Merge branch 'master' into customizeEntrydlg

* master: reference to issue added (#5911) Fix properly resolves OrFields of required fields (#5903) IDE setup updated and extended (#5901) Squashed 'src/main/resources/csl-styles/' changes from e71363e..c531528 Fixes problems with managing external file types (issue 5846) (#5894) Squashed 'src/main/resources/csl-locales/' changes from 41da445acc..4fa753374e Squashed 'src/main/resources/csl-styles/' changes from f0c7374..e71363e Update development-strategy.md Replace link to Workspace set-up with new one (#5896) Fixes making paths of linked files relative (web urls will not be touched anymore) (#5879)
JabRef · Feb 3, 2020 · 50c054d · 50c054d
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diff --git a/AUTHORS b/AUTHORS
@@ -301,6 +301,7 @@ Stephen Beitzel
 Stéphane Curet
 Super-Tang
 Sven Jäger
+systemoperator
 Thiago Toledo
 Thomas Arildsen
 Thomas Ilsche

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -27,6 +27,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where an erroneous "The library has been modified by another program" message was shown when saving. [#4877](https://github.com/JabRef/jabref/issues/4877)
 - We fixed an issue where the file extension was missing after downloading a file (we now fall-back to pdf). [#5816](https://github.com/JabRef/jabref/issues/5816)
 - We fixed an issue where cleaning up entries broke web URLs, if "Make paths of linked files relative (if possible)" was enabled, which resulted in various other issues subsequently. [#5861](https://github.com/JabRef/jabref/issues/5861)
+- We fixed an issue where the tab "Required fields" of the entry editor did not show all required fields, if at least two of the defined required fields are linked with a logical or. [#5859](https://github.com/JabRef/jabref/issues/5859)
+- 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)
 
 ### Removed
 - Ampersands are no longer escaped by default in the `bib` file. If you want to keep the current behaviour, you can use the new "Escape Ampersands" formatter as a save action.

diff --git a/docs/development-strategy.md b/docs/development-strategy.md
@@ -6,9 +6,9 @@ To ensure high code-quality,
 
 - we follow the priniciples of [Java by Comparison](https://java.by-comparison.com/).
 - we follow the principles of [Effetcive Java](https://www.oreilly.com/library/view/effective-java-3rd/9780134686097/).
-- we use [Design Pattners](https://java-design-patterns.com/patterns/) wherever possible.
+- we use [Design Pattners](https://java-design-patterns.com/patterns/) when applicable.
 - we document our design decisions using the lightweight architectural decision records [MADR](https://adr.github.io/madr/).
-- we review each pull request by at least two [JabRef Core Developers](https://github.com/JabRef/jabref/blob/master/DEVELOPERS).
+- we review each external pull request by at least two [JabRef Core Developers](https://github.com/JabRef/jabref/blob/master/DEVELOPERS).
 
 ## Continuos integration
 
@@ -22,6 +22,7 @@ The branch [master](https://builds.jabref.org/master/) is the main development l
 
 Other branches are used for discussing improvements with the help of [pull requests](https://github.com/JabRef/jabref/pulls).
 One can see the binaries of each branch at <https://builds.jabref.org/>.
+Releases mark milestones and are based on the master at a point in time.
 
 ## How JabRef aquires contributors
 

diff --git a/docs/guidelines-for-setting-up-a-local-workspace.md b/docs/guidelines-for-setting-up-a-local-workspace.md
@@ -45,55 +45,158 @@ Under Ubuntu Linux, you can follow the [documentation from the Ubuntu Community]
 * Go to the newly created jabref folder: `cd jabref`
 * Generate additional source code: `./gradlew assemble`
 * Start JabRef: `./gradlew run`
+  * The JabRef's GUI should now start up.
 
 ## Configure your IDE
 
-### IntelliJ
+### Setup for IntelliJ
 
 1. Open `jabref/build.gradle` as a project
 2. Enable annotation processors:
-   * File -> Settings -> Compiler -> Annotation processors -> Check "Enable annotation processing"
-3. Configure module settings: Right click on project -> Open Module Settings
-   * Ensure that the projects SDK is Java 13: Project Settings -> Project -> Project SDK: Choose Java 13
-   * Ensure that standard SDK is Java 13: Platform Settings -> SDK -> Choose Java 13
-4. Specify additional compiler arguments: File -> Settings -> Build, Execution, Deployment -> Compiler -> Java Compiler -> Under "Override compiler parameters per-module" add the following compiler arguments for the `JabRef.main` module:
-   ```text
-   --patch-module test=fastparse_2.12-1.0.0.jar
-   --patch-module test2=fastparse-utils_2.12-1.0.0.jar
-   --patch-module test3=sourcecode_2.12-0.1.4.jar
-   --add-exports javafx.controls/com.sun.javafx.scene.control=org.jabref
-   --add-exports org.controlsfx.controls/impl.org.controlsfx.skin=org.jabref
-   --add-exports javafx.graphics/com.sun.javafx.scene=org.controlsfx.controls
-   --add-exports javafx.graphics/com.sun.javafx.scene.traversal=org.controlsfx.controls
-   --add-exports javafx.graphics/com.sun.javafx.css=org.controlsfx.controls
-   --add-exports javafx.controls/com.sun.javafx.scene.control.behavior=org.controlsfx.controls
-   --add-exports javafx.controls/com.sun.javafx.scene.control=org.controlsfx.controls
-   --add-exports javafx.controls/com.sun.javafx.scene.control.inputmap=org.controlsfx.controls
-   --add-exports javafx.base/com.sun.javafx.event=org.controlsfx.controls
-   --add-exports javafx.base/com.sun.javafx.collections=org.controlsfx.controls
-   --add-exports javafx.base/com.sun.javafx.runtime=org.controlsfx.controls
-   --add-exports javafx.web/com.sun.webkit=org.controlsfx.controls
-   --add-exports javafx.graphics/com.sun.javafx.css=org.controlsfx.controls
-   --add-exports javafx.controls/com.sun.javafx.scene.control.behavior=com.jfoenix
-   --patch-module org.jabref=build/resources/main
+   * File -> Settings -> Build, Execution, Deployment -> Compiler -> Annotation processors:
+     * Check "Enable annotation processing"
+3. Configure module settings: Right click on project -> Open Module Settings:
+   * Ensure that the projects' SDK is Java 13:
+     * Project Settings -> Project -> Project SDK: Choose Java 13
+   * Ensure that standard SDK is Java 13:
+     * Platform Settings -> SDK -> Choose Java 13
+4. Specify additional compiler arguments:
+   * File -> Settings -> Build, Execution, Deployment -> Compiler -> Java Compiler:
+     * Under "Override compiler parameters per-module" add ([+]) the following compiler arguments for the `JabRef.main` module:
+
+   ```
+   --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref
+   --add-exports=org.controlsfx.controls/impl.org.controlsfx.skin=org.jabref
    ```
-4. Use IntellJ to build and run (instead of gradle): File -> Settings -> Build, Execution, Deployment ->  Build Tools -> Gradle -> At "Build and run using" and "Run tests using" choose "Intellj IDEA"
-4. Ensure that JDK13 is enabled for Gradle: Use IntellJ to build and run (instead of gradle): File -> Settings -> Build, Execution, Deployment ->  Build Tools -> Gradle -> Gradle -> Gradle JVM
-5. Use the provided code style:
-   1. Install the [CheckStyle-IDEA plugin](http://plugins.jetbrains.com/plugin/1065?pr=idea), it can be found via plug-in repository (File > Settings > Plugins > Marketplace -> Search for "Checkstyle" and choose "CheckStyle-IDEA). Close the settings afterwards and restart IntelliJ.
-   2. Go to File > Settings > Editor > Code Style, choose a code style (or create a new one) 
-   3. Click on the settings wheel (next to the scheme chooser), then click "Import Scheme" and choose "IntelliJ Code Style xml". Select the IntelliJ configuration file `config/IntelliJ Code Style.xml`. Click OK.
-   4. Go to File -> Settings -> Checkstyle and import the CheckStyle configuration file. Activate it.
-6. Use the provided run configuration: Run -> Run "JabRef Main"
-
-### Set-up Eclipse
-
-1. Run `./gradlew run` to generate all resources and to check if jabref runs. (This step is only required once)
-2. Run `./gradlew eclipse` (This has to be always execute, when there are new upstream changes)
-7. Copy the file Log4jPlugins.java from `build\generated\sources\annotationProcessor\java\main\org\jabref\gui\logging\plugins` to `org.jabref.gui.logging.plugins`
-8. Create a run/debug configuration for main class `org.jabref.JabRefLauncher` 
-9. In the arguments tab enter the same runtime arguments as above for intellij.
-10. Optional: Install the [e(fx)clipse plugin](http://www.eclipse.org/efxclipse/index.html) from the eclipse marketplace
+
+5. Use IntellJ to build and run (instead of gradle):
+   * File -> Settings -> Build, Execution, Deployment -> Build Tools -> Gradle:
+     * Set "Build and run using" and "Run tests using" both to "IntelliJ IDEA"
+6. Ensure that the JDK13 is enabled for Gradle: Use IntellJ to build and run (instead of gradle):
+   * File -> Settings -> Build, Execution, Deployment -> Build Tools -> Gradle -> Gradle:
+     * Set "Gradle JVM" to "JDK13"
+7. Use the provided code style:
+   1. Install the [CheckStyle-IDEA plugin](http://plugins.jetbrains.com/plugin/1065?pr=idea), it can be found via the plug-in repository:
+      1. File > Settings > Plugins > Marketplace
+      2. Search for "Checkstyle" and choose "CheckStyle-IDEA"
+      3. Close the settings afterwards and restart IntelliJ
+   2. Go to File > Settings > Editor > Code Style:
+      1. Click on the settings wheel (next to the scheme chooser), then click "Import Scheme" and choose "IntelliJ Code Style.xml".
+      2. Select the IntelliJ configuration file `config/IntelliJ Code Style.xml`.
+      3. Click "OK".
+   4. Go to File -> Settings -> Other Settings -> Checkstyle -> Configuration File:
+      1. Import the CheckStyle configuration file by clicking the [+] button
+      2. For the description provide e.g. "CheckStyle"
+      3. Click "Browse" and choose `config/checkstyle/checkstyle.xml`
+      4. Click "Next" and "Finish"
+      5. Activate the CheckStyle configuration file by ticking it in the list
+      6. Save settings by clicking "OK"
+8. Open Run -> Edit Configurations... -> Select Application -> JabRef Main
+   * Verify, that "JRE" is set to "Default (JDK 13)" or to JDK 13
+   * Set "VM Options" to the following:
+
+    ```
+    --patch-module org.jabref=build/resources/main
+    --add-exports javafx.controls/com.sun.javafx.scene.control=org.jabref
+    --add-exports org.controlsfx.controls/impl.org.controlsfx.skin=org.jabref
+    --add-exports javafx.graphics/com.sun.javafx.scene=org.controlsfx.controls
+    --add-exports javafx.graphics/com.sun.javafx.scene.traversal=org.controlsfx.controls
+    --add-exports javafx.graphics/com.sun.javafx.css=org.controlsfx.controls
+    --add-exports javafx.controls/com.sun.javafx.scene.control.behavior=org.controlsfx.controls
+    --add-exports javafx.controls/com.sun.javafx.scene.control=org.controlsfx.controls
+    --add-exports javafx.controls/com.sun.javafx.scene.control.inputmap=org.controlsfx.controls
+    --add-exports javafx.base/com.sun.javafx.event=org.controlsfx.controls
+    --add-exports javafx.base/com.sun.javafx.collections=org.controlsfx.controls
+    --add-exports javafx.base/com.sun.javafx.runtime=org.controlsfx.controls
+    --add-exports javafx.web/com.sun.webkit=org.controlsfx.controls
+    --add-exports javafx.graphics/com.sun.javafx.css=org.controlsfx.controls
+    --add-exports javafx.controls/com.sun.javafx.scene.control.behavior=com.jfoenix
+    --add-exports com.oracle.truffle.regex/com.oracle.truffle.regex=org.graalvm.truffle
+    --add-opens javafx.controls/javafx.scene.control=org.jabref
+    --add-opens org.controlsfx.controls/org.controlsfx.control.textfield=org.jabref
+    --add-opens javafx.controls/javafx.scene.control.skin=org.controlsfx.controls
+    --add-opens javafx.graphics/javafx.scene=org.controlsfx.controls
+    --add-opens javafx.controls/com.sun.javafx.scene.control=org.jabref
+    --add-opens javafx.controls/com.sun.javafx.scene.control.behavior=com.jfoenix
+    --add-opens javafx.base/com.sun.javafx.binding=com.jfoenix
+    --add-opens javafx.graphics/com.sun.javafx.stage=com.jfoenix
+    --add-opens javafx.base/com.sun.javafx.event=com.jfoenix
+    ```
+
+     Optionally the following entries can also be added (but they currently only produce warnings and they are not needed):
+
+   ```
+    --patch-module test=fastparse_2.12-1.0.0.jar
+    --patch-module test2=fastparse-utils_2.12-1.0.0.jar
+    --patch-module test3=sourcecode_2.12-0.1.4.jar
+   ```
+
+9. If you have configured Eclipse for the same project (the required steps are described below), then the additionally added file `Log4jPlugins.java` must be excluded from the compilation process, otherwise an error will occur during the compilation of the project:
+   * File -> Settings -> Build, Execution, Deployment -> Compiler -> Excludes: Add the following file to the list ([+]), in order to exclude it:
+     * `src/main/java/org/jabref/gui/logging/plugins/Log4jPlugins.java`
+10. Use the provided run configuration: Run -> Run "JabRef Main"
+    * This uses now IntelliJ for building and running/debugging the application, which is recommended, since the application starts quite fast.
+11. Alternatively, the project can also be built and run/debugged by using gradle from within the IDE, which is not recommended, since the application starts significantly slower:
+    1. Open the gradle tool window:
+       * View -> Tool Windows -> Gradle
+    2. Navigate to the following entry in the gradle tool window:
+       * JabRef -> Tasks -> application -> run
+    3. Double click "run" to build and run the application
+    4. After that a new entry called "jabref [run]" will appear in the run configurations.
+    5. Now you can also select "jabref [run]" and either run or debug the application from within IntelliJ.
+       * Equivalently, this can also be executed from the terminal by running `./gradlew run`.
+
+
+### Setup for Eclipse
+
+1. Run `./gradlew run` to generate all resources and to check if jabref runs.
+   * The JabRef GUI should finally appear.
+   * This step is only required once.
+2. Run `./gradlew eclipse`
+   * **This must always be executed, when there are new upstream changes.**
+3. Copy the file `Log4jPlugins.java` from `build\generated\sources\annotationProcessor\java\main\org\jabref\gui\logging\plugins` to `src/main/java/org/jabref/gui/logging/plugins/`
+   * Usually, the folder `plugins` must be created for that.
+4. Open or import the existing project in Eclipse as Java project. Import as gradle project will not work correctly.
+5. Create a run/debug configuration for the main class `org.jabref.JabRefLauncher` and/or for `org.jabref.JabRefMain` (both can be used equivalently)
+   * In the tab "Arguments" of the run/debug configuration, enter the same runtime VM arguments as above for intelliJ:
+     * Set "VM Arguments" to:
+
+    ```
+    --patch-module org.jabref=build/resources/main
+    --add-exports javafx.controls/com.sun.javafx.scene.control=org.jabref
+    --add-exports org.controlsfx.controls/impl.org.controlsfx.skin=org.jabref
+    --add-exports javafx.graphics/com.sun.javafx.scene=org.controlsfx.controls
+    --add-exports javafx.graphics/com.sun.javafx.scene.traversal=org.controlsfx.controls
+    --add-exports javafx.graphics/com.sun.javafx.css=org.controlsfx.controls
+    --add-exports javafx.controls/com.sun.javafx.scene.control.behavior=org.controlsfx.controls
+    --add-exports javafx.controls/com.sun.javafx.scene.control=org.controlsfx.controls
+    --add-exports javafx.controls/com.sun.javafx.scene.control.inputmap=org.controlsfx.controls
+    --add-exports javafx.base/com.sun.javafx.event=org.controlsfx.controls
+    --add-exports javafx.base/com.sun.javafx.collections=org.controlsfx.controls
+    --add-exports javafx.base/com.sun.javafx.runtime=org.controlsfx.controls
+    --add-exports javafx.web/com.sun.webkit=org.controlsfx.controls
+    --add-exports javafx.graphics/com.sun.javafx.css=org.controlsfx.controls
+    --add-exports javafx.controls/com.sun.javafx.scene.control.behavior=com.jfoenix
+    --add-exports com.oracle.truffle.regex/com.oracle.truffle.regex=org.graalvm.truffle
+    --add-opens javafx.controls/javafx.scene.control=org.jabref
+    --add-opens org.controlsfx.controls/org.controlsfx.control.textfield=org.jabref
+    --add-opens javafx.controls/javafx.scene.control.skin=org.controlsfx.controls
+    --add-opens javafx.graphics/javafx.scene=org.controlsfx.controls
+    --add-opens javafx.controls/com.sun.javafx.scene.control=org.jabref
+    --add-opens javafx.controls/com.sun.javafx.scene.control.behavior=com.jfoenix
+    --add-opens javafx.base/com.sun.javafx.binding=com.jfoenix
+    --add-opens javafx.graphics/com.sun.javafx.stage=com.jfoenix
+    --add-opens javafx.base/com.sun.javafx.event=com.jfoenix
+    ```
+
+6. Optional: Install the [e(fx)clipse plugin](http://www.eclipse.org/efxclipse/index.html) from the eclipse marketplace:
+   1. Help -> Eclipse Marketplace... -> Search tab
+   2. Enter "e(fx)clipse" in the search dialogue
+   3. Click "Go"
+   4. Click "Install" button next to the plugin
+   5. Click "Finish"
+7. Now you can build and run/debug the application by either using "JabRefLauncher" or "JabRefMain". This is the recommended way, since the application starts quite fast.
+   * Alternatively, it is still possible to start the application from the terminal by executing `./gradlew run`, but the application will start significantly slower.
 
 ## Final comments
 

diff --git a/src/main/java/org/jabref/gui/entryeditor/RequiredFieldsTab.java b/src/main/java/org/jabref/gui/entryeditor/RequiredFieldsTab.java
@@ -4,7 +4,6 @@
 import java.util.Optional;
 import java.util.SortedSet;
 import java.util.TreeSet;
-import java.util.stream.Collectors;
 
 import javax.swing.undo.UndoManager;
 
@@ -43,7 +42,9 @@ protected SortedSet<Field> determineFieldsToShow(BibEntry entry) {
         Optional<BibEntryType> entryType = entryTypesManager.enrich(entry.getType(), databaseContext.getMode());
         SortedSet<Field> fields = new TreeSet<>(Comparator.comparing(Field::getName));
         if (entryType.isPresent()) {
-            fields.addAll(entryType.get().getRequiredFields().stream().map(OrFields::getPrimary).collect(Collectors.toSet()));
+            for (OrFields orFields : entryType.get().getRequiredFields()) {
+                fields.addAll(orFields);
+            }
             // Add the edit field for Bibtex-key.
             fields.add(InternalField.KEY_FIELD);
         } else {

diff --git a/src/main/java/org/jabref/gui/externalfiletype/CustomizeExternalFileTypesViewModel.java b/src/main/java/org/jabref/gui/externalfiletype/CustomizeExternalFileTypesViewModel.java
@@ -49,6 +49,8 @@ private void showEditDialog(ExternalFileType type, String dialogTitle) {
             typeForEdit = (CustomExternalFileType) type;
         } else {
             typeForEdit = new CustomExternalFileType(type);
+            fileTypes.add(fileTypes.indexOf(type), typeForEdit);
+            fileTypes.remove(type);
         }
 
         EditExternalFileTypeEntryDialog dlg = new EditExternalFileTypeEntryDialog(typeForEdit, dialogTitle);

diff --git a/src/main/java/org/jabref/gui/externalfiletype/EditExternalFileTypeEntryDialog.java b/src/main/java/org/jabref/gui/externalfiletype/EditExternalFileTypeEntryDialog.java
@@ -62,6 +62,7 @@ public void initialize() {
         icon.setGraphic(viewModel.getIcon());
 
         defaultApplication.selectedProperty().bindBidirectional(viewModel.defaultApplicationSelectedProperty());
+        customApplication.selectedProperty().bindBidirectional(viewModel.customApplicationSelectedProperty());
         selectedApplication.disableProperty().bind(viewModel.defaultApplicationSelectedProperty());
         btnBrowse.disableProperty().bind(viewModel.defaultApplicationSelectedProperty());