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

* upstream/master: (71 commits)
  New translations JabRef_en.properties (French)
  Add Gitter badge and hint (#3630)
  New translations JabRef_en.properties (Vietnamese)
  New translations JabRef_en.properties (Chinese Simplified)
  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 (Norwegian)
  New translations JabRef_en.properties (Persian)
  New translations JabRef_en.properties (Portuguese, Brazilian)
  New translations JabRef_en.properties (Russian)
  New translations JabRef_en.properties (Spanish)
  New translations JabRef_en.properties (Swedish)
  New translations JabRef_en.properties (Turkish)
  New translations JabRef_en.properties (Danish)
  Update CHANGELOG.md
  ...

Author: Siedlerchr

CHANGELOG.md

@@ -12,14 +12,16 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- We now show a small notification icon in the entry editor when we detect data inconsistency or other problems. [#3145](https://github.com/JabRef/jabref/issues/3145)
 - We added [oaDOI](https://oadoi.org/) as a fulltext provider, so that JabRef is now able to provide fulltexts for more than 90 million open-access articles.
-
+- We changed one default of [Cleanup entries dialog](http://help.jabref.org/en/CleanupEntries): Per default, the PDF are not moved to the default file directory anymore. [#3619](https://github.com/JabRef/jabref/issues/3619)
 
 ### Fixed
 - We fixed the missing dot in the name of an exported file. [#3576](https://github.com/JabRef/jabref/issues/3576)
+- Autocompletion in the search bar can now be disabled via the preferences. [#3598](https://github.com/JabRef/jabref/issues/3598)
 
 ### Removed
-- We removed the Look and Feels from jgoodies, because these are not compatible with Java 9
+- We removed the [Look and Feels from JGoodies](http://www.jgoodies.com/freeware/libraries/looks/), because the open source version is not compatible with Java 9.
 
 
 
@@ -115,7 +117,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
  - 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 improved the auto link algorithm so that files starting with a similar key are no longer found (e.g, `Einstein1902` vs `Einstein1902a`). [#3472](https://github.com/JabRef/jabref/issues/3472) 
+ - We improved the auto link algorithm so that files starting with a similar key are no longer found (e.g, `Einstein1902` vs `Einstein1902a`). [#3472](https://github.com/JabRef/jabref/issues/3472)
  - 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)

CONTRIBUTING.md

@@ -6,6 +6,7 @@ Take a look at GitHub's excellent [help documentation] for a detailed explanatio
 We also have [code howtos](https://github.com/JabRef/jabref/wiki/Code-Howtos) and [guidelines for setting up a local workspace](https://github.com/JabRef/jabref/wiki/Guidelines-for-setting-up-a-local-workspace).
 
 In case you have any question, do not hesitate to write one of our [JabRef developers](https://github.com/orgs/JabRef/teams/developers) an email.
+We should also be online at [gitter](https://gitter.im/JabRef/jabref).
 
 
 ## Formal requirements for a pull request

README.md

@@ -3,6 +3,8 @@
 [![Build Status](https://travis-ci.org/JabRef/jabref.svg?branch=master)](https://travis-ci.org/JabRef/jabref)
 [![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=master)
 [![Donation](https://img.shields.io/badge/donate%20to-jabref-orange.svg)](https://donations.jabref.org)
+[![Help Contribute to Open Source](https://www.codetriage.com/jabref/jabref/badges/users.svg)](https://www.codetriage.com/jabref/jabref)
+[![Join the chat at https://gitter.im/JabRef/jabref](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/JabRef/jabref?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 This version is a development version. Features may not work as expected.
 

build.gradle

@@ -1,7 +1,8 @@
 import groovy.json.JsonSlurper
 import org.gradle.internal.os.OperatingSystem
 
-// to update the gradle wrapper, execute ./gradlew wrapper --gradle-version 4.0
+// to update the gradle wrapper, execute
+// ./gradlew wrapper --gradle-version=4.4.1 --distribution-type=bin
 
 buildscript {
     repositories {
@@ -95,7 +96,7 @@ 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:1.58'
+    compile 'org.bouncycastle:bcprov-jdk15on:1.59'
 
     compile 'commons-cli:commons-cli:1.4'
 
@@ -132,7 +133,7 @@ dependencies {
     compile 'org.fxmisc.richtext:richtextfx:0.8.1'
 
     // Cannot be updated to 9.*.* until Jabref works with Java 9
-    compile 'org.controlsfx:controlsfx:8.40.14'
+    compile 'org.controlsfx:controlsfx:8.40.15-SNAPSHOT'
 
     compile 'org.jsoup:jsoup:1.11.2'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
@@ -160,7 +161,7 @@ dependencies {
     testRuntime 'org.apache.logging.log4j:log4j-core:2.10.0'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.10.0'
     testCompile 'org.mockito:mockito-core:2.13.0'
-    testCompile 'com.github.tomakehurst:wiremock:2.12.0'
+    testCompile 'com.github.tomakehurst:wiremock:2.13.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.5.1'
@@ -170,7 +171,7 @@ dependencies {
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.5'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.7'
 }
 
 dependencyUpdates {
@@ -389,6 +390,7 @@ afterEvaluate {
     def junitPlatformTest = tasks.junitPlatformTest
 
     jacoco {
+        toolVersion = '0.8.0'
         applyTo(junitPlatformTest)
     }
 
@@ -502,7 +504,7 @@ task releaseJar(dependsOn: "shadowJar") {
             }
         }
         // set executable with read permissions (first true) and for all (false)
-        file("$buildDir/releases/JabRef-${project.version}.jar").setExecutable(true, false);
+        file("$buildDir/releases/JabRef-${project.version}.jar").setExecutable(true, false)
     }
 }
 

docs/adr/0001-use-crowdin-for-translations.md

@@ -0,0 +1,14 @@
+# Use Crowdin for tranlsations
+
+The JabRef UI is offered in multiple languages. It should be easy for translators to translate the strings.
+
+## Considered Alternatives
+
+* Use [Crowdin](http://crowdin.com/)
+* Use [popeye](https://github.com/JabRef/popeye)
+* Use [Lingohub](https://lingohub.com/)
+
+## Decision Outcome
+
+* Chosen Alternative: Crowdin
+* Crowdin is easy to use, integrates in our GitHub workflow, and is free for OSS projects.

gradle/wrapper/gradle-wrapper.jar

@@ -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-4.4-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.4.1-bin.zip

gradle/wrapper/gradle-wrapper.properties

@@ -80,6 +80,10 @@ private static void ensureCorrectJavaVersion() {
                             buildInfo.getMinRequiredJavaVersion()
                     )
             );
+
+            versionError.append("\n");
+            versionError.append(Localization.lang("Your Java Runtime Environment is located at %0.", checker.getJavaInstallationDirectory()));
+
             if (!buildInfo.isAllowJava9()) {
                 versionError.append("\n");
                 versionError.append(Localization.lang("Note that currently, JabRef does not run with Java 9."));

src/main/java/org/jabref/JabRefMain.java

@@ -1619,7 +1619,6 @@ public void ensureNotShowingBottomPanel(BibEntry entry) {
     public void updateEntryEditorIfShowing() {
         if (mode == BasePanelMode.SHOWING_EDITOR) {
             BibEntry currentEntry = entryEditor.getEntry();
-            showAndEdit(null);
             showAndEdit(currentEntry);
         }
     }
@@ -2013,18 +2012,19 @@ public void searchAndOpen() {
 
             // Run the search operation:
             FileFinder fileFinder = FileFinders.constructFromConfiguration(Globals.prefs.getAutoLinkPreferences());
+            try {
             List<Path> files = fileFinder.findAssociatedFiles(entry, dirs, extensions);
-            if (!files.isEmpty()) {
-                Path file = files.get(0);
-                Optional<ExternalFileType> type = ExternalFileTypes.getInstance().getExternalFileTypeByFile(file);
-                if (type.isPresent()) {
-                    try {
+                if (!files.isEmpty()) {
+                    Path file = files.get(0);
+                    Optional<ExternalFileType> type = ExternalFileTypes.getInstance().getExternalFileTypeByFile(file);
+                    if (type.isPresent()) {
                         JabRefDesktop.openExternalFileAnyFormat(file, basePanel.getBibDatabaseContext(), type);
                         basePanel.output(Localization.lang("External viewer called") + '.');
-                    } catch (IOException ex) {
-                        basePanel.output(Localization.lang("Error") + ": " + ex.getMessage());
                     }
                 }
+            } catch (IOException ex) {
+                LOGGER.error("Problems with finding/or opening files ", ex);
+                basePanel.output(Localization.lang("Error") + ": " + ex.getMessage());
             }
         }
     }

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

@@ -166,7 +166,7 @@ public static List<java.awt.Image> getLogoSet() {
 
         return jabrefLogos;
     }
-	
+
     public enum JabRefIcon {
 
         ADD(MaterialDesignIcon.PLUS_BOX),
@@ -260,6 +260,9 @@ public enum JabRefIcon {
         KEY_BINDINGS(MaterialDesignIcon.KEYBOARD), /*css: keyboard */
         FIND_DUPLICATES(MaterialDesignIcon.CODE_EQUAL), /*css: code-equal */
         PULL(MaterialDesignIcon.SOURCE_PULL), /*source-pull*/
+        SUCCESS(MaterialDesignIcon.CHECK_CIRCLE),
+        WARNING(MaterialDesignIcon.ALERT),
+        ERROR(MaterialDesignIcon.ALERT_CIRCLE),
         OPEN_IN_NEW_WINDOW(MaterialDesignIcon.OPEN_IN_NEW), /*css: open-in-new */
         CASE_SENSITIVE(MaterialDesignIcon.ALPHABETICAL), /* css: mdi-alphabetical */
         REG_EX(MaterialDesignIcon.REGEX), /*css: mdi-regex */