jabref/issues/494
+- Sorting in the main table now takes information from cross-referenced entries into account. https://github.com/JabRef/jabref/issues/2808
+- If a group has a color specified, then entries matched by this group have a small colored bar in front of them in the main table.
+- Change default icon for groups to a circle because a colored version of the old icon was hard to distinguish from its black counterpart.
+- In the main table, the context menu appears now when you press the "context menu" button on the keyboard. [feature request in the forum](http://discourse.jabref.org/t/how-to-enable-keyboard-context-key-windows)
+- We added icons to the group side panel to quickly switch between `union` and `intersection` group view mode https://github.com/JabRef/jabref/issues/3269.
+- We use `https` for [fetching from most online bibliographic database](https://help.jabref.org/en/#-using-online-bibliographic-database).
 
 ### Fixed
-We fixed an issue where the export to clipboard functionality could not be invoked [#3994](https://github.com/JabRef/jabref/issues/3994)
-We fixed an issue with the migration of invalid Look and Feels [#3995, comment](https://github.com/JabRef/jabref/issues/3995#issuecomment-385649448)
-We fixed an issue where JabRef would no longer start, when the option "Override default font settings" was activated [#3986](https://github.com/JabRef/jabref/issues/3986)
-We fixed an issue where fetched entries from the ACM fetcher could not be imported. [#4018](https://github.com/JabRef/jabref/issues/4018)
+- 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
+- The entry editor no longer gets corrupted after using the source tab. https://github.com/JabRef/jabref/issues/3532 https://github.com/JabRef/jabref/issues/3608 https://github.com/JabRef/jabref/issues/3616
+- We fixed multiple issues where entries did not show up after import if a search was active. https://github.com/JabRef/jabref/issues/1513 https://github.com/JabRef/jabref/issues/3219
+- We fixed an issue where the group tree was not updated correctly after an entry was changed. https://github.com/JabRef/jabref/issues/3618
+- We fixed an issue where a right-click in the main table selected a wrong entry. https://github.com/JabRef/jabref/issues/3267
+- We fixed an issue where in rare cases entries where overlayed in the main table. https://github.com/JabRef/jabref/issues/3281
+- 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 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
+- We fixed an issue where the menu on Mac OS was not displayed in the usual Mac-specific way. https://github.com/JabRef/jabref/issues/3146
+- We fixed an issue where the groups tree of the last database was still shown even after the database was already closed.
+- We fixed an issue where the "Open file dialog" may disappear behind other windows. https://github.com/JabRef/jabref/issues/3410
+- We fixed an issue where the default icon of a group was not colored correctly.
+- 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 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)
 
 ### Removed
-We removed the GTK Look and Feel from the Options, as it leads to freezes in JabRef on MacOSX and Linux [#3995](https://github.com/JabRef/jabref/issues/3995)
-The GTK Look and Feel is now replaced with the "Nimbus" style as default.
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+- 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 coloring of cells in the maintable according to whether the field is optional/required.
+- 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
 
 
 
@@ -87,9 +81,30 @@ The GTK Look and Feel is now replaced with the "Nimbus" style as default.
 
 
 
+## [4.3] - 2018-06-01
 
+### Changed
+- We changed the minimum required version of Java to 1.8.0_172, as 1.8.0_162 has introduced a CPU leak [3943](https://github.com/JabRef/jabref/issues/3943)
+- We added a validity check for dates in the `date` and `urldate` fields.
+- We added a text file export for 'Find Unlinked Files'. [#3341](https://github.com/JabRef/jabref/issues/3341)
+- We added a fetcher based on RFC-IDs. [#3971](https://github.com/JabRef/jabref/issues/3971)
+- We changed the implementation of the `[shorttitle]` key pattern. It now removes small words like `a`, `an`, `on`, `the` etc. Refer to the help page for a complete overview. [Feature request in the forum](http://discourse.jabref.org/t/jabref-differences-in-shorttitle-between-versions-3-8-1-and-4-not-discounting-the-a-an-of-in-titles/1147)
+- We added a formatter for adding braces around the `title` field. E.g., `title = {ExamPle}` becomes `title = {{ExamPle}}`, which prevents BibTeX to convert it to lower case. You can use it at the [cleanup entries](http://help.jabref.org/en/CleanupEntries) functionality.
+- We added a formatter to ensure correct en dashes in the `title` field. E.g., `title = {Example - illustrative}` becomes `title = {Example -- illustrative}`.
+- We streamlined the defaults for a [cleanup of entries](http://help.jabref.org/en/CleanupEntries) in the case of BibTeX.
+- The import inspection window now uses the same font size setting as the maintable [Feature request in the forum](http://discourse.jabref.org/t/inspection-window-and-others-line-height-of-table-too-small-for-fonts/1168)
 
+### Fixed
+- We fixed an issue where the export to clipboard functionality could not be invoked. [#3994](https://github.com/JabRef/jabref/issues/3994)
+- We fixed an issue with the migration of invalid Look and Feels. [#3995, comment](https://github.com/JabRef/jabref/issues/3995#issuecomment-385649448)
+- We fixed an issue where JabRef would no longer start, when the option "Override default font settings" was activated. [#3986](https://github.com/JabRef/jabref/issues/3986)
+- We fixed an issue where JabRef removed whitespace from the Title-fetcher which resulting in no entries being found. [#4014](https://github.com/JabRef/jabref/issues/4014)
+- We fixed an issue where fetched entries from the ACM fetcher could not be imported. [#4018](https://github.com/JabRef/jabref/issues/4018)
+- We fixed an issue to enable push to application on macOs again [#4041](https://github.com/JabRef/jabref/issues/4041)
 
+### Removed
+- We removed the GTK Look and Feel from the Options, as it leads to freezes in JabRef on MacOSX and Linux [#3995](https://github.com/JabRef/jabref/issues/3995).
+The GTK Look and Feel is now replaced with the "Nimbus" style as default.
 
 
 ## [4.2] - 2018-04-26
@@ -426,7 +441,8 @@ The new default removes the linked file from the entry instead of deleting the f
 The changelog of versions 3.x is available at the [v3.8.2 tag](https://github.com/JabRef/jabref/blob/v3.8.2/CHANGELOG.md).
 The changelog of 2.11 and versions before is available as [text file in the v2.11.1 tag](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG).
 
-[Unreleased]: https://github.com/JabRef/jabref/compare/v4.2...HEAD
+[Unreleased]: https://github.com/JabRef/jabref/compare/v4.3...HEAD
+[4.3]: https://github.com/JabRef/jabref/compare/v4.2...v4.3
 [4.2]: https://github.com/JabRef/jabref/compare/v4.1...v4.2
 [4.1]: https://github.com/JabRef/jabref/compare/v4.0...v4.1
 [4.0]: https://github.com/JabRef/jabref/compare/v4.0-beta3...v4.0

diff --git a/build.gradle b/build.gradle
@@ -44,15 +44,15 @@ apply from: 'localization.gradle'
 apply from: 'xjc.gradle'
 
 group = "org.jabref"
-version = "4.3-dev"
-project.ext.threeDotVersion = "4.2.0.1"
+version = "4.4-dev"
+project.ext.threeDotVersion = "4.3.0.1"
 project.ext.install4jDir = hasProperty("install4jDir") ? getProperty("install4jDir") : (OperatingSystem.current().isWindows() ? 'C:/Program Files/install4j7' : 'install4j7')
 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.minRequiredJavaVersion = "1.8.0_171"
 ext.allowJava9 = false
 
 sourceSets {
@@ -113,14 +113,13 @@ dependencies {
     // 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:5.1.46'
 
-    compile 'com.impossibl.pgjdbc-ng:pgjdbc-ng:0.7.1'
+    compile 'org.postgresql:postgresql:42.2.2'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:25.0-jre'
+    compile 'com.google.guava:guava:25.1-jre'
 
     // JavaFX stuff
-    compile 'de.codecentric.centerdevice:javafxsvg:1.3.0'
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
     compile 'de.saxsys:mvvmfx-validation:1.7.0'
     compile 'de.saxsys:mvvmfx:1.7.0'
@@ -150,14 +149,15 @@ dependencies {
 
     compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'
 
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.1.0'
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.1.0'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.1.1'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.1.1'
 
     testImplementation 'org.junit.jupiter:junit-jupiter-api:5.2.0'
     testCompile 'org.junit.jupiter:junit-jupiter-params:5.2.0'
     testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.2.0'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.2.0'
     testCompile 'org.junit.platform:junit-platform-launcher:1.2.0'
+    testCompile 'org.junit-pioneer:junit-pioneer:0.1-SNAPSHOT'
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.0'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.0'
     testCompile 'org.mockito:mockito-core:2.18.3'
@@ -166,11 +166,11 @@ dependencies {
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.0'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.0'
-    testCompile 'com.tngtech.archunit:archunit-junit:0.5.0'
+    testCompile 'com.tngtech.archunit:archunit-junit:0.8.0'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.10'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.10.1'
 }
 
 jacoco {
@@ -314,7 +314,7 @@ test {
     useJUnitPlatform {
         excludeTags 'DatabaseTest', 'FetcherTest', 'GUITest', 'org.jabref.testutils.category.FetcherTest', 'org.jabref.testutils.category.GUITest'
     }
-    
+
     testLogging {
         // set options for log level LIFECYCLE
         events "failed"
@@ -375,7 +375,7 @@ checkstyle {
     // do not use other packages for checkstyle, excluding gen(erated) sources
     checkstyleMain.source = "src/main/java"
     toolVersion = '8.5'
-    
+
     // do not perform checkstyle checks by default
     sourceSets = []
 }
@@ -487,3 +487,19 @@ jmh {
     iterations = 10
     fork = 2
 }
+
+// Source: https://stackoverflow.com/a/44168582/873282
+task downloadDependencies {
+  description "Pre-downloads *most* dependencies"
+  doLast {
+    configurations.getAsMap().each { name, config ->
+      println "Retrieving dependencies for $name"
+      try {
+        config.files
+      } catch (e) {
+        // some cannot be resolved, just log them
+        project.logger.info e.message
+      }
+    }
+  }
+}
diff --git a/circle.yml b/circle.yml
@@ -13,19 +13,14 @@ dependencies:
     - install4j7/bin/install4jc --verbose --license=$INSTALL4J_KEY 
     #--win-keystore-password $CERTIFICATE_PW --mac-keystore-password $CERTIFICATE_PW
   override:
-    # We do this to decrease build time by using CircleCI's cache. See https://discuss.circleci.com/t/effective-caching-for-gradle/540 for a longer motivation.
-    - ./gradlew compileJava
+    - ./gradlew downloadDependencies
   cache_directories:
     - "~/.install4j7"
     - "~/downloads"
 
 test:
   override:
-    - ./gradlew -Pdev=true -Pinstall4jDir="install4j7" release --stacktrace
-  post:
-    # save test reports as build artifacts
-    - mkdir -p $CIRCLE_TEST_REPORTS/junit/
-    - find . -type f -regex ".*/build/test-results/.*xml" -exec cp {} $CIRCLE_TEST_REPORTS/junit/ \;
+    - "true"
 
 deployment:
   release:
@@ -34,18 +29,19 @@ deployment:
    commands:
       # we have to do a clean build as changing gradle's "project.version" does not lead to a rebuild of resources (mirroring project.version)
       - ./gradlew -Pinstall4jDir="install4j7" clean release --stacktrace
-      # upload at all circumstances
-      - scripts/upload-to-builds.jabref.org.sh
+      # if upload fails, it is accepted; CircleCI provides deep links to the binaries as fallback.
+      - timeout 580 scripts/upload-to-builds.jabref.org.sh || exit 0
+      # generate dependency information. This is not published on our buid server, but can be collected as logged in user at CircleCI
       - ./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: /.*/
     commands:
+      # generate binaries
+      - ./gradlew -Pdev=true -Pinstall4jDir="install4j7" release --stacktrace
       # if upload fails, it is accepted; CircleCI provides deep links to the binaries as fallback
       - timeout 580 scripts/upload-to-builds.jabref.org.sh || exit 0
 
-
-
 general:
   artifacts:
     - "build/releases"
diff --git a/crowdin.yml b/crowdin.yml
@@ -1,10 +1,4 @@
 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:

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
@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.8-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.6-bin.zip
diff --git a/src/main/java/org/jabref/JabRefExecutorService.java b/src/main/java/org/jabref/JabRefExecutorService.java
@@ -140,7 +140,7 @@ public void shutdownEverything() {
         this.lowPriorityExecutorService.shutdownNow();
         // kill the remote thread
         stopRemoteThread();
-        // timer doesn't need to be canceled as it is run in daemon mode, which ensures that it is stopped if the application is shut down
+        timer.cancel();
     }
 
     private class NamedRunnable implements Runnable {