Merge branch 'master' into remote-db-menu

.github/workflows/tests.yml

@@ -208,3 +208,11 @@ jobs:
           CI: "false" # we pretend to run locally - even if tests fail on the CI, they count towards test coverage
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
           DBMS: "postgresql"
+  # This is https://github.com/marketplace/actions/gradle-wrapper-validation
+  # It ensures that the jar file is from gradle and not by a strange third party.
+  gradlevalidation:
+    name: "Validate Gradle Wrapper"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: gradle/wrapper-validation-action@v1

.sonarcloud.properties

@@ -0,0 +1 @@
+

CHANGELOG.md

@@ -13,7 +13,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 ### Changed
 
-- We reintroduced the possibility to extract references from plain text (using GROBID) [#5614](https://github.com/JabRef/jabref/pull/5614) 
+- We reintroduced the possibility to extract references from plain text (using GROBID) [#5614](https://github.com/JabRef/jabref/pull/5614)
 - We changed the open office panel to show buttons in rows of three instead of going straight down to save space as the button expanded out to take up unnecessary horizontal space. [#5479](https://github.com/JabRef/jabref/issues/5479)
 - We cleaned up the group add/edit dialog. [#5826](https://github.com/JabRef/jabref/pull/5826)
 - We reintroduced the index column. [#5844](https://github.com/JabRef/jabref/pull/5844)
@@ -37,8 +37,15 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed several issues concerning managing external file types: Now everything is usable and fully functional. Previously, there were problems with the radio buttons, with saving the settings and with loading an input field value. Furthermore, different behavior for Windows and other operating systems was given, which was unified as well. [#5846](https://github.com/JabRef/jabref/issues/5846)
 - We fixed an issue where entries containing Unicode charaters were not parsed correctly [#5899](https://github.com/JabRef/jabref/issues/5899)
 - We fixed an issue where an entry containing an external filename with curly braces could not be saved. Curly braces are now longer allowed in filenames. [#5899](https://github.com/JabRef/jabref/issues/5899)
+- We fixed an issue where changing the type of an entry did not update the main table [#5906](https://github.com/JabRef/jabref/issues/5906)
+- We fixed an issue where opening a library from the recent libraries menu was not possible [#5939](https://github.com/JabRef/jabref/issues/5939)
+- We fixed an issue in the optics of the library properties, that cropped the dialog on scaled displays. [#5969](https://github.com/JabRef/jabref/issues/5969)
 - We fixed an issue where changing the type of an entry did not update the main table. [#5906](https://github.com/JabRef/jabref/issues/5906)
 - We fixed an issue where opening a library from the recent libraries menu was not possible. [#5939](https://github.com/JabRef/jabref/issues/5939)
+- We fixed an issue where the most bottom group in the list got lost, if it was dragged on itself. [#5983](https://github.com/JabRef/jabref/issues/5983)
+- We fixed an issue where changing entry type doesn't always work when biblatex source is shown. [#5905](https://github.com/JabRef/jabref/issues/5905)
+- We fixed an issue where the group and the link column were not updated after changing the entry in the main table. [#5985](https://github.com/JabRef/jabref/issues/5985)
+- We fixed an issue where reordering the groups was not possible after inserting an article. [#6008](https://github.com/JabRef/jabref/issues/6008)
 
 ### Removed
 

docs/README.md

@@ -2,9 +2,15 @@
 
 This page presents all development informatation around JabRef. For users documentation see <https://docs.jabref.org>.
 
+## Excersises
+
+Uni Basel offers a German (🇩🇪) Software Engineering course which uses JabRef as one example.
+Look at [Exercise 5](https://github.com/unibas-marcelluethi/software-engineering/blob/master/docs/week5/exercises/practical-exercises.md) for an exercise where some important points of JabRef are touched.
+
 ## How tos
 
-- [Sync your fork with the JabRef repository](https://help.github.com/articles/syncing-a-fork/)
+- External: [Sync your fork with the JabRef repository](https://help.github.com/articles/syncing-a-fork/)
+- External (🇩🇪): Branches and pull requests: <https://github.com/unibas-marcelluethi/software-engineering/blob/master/docs/week2/exercises/practical-exercises.md>
 
 ## Command Line
 

docs/code-quality.md

@@ -0,0 +1,12 @@
+# Code Quality
+
+We monitor the general source code quality at three places:
+
+* [codacy](https://www.codacy.com/) is a hosted service to monitor code quality. It thereby combines the results of available open source code quality checkers such as [Checkstyle](https://checkstyle.sourceforge.io/) or [PMD](https://pmd.github.io/). The code quality analysis for JabRef is available at <https://app.codacy.com/gh/JabRef/jabref/dashboard>, especially the [list of open issues](https://app.codacy.com/gh/JabRef/jabref/issues/index). In case a rule feels wrong, it is most likely a PMD rule. The JabRef team can change the configuration at <https://app.codacy.com/p/306789/patterns/list?engine=9ed24812-b6ee-4a58-9004-0ed183c45b8f>.
+* [codecov](https://codecov.io/) is a solution to check code coverage of test cases. The code coverage metrics for JabRef are available at <https://codecov.io/github/JabRef/jabref>.
+* [Teamscale](https://www.cqse.eu/de/produkte/teamscale/landing/) is a popular German product analyzing code quality. The analysis results are available at <https://demo.teamscale.com/findings.html#/jabref/?>.
+
+We strongly recommend to read following two books on code quality:
+
+* [Java by Comparison](java.by-comparison.com/) is a book by three JabRef developers which focuses on code improvements close to single statements. It is fast to read and one gains much information from each recommendation discussed in the book.
+* [Effective Java](https://www.oreilly.com/library/view/effective-java-3rd/9780134686097/) is the standard book for advanced Java programming. Did you know that `enum` is the [recommended way to enforce a singleton instance of a class](https://learning.oreilly.com/library/view/effective-java-3rd/9780134686097/ch2.xhtml#lev3)? Did you know that one should [refer to objects by their interfaces](https://learning.oreilly.com/library/view/effective-java-3rd/9780134686097/ch9.xhtml#lev64)?

docs/guidelines-for-setting-up-a-local-workspace.md

@@ -1,12 +1,12 @@
-# Setup a local workspace
+# Set up a local workspace
 
 This guide explains how to set up your environment for development of JabRef. It includes information about prerequisites, configuring your IDE, and running JabRef locally to verify your setup.
 
-For a complete step-by-step guide (using IntellJ as the IDE), have a look at the following video instructions:
+For a complete step-by-step guide for Linux using IntellJ IDEA as the IDE, have a look at the following video instructions:
 
-<p align="center">
-  <a href="http://www.youtube.com/watch?v=FeQpygT0314"><img src="http://img.youtube.com/vi/FeQpygT0314/0.jpg" /></a>
-</p>
+<a href="https://youtu.be/JkFVJ6p0urw">
+<img src="https://img.youtube.com/vi/JkFVJ6p0urw/mqdefault.jpg" alt="JabRef development video tutorial"/>
+</a>
 
 ## Prerequisites
 

src/main/java/module-info.java

@@ -6,6 +6,7 @@
     requires java.sql;
 
     // JavaFX
+    requires javafx.base;
     requires javafx.graphics;
     requires javafx.swing;
     requires javafx.controls;
@@ -17,6 +18,7 @@
     requires de.jensd.fx.fontawesomefx.commons;
     requires de.jensd.fx.fontawesomefx.materialdesignicons;
     requires org.controlsfx.controls;
+    requires org.fxmisc.richtext;
 
     provides com.airhacks.afterburner.views.ResourceLocator
             with org.jabref.gui.util.JabRefResourceLocator;
@@ -62,7 +64,6 @@
     requires org.graalvm.js;
     requires org.apache.xmpbox;
     requires de.saxsys.mvvmfx.validation;
-    requires richtextfx;
     requires com.google.gson;
     requires unirest.java;
     requires org.apache.httpcomponents.httpclient;
@@ -72,9 +73,10 @@
     requires java.string.similarity;
     requires ojdbc10;
     requires org.postgresql.jdbc;
+    requires org.mariadb.jdbc;
+    uses org.mariadb.jdbc.credential.CredentialPlugin;
     requires org.apache.commons.lang3;
     requires org.antlr.antlr4.runtime;
     requires flowless;
     requires org.apache.tika.core;
-    requires javafx.base;
 }

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

@@ -494,7 +494,7 @@ private Node createToolbar() {
                 factory.createIconButton(StandardActions.GENERATE_CITE_KEYS, new OldDatabaseCommandWrapper(Actions.MAKE_KEY, this, stateManager)),
                 factory.createIconButton(StandardActions.CLEANUP_ENTRIES, new OldDatabaseCommandWrapper(Actions.CLEANUP, this, stateManager)),
                 new Separator(Orientation.VERTICAL),
-                factory.createIconButton(StandardActions.FORK_ME, new OpenBrowserAction("https://github.com/JabRef/jabref")),
+                factory.createIconButton(StandardActions.OPEN_GITHUB, new OpenBrowserAction("https://github.com/JabRef/jabref")),
                 factory.createIconButton(StandardActions.OPEN_FACEBOOK, new OpenBrowserAction("https://www.facebook.com/JabRef/")),
                 factory.createIconButton(StandardActions.OPEN_TWITTER, new OpenBrowserAction("https://twitter.com/jabref_org"))
         );
@@ -653,6 +653,7 @@ private MenuBar createMenu() {
         Menu edit = new Menu(Localization.lang("Edit"));
         Menu library = new Menu(Localization.lang("Library"));
         Menu quality = new Menu(Localization.lang("Quality"));
+        Menu lookup = new Menu(Localization.lang("Lookup"));
         Menu view = new Menu(Localization.lang("View"));
         Menu tools = new Menu(Localization.lang("Tools"));
         Menu options = new Menu(Localization.lang("Options"));
@@ -716,18 +717,23 @@ private MenuBar createMenu() {
 
                 new SeparatorMenuItem(),
 
+                factory.createMenuItem(StandardActions.REPLACE_ALL, new OldDatabaseCommandWrapper(Actions.REPLACE_ALL, this, stateManager)),
+                factory.createMenuItem(StandardActions.GENERATE_CITE_KEYS, new OldDatabaseCommandWrapper(Actions.MAKE_KEY, this, stateManager)),
+
+                new SeparatorMenuItem(),
+
                 factory.createMenuItem(StandardActions.MANAGE_KEYWORDS, new ManageKeywordsAction(stateManager))
         );
 
         if (Globals.prefs.getBoolean(JabRefPreferences.SPECIALFIELDSENABLED)) {
             edit.getItems().addAll(
+                    new SeparatorMenuItem(),
                     SpecialFieldMenuItemFactory.createSpecialFieldMenuForActiveDatabase(SpecialField.RANKING, factory, undoManager),
                     SpecialFieldMenuItemFactory.getSpecialFieldSingleItemForActiveDatabase(SpecialField.RELEVANCE, factory),
                     SpecialFieldMenuItemFactory.getSpecialFieldSingleItemForActiveDatabase(SpecialField.QUALITY, factory),
                     SpecialFieldMenuItemFactory.getSpecialFieldSingleItemForActiveDatabase(SpecialField.PRINTED, factory),
                     SpecialFieldMenuItemFactory.createSpecialFieldMenuForActiveDatabase(SpecialField.PRIORITY, factory, undoManager),
-                    SpecialFieldMenuItemFactory.createSpecialFieldMenuForActiveDatabase(SpecialField.READ_STATUS, factory, undoManager),
-                    new SeparatorMenuItem()
+                    SpecialFieldMenuItemFactory.createSpecialFieldMenuForActiveDatabase(SpecialField.READ_STATUS, factory, undoManager)
             );
         }
 
@@ -763,6 +769,10 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction(this, prefs, stateManager, undoManager, Globals.TASK_EXECUTOR))
         );
 
+        lookup.getItems().addAll(
+                factory.createMenuItem(StandardActions.FIND_DUPLICATES, new DuplicateSearch(this, dialogService, stateManager))
+        );
+
         // PushToApplication
         final PushToApplicationAction pushToApplicationAction = pushToApplicationsManager.getPushToApplicationAction();
         final MenuItem pushToApplicationMenuItem = factory.createMenuItem(pushToApplicationAction.getActionInformation(), pushToApplicationAction);
@@ -771,6 +781,9 @@ private MenuBar createMenu() {
         tools.getItems().addAll(
                 factory.createMenuItem(StandardActions.PARSE_TEX, new ParseTexAction(stateManager)),
                 factory.createMenuItem(StandardActions.NEW_SUB_LIBRARY_FROM_AUX, new NewSubLibraryAction(this, stateManager)),
+
+                new SeparatorMenuItem(),
+
                 factory.createMenuItem(StandardActions.FIND_UNLINKED_FILES, new FindUnlinkedFilesAction(this, stateManager)),
                 factory.createMenuItem(StandardActions.WRITE_XMP, new OldDatabaseCommandWrapper(Actions.WRITE_XMP, this, stateManager)),
                 factory.createMenuItem(StandardActions.COPY_LINKED_FILES, new CopyFilesAction(stateManager, this.getDialogService())),
@@ -782,8 +795,6 @@ private MenuBar createMenu() {
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.GENERATE_CITE_KEYS, new OldDatabaseCommandWrapper(Actions.MAKE_KEY, this, stateManager)),
-                factory.createMenuItem(StandardActions.REPLACE_ALL, new OldDatabaseCommandWrapper(Actions.REPLACE_ALL, this, stateManager)),
                 factory.createMenuItem(StandardActions.SEND_AS_EMAIL, new OldDatabaseCommandWrapper(Actions.SEND_AS_EMAIL, this, stateManager)),
                 pushToApplicationMenuItem,
 
@@ -849,23 +860,19 @@ private MenuBar createMenu() {
 
                 new SeparatorMenuItem(),
 
+                factory.createMenuItem(StandardActions.DONATE, new OpenBrowserAction("https://donations.jabref.org")),
                 factory.createMenuItem(StandardActions.SEARCH_FOR_UPDATES, new SearchForUpdateAction(Globals.BUILD_INFO, prefs.getVersionPreferences(), dialogService, Globals.TASK_EXECUTOR)),
                 factory.createSubMenu(StandardActions.WEB_MENU,
                         factory.createMenuItem(StandardActions.OPEN_WEBPAGE, new OpenBrowserAction("https://jabref.org/")),
                         factory.createMenuItem(StandardActions.OPEN_BLOG, new OpenBrowserAction("https://blog.jabref.org/")),
                         factory.createMenuItem(StandardActions.OPEN_FACEBOOK, new OpenBrowserAction("https://www.facebook.com/JabRef/")),
                         factory.createMenuItem(StandardActions.OPEN_TWITTER, new OpenBrowserAction("https://twitter.com/jabref_org")),
+                        factory.createMenuItem(StandardActions.OPEN_GITHUB, new OpenBrowserAction("https://github.com/JabRef/jabref")),
 
                         new SeparatorMenuItem(),
 
-                        factory.createMenuItem(StandardActions.FORK_ME, new OpenBrowserAction("https://github.com/JabRef/jabref")),
                         factory.createMenuItem(StandardActions.OPEN_DEV_VERSION_LINK, new OpenBrowserAction("https://builds.jabref.org/master/")),
-                        factory.createMenuItem(StandardActions.OPEN_CHANGELOG, new OpenBrowserAction("https://github.com/JabRef/jabref/blob/master/CHANGELOG.md")),
-
-                        new SeparatorMenuItem(),
-
-                        factory.createMenuItem(StandardActions.DONATE, new OpenBrowserAction("https://donations.jabref.org"))
-
+                        factory.createMenuItem(StandardActions.OPEN_CHANGELOG, new OpenBrowserAction("https://github.com/JabRef/jabref/blob/master/CHANGELOG.md"))
                 ),
                 factory.createMenuItem(StandardActions.ABOUT, new AboutAction())
         );

src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml

@@ -24,37 +24,38 @@
     <RadioButton fx:id="exportInSpecifiedOrder"
                  text="%Export entries ordered as specified" toggleGroup="$saveOrderToggleGroup"/>
 
-    <GridPane alignment="CENTER_LEFT" hgap="10.0">
+    <GridPane hgap="10.0" vgap="4.0">
         <columnConstraints>
-            <ColumnConstraints hgrow="SOMETIMES" minWidth="-Infinity" prefWidth="100.0"/>
-            <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0"/>
-            <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0"/>
+            <ColumnConstraints hgrow="NEVER" minWidth="25.0" maxWidth="25.0"/>
+            <ColumnConstraints hgrow="SOMETIMES" percentWidth="30.0" />
+            <ColumnConstraints hgrow="SOMETIMES" />
+            <ColumnConstraints hgrow="SOMETIMES" halignment="LEFT"/>
         </columnConstraints>
         <rowConstraints>
-            <RowConstraints prefHeight="30.0"/>
-            <RowConstraints prefHeight="30.0"/>
-            <RowConstraints prefHeight="30.0"/>
-            <RowConstraints prefHeight="30.0"/>
-            <RowConstraints prefHeight="30.0"/>
-            <RowConstraints prefHeight="30.0"/>
+            <RowConstraints minHeight="30.0" vgrow="SOMETIMES" />
+            <RowConstraints minHeight="30.0" vgrow="SOMETIMES" />
+            <RowConstraints minHeight="30.0" vgrow="SOMETIMES" />
         </rowConstraints>
 
-        <Label disable="${!exportInSpecifiedOrder.selected}" text="%Primary sort criterion" GridPane.rowIndex="0"/>
-        <Label disable="${!exportInSpecifiedOrder.selected}" text="%Secondary sort criterion" GridPane.rowIndex="1"/>
-        <Label disable="${!exportInSpecifiedOrder.selected}" text="%Tertiary sort criterion" GridPane.rowIndex="2"/>
+        <Label text="%Primary sort criterion" GridPane.columnIndex="1" GridPane.rowIndex="0"
+               disable="${!exportInSpecifiedOrder.selected}"/>
+        <Label text="%Secondary sort criterion" GridPane.columnIndex="1" GridPane.rowIndex="1"
+               disable="${!exportInSpecifiedOrder.selected}"/>
+        <Label text="%Tertiary sort criterion" GridPane.columnIndex="1" GridPane.rowIndex="2"
+               disable="${!exportInSpecifiedOrder.selected}"/>
 
-        <ComboBox fx:id="savePriSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="0"
+        <ComboBox fx:id="savePriSort" editable="true" GridPane.columnIndex="2" GridPane.rowIndex="0"
                   disable="${!exportInSpecifiedOrder.selected}"/>
-        <ComboBox fx:id="saveSecSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="1"
+        <ComboBox fx:id="saveSecSort" editable="true" GridPane.columnIndex="2" GridPane.rowIndex="1"
                   disable="${!exportInSpecifiedOrder.selected}"/>
-        <ComboBox fx:id="saveTerSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="2"
+        <ComboBox fx:id="saveTerSort" editable="true" GridPane.columnIndex="2" GridPane.rowIndex="2"
                   disable="${!exportInSpecifiedOrder.selected}"/>
 
         <CheckBox fx:id="savePriDesc" disable="${!exportInSpecifiedOrder.selected}" mnemonicParsing="false"
-                  text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="0"/>
+                  text="%Descending" GridPane.columnIndex="3" GridPane.rowIndex="0"/>
         <CheckBox fx:id="saveSecDesc" disable="${!exportInSpecifiedOrder.selected}" mnemonicParsing="false"
-                  text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="1"/>
+                  text="%Descending" GridPane.columnIndex="3" GridPane.rowIndex="1"/>
         <CheckBox fx:id="saveTerDesc" disable="${!exportInSpecifiedOrder.selected}" mnemonicParsing="false"
-                  text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="2"/>
+                  text="%Descending" GridPane.columnIndex="3" GridPane.rowIndex="2"/>
     </GridPane>
 </fx:root>