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

* upstream/master: (30 commits)
  Update README.md (#4419)
  Fix generate bibtex key overwrite warning dialog (#4418)
  Fix group hit counter when adding entries (#4413)
  Update README.md
  fix java.nio.file.FileSystemNotFoundException and reorganize code (#4416)
  fixed an issue where corresponding groups are sometimes not highlighted when clicking on entries (#4404)
  Add a few journal abbreviations (#4412)
  Fix display of radio buttons (#4411)
  Update issue templates
  Delete ISSUE_TEMPLATE.md
  Update issue templates
  Integrate mrdlib redesign (#4361)
  fix "save" button in preference dialog not response (#4406)
  show dialog before creating entry (#4405)
  Scrollbar invisible in Preferences -> BibTex Key Pattern (#4287) (#4398)
  Updates (#4402)
  Fixes for all mods exporter tests (#4396)
  Fix EntryType dialog not closed after generate button (#4390)
  Make rank image narrower (#4395)
  Fix showing multiple icons for one menu entry - fixes #4384 (#4392)
  ...

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,32 @@
+---
+name: Bug report
+about: Create a report to help us improve
+
+---
+
+<!-- 
+Note: Please use the GitHub issue tracker only for bug reports. 
+Feature requests, questions and general feedback is now handled at http://discourse.jabref.org.
+Thanks! 
+--> 
+
+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. -->
+- [ ] I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists
+
+<!-- Add a clear and concise description of what the bug is. -->
+
+Steps to reproduce the behavior:
+1. ...
+2. ...
+3. ...
+
+<!-- If applicable, add excerpt of the bibliography file, screenshot, and excerpt of log (available in the error console) -->
+
+<details>
+  <summary>Log File</summary>
+
+  ```
+  Paste an excerpt of your log file here
+  ```
+</details>

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,9 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+
+---
+
+Please use the GitHub issue tracker only for bug reports and suggestions for improvements.
+Feature requests, questions and general feedback is now handled at http://discourse.jabref.org.
+Thanks!

.github/ISSUE_TEMPLATE/question.md

@@ -0,0 +1,9 @@
+---
+name: Question
+about: Ask a question about JabRef
+
+---
+
+Please use the GitHub issue tracker only for bug reports and suggestions for improvements.
+Feature requests, questions and general feedback is now handled at http://discourse.jabref.org.
+Thanks!

.github/ISSUE_TEMPLATE/suggestion-for-improvement.md

@@ -0,0 +1,20 @@
+---
+name: Suggestion for improvement
+about: Suggest an enhancement
+
+---
+
+<!--
+Please use the GitHub issue tracker only for bug reports and smaller suggestions for improvements.
+Requests for completely new features, questions and general feedback is now handled at http://discourse.jabref.org.
+Thanks!
+-->
+
+**Is your suggestion for improvement related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.travis.yml

@@ -47,7 +47,7 @@ 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" ] && [ "$TEST_SUITE" != "codecov" ]; then ./gradlew $TEST_SUITE $OPTIONS --scan; fi
+  - if [ "$TEST_SUITE" != "guiTest" ] && [ "$TEST_SUITE" != "checkstyle" ] && [ "$TEST_SUITE" != "codecov" ]; then ./gradlew $TEST_SUITE $OPTIONS -x checkstyleJmh -x checkstyleMain -x checkstyleTest --scan; fi
   - if [ "$TEST_SUITE" == "checkstyle" ]; then ./gradlew checkstyleMain checkstyleTest checkstyleJmh; fi
   - if [ "$TEST_SUITE" == "guiTest" ]; then ./buildres/gui-tests.sh; fi
   - if [ "$TEST_SUITE" == "codecov" ]; then ./gradlew jacocoTestReport; bash <(curl -s https://codecov.io/bash); fi

CHANGELOG.md

@@ -34,14 +34,16 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We add auto url formatting when user paste link to URL field in entry editor. [#254](https://github.com/koppor/jabref/issues/254)
 - We added a minimal height for the entry editor so that it can no longer be hidden by accident. [#4279](https://github.com/JabRef/jabref/issues/4279)
 - We added a new keyboard shortcut so that the entry editor could be closed by <kbd>Ctrl<kbd> + <kbd>E<kbd>. [#4222] (https://github.com/JabRef/jabref/issues/4222)
-
+- We added an option in the preference dialog box, that allows user to pick the dark or light theme option. [#4130] (https://github.com/JabRef/jabref/issues/4130)
+- We updated updated the Related Articles tab to accept JSON from the new version of the Mr. DLib service
 
 
 
 
 
 
 ### Fixed
+- 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
 - 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
@@ -59,6 +61,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the order of fields in customized entry types was not saved correctly. [#4033](http://github.com/JabRef/jabref/issues/4033)
 - 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 number of entries matched was not updated correctly upon adding or removing an entry. [#3537](https://github.com/JabRef/jabref/issues/3537)
 - 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

README.md

@@ -101,9 +101,7 @@ When you want to develop, it is necessary to generate additional sources using `
 and then generate the Eclipse `gradlew eclipse`.
 For IntelliJ IDEA, just import the project via a Gradle Import by pointing at the `build.gradle`.
 
-`gradlew test` executes the normal unit tests.
-If you want to test the UI, execute `gradlew integrationTest`.
-Sources for the integration test are kept in `src/integrationTest`.
+`gradlew test` executes all tests. We use [Travis CI](https://travis-ci.org/) for executing the tests after each commit. For developing, it is sufficient to locally only run the associated test for the classes you changed. Travis will report any other failure.
 
 
 ## Acknowledgements

build.gradle

@@ -16,8 +16,8 @@ buildscript {
 
 plugins {
     id 'com.gradle.build-scan' version '1.16'
-    id 'com.install4j.gradle' version '7.0.7'
-    id 'com.github.johnrengelman.shadow' version '4.0.0'
+    id 'com.install4j.gradle' version '7.0.8'
+    id 'com.github.johnrengelman.shadow' version '2.0.4'
     id "de.sebastianboegl.shadow.transformer.log4j" version "2.1.1"
     id "com.simonharrer.modernizer" version '1.6.0-1'
     id 'me.champeau.gradle.jmh' version '0.4.7'
@@ -119,13 +119,13 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.7.1'
     compile 'org.antlr:antlr4-runtime:4.7.1'
 
-    compile 'mysql:mysql-connector-java:8.0.12'
+    compile 'mysql:mysql-connector-java:8.0.13'
 
     compile 'org.postgresql:postgresql:42.2.5'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:26.0-jre'
+    compile 'com.google.guava:guava:27.0-jre'
 
     // JavaFX stuff
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
@@ -168,7 +168,7 @@ dependencies {
     testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.3.1'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.3.1'
     testCompile 'org.junit.platform:junit-platform-launcher:1.3.1'
-    testCompile 'org.junit-pioneer:junit-pioneer:0.2.1'
+    testCompile 'org.junit-pioneer:junit-pioneer:0.2.2'
     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:2.23.0'
@@ -177,11 +177,12 @@ dependencies {
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
-    testCompile 'com.tngtech.archunit:archunit-junit:0.8.3'
+    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.9.1'
+    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.9.1'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.13'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.14'
 }
 
 jacoco {
@@ -203,6 +204,11 @@ 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")
@@ -215,8 +221,8 @@ dependencyUpdates.resolutionStrategy = {
             }
         }
         rules.withModule("com.github.johnrengelman.shadow:com.github.johnrengelman.shadow.gradle.plugin") { ComponentSelection selection ->
-            if (selection.candidate.version == /4.0.1/) {
-                selection.reject("Version 4.0.1 breaks the release process.")
+            if (selection.candidate.version ==~ /4.*/) {
+                selection.reject("Version 4.X breaks the release process.")
             }
         }
         rules.withModule("de.jensd:fontawesomefx-materialdesignfont") { ComponentSelection selection ->
@@ -402,12 +408,7 @@ jacocoTestReport {
 
 // Code quality tasks
 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 = []
 }
 
 modernizer {

config/checkstyle/suppressions.xml

@@ -6,5 +6,4 @@
 
 <suppressions>
     <suppress checks="[a-zA-Z0-9]*" files="[\\/]gen[\\/]" />
-    <suppress checks="[a-zA-Z0-9]*" files="[\\/]test[\\/]" />
 </suppressions>

src/main/java/org/jabref/Globals.java

@@ -75,11 +75,11 @@ public static synchronized KeyBindingRepository getKeyPrefs() {
     }
 
     // Background tasks
-    public static void startBackgroundTasks() {
+    public static void startBackgroundTasks() throws JabRefException {
         Globals.fileUpdateMonitor = new DefaultFileUpdateMonitor();
         JabRefExecutorService.INSTANCE.executeInterruptableTask(Globals.fileUpdateMonitor, "FileUpdateMonitor");
 
-        themeLoader = new ThemeLoader(fileUpdateMonitor);
+        themeLoader = new ThemeLoader(fileUpdateMonitor, prefs);
 
         if (Globals.prefs.shouldCollectTelemetry() && !GraphicsEnvironment.isHeadless()) {
             startTelemetryClient();

src/main/java/org/jabref/gui/Base.css

@@ -247,6 +247,7 @@
     -fx-underline: false;
     -fx-border-style: null;
     -fx-border-color: null;
+    -fx-text-fill: -jr-theme;
 }
 
 .hyperlink:visited {
@@ -390,12 +391,32 @@
 }
 
 .check-box > .box > .mark {
-    -fx-background-color: white;
+    -fx-background-color: -fx-control-inner-background;
     -fx-padding: 0.2em 0.2em 0.2em 0.2em;
     -fx-shape: "M6.61 11.89L3.5 8.78 2.44 9.84 6.61 14l8.95-8.95L14.5 4z";
     -fx-stroke-width: 5;
 }
 
+.radio-button > .radio {
+    -fx-background-radius: 1.0em; /* large value to make sure this remains circular */
+    -fx-padding: 0.35em; /* padding from outside edge to the inner dot */
+    -fx-background-color: rgba(0, 0, 0, 0.54), -fx-control-inner-background;
+    -fx-background-insets: 0, 2px;
+}
+
+.radio-button:selected > .radio {
+    -fx-background-color: -jr-checked, -fx-background;
+}
+
+.radio-button > .radio > .dot {
+    -fx-padding: 0.25em; /* radius of the inner dot when selected */
+    -fx-background-insets: 0;
+}
+
+.radio-button:selected > .radio > .dot {
+    -fx-background-color: -jr-checked;
+}
+
 .menu-bar {
     -fx-background-color: -jr-menu-background;
     -fx-background-insets: 0;
@@ -667,6 +688,7 @@
     -fx-background-radius: 0em;
 }
 
+
 .scroll-bar:horizontal .thumb,
 .scroll-bar:vertical .thumb {
     -fx-background-color: -jr-scrollbar-thumb;
@@ -714,7 +736,8 @@
 .tree-view:hover .scroll-bar,
 .table-view:hover .scroll-bar,
 .tree-table-view:hover .scroll-bar,
-.text-input:hover .scroll-bar {
+.text-input:hover .scroll-bar,
+.scroll-pane:hover .scroll-bar {
     -fx-opacity: 1;
 }
 

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

@@ -74,6 +74,13 @@ public EntryTypeView(BasePanel basePanel, DialogService dialogService, JabRefPre
 
         btnGenerate.textProperty().bind(EasyBind.map(viewModel.searchingProperty(), searching -> (searching) ? Localization.lang("Searching...") : Localization.lang("Generate")));
         btnGenerate.disableProperty().bind(viewModel.searchingProperty());
+
+        EasyBind.subscribe(viewModel.searchSuccesfulProperty(), value -> {
+            if (value) {
+                setEntryTypeForReturnAndClose(null);
+            }
+        });
+
     }
 
     private void addEntriesToPane(FlowPane pane, Collection<? extends EntryType> entries) {

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

@@ -36,6 +36,7 @@ public class EntryTypeViewModel {
 
     private final JabRefPreferences prefs;
     private final BooleanProperty searchingProperty = new SimpleBooleanProperty();
+    private final BooleanProperty searchSuccesfulProperty = new SimpleBooleanProperty();
     private final ObjectProperty<IdBasedFetcher> selectedItemProperty = new SimpleObjectProperty<>();
     private final ListProperty<IdBasedFetcher> fetchers = new SimpleListProperty<>(FXCollections.observableArrayList());
     private final StringProperty idText = new SimpleStringProperty();
@@ -53,6 +54,10 @@ public EntryTypeViewModel(JabRefPreferences preferences, BasePanel basePanel, Di
 
     }
 
+    public BooleanProperty searchSuccesfulProperty() {
+        return searchSuccesfulProperty;
+    }
+
     public BooleanProperty searchingProperty() {
         return searchingProperty;
     }
@@ -110,6 +115,7 @@ protected Optional<BibEntry> call() throws InterruptedException, FetcherExceptio
     }
 
     public void runFetcherWorker() {
+        searchSuccesfulProperty.set(false);
         fetcherWorker.run();
         fetcherWorker.setOnFailed(event -> {
             Throwable exception = fetcherWorker.getException();
@@ -124,7 +130,9 @@ public void runFetcherWorker() {
             LOGGER.error(String.format("Exception during fetching when using fetcher '%s' with entry id '%s'.", searchId, fetcher), exception);
 
             searchingProperty.set(false);
+
             fetcherWorker = new FetcherWorker();
+
         });
 
         fetcherWorker.setOnSucceeded(evt -> {
@@ -143,8 +151,8 @@ public void runFetcherWorker() {
                     new BibtexKeyGenerator(basePanel.getBibDatabaseContext(), prefs.getBibtexKeyPatternPreferences()).generateAndSetKey(bibEntry);
                     basePanel.insertEntry(bibEntry);
                 }
+                searchSuccesfulProperty.set(true);
 
-                // close();
             } else if (StringUtil.isBlank(idText.getValue())) {
                 dialogService.showWarningDialogAndWait(Localization.lang("Empty search ID"), Localization.lang("The given search ID was empty."));
             }