Merge remote-tracking branch 'upstream/main' into oo-architecture

* upstream/main:
  Fix NPE when saving preferences (JabRef#11509)
  Switch to stream-based loading (JabRef#11479)
  Save unlinked local files dialog prefs (JabRef#11493)
  Add minimal support for biblatex data annotations (JabRef#11506)
  Fix handling of relative-file storage and auto linking (JabRef#11492)
  New Crowdin updates (JabRef#11504)
  Add missing issue numbers
  CSL4LibreOffice - A [GSoC '24] (JabRef#11477)
  Bump src/main/resources/csl-styles from `b2be5ae` to `fd6cb3e` (JabRef#11501)
  Bump gittools/actions from 1.1.1 to 1.2.0 (JabRef#11500)
  Bump com.kohlschutter.junixsocket:junixsocket-core from 2.9.1 to 2.10.0 (JabRef#11498)
  Bump commons-logging:commons-logging from 1.3.2 to 1.3.3 (JabRef#11499)
  Bump org.jsoup:jsoup from 1.17.2 to 1.18.1 (JabRef#11497)
  Bump com.kohlschutter.junixsocket:junixsocket-mysql from 2.9.1 to 2.10.0 (JabRef#11496)
  Bump org.openrewrite.recipe:rewrite-recipe-bom from 2.14.0 to 2.15.0 (JabRef#11495)
  FAQ updates (JabRef#11486)
  Update Gradle Wrapper from 8.8 to 8.9.
  Fix Chocolate.bib (JabRef#11491)

# Conflicts:
#	src/main/java/org/jabref/gui/openoffice/OOBibBase.java
#	src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java
#	src/main/java/org/jabref/gui/openoffice/StyleSelectDialogView.java
#	src/main/java/org/jabref/gui/openoffice/StyleSelectDialogViewModel.java
#	src/main/java/org/jabref/preferences/JabRefPreferences.java

.github/workflows/deployment-arm64.yml

@@ -66,12 +66,12 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v1.1.1
+        uses: gittools/actions/gitversion/setup@v1.2.0
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v1.1.1
+        uses: gittools/actions/gitversion/execute@v1.2.0
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

.github/workflows/deployment-jdk-ea.yml

@@ -84,12 +84,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v1.1.1
+        uses: gittools/actions/gitversion/setup@v1.2.0
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v1.1.1
+        uses: gittools/actions/gitversion/execute@v1.2.0
 
       # JDK
       - name: 'Set up JDK ${{ matrix.jdk }}'

.github/workflows/deployment.yml

@@ -79,12 +79,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v1.1.1
+        uses: gittools/actions/gitversion/setup@v1.2.0
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v1.1.1
+        uses: gittools/actions/gitversion/execute@v1.2.0
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

CHANGELOG.md

@@ -12,11 +12,18 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 ### Added
 
 - We added support for selecting and using CSL Styles in JabRef's OpenOffice/LibreOffice integration for inserting bibliographic and in-text citations into a document.
+- We added support for selecting and using CSL Styles in JabRef's OpenOffice/LibreOffice integration for inserting bibliographic and in-text citations into a document. [#2146](https://github.com/JabRef/jabref/issues/2146), [#8893](https://github.com/JabRef/jabref/issues/8893)
+- Added minimal support for [biblatex data annotation](https://mirrors.ctan.org/macros/latex/contrib/biblatex/doc/biblatex.pdf#subsection.3.7) fields in .layout files. [#11505](https://github.com/JabRef/jabref/issues/11505)
+- Added saving of selected options in the [Lookup -> Search for unlinked local files dialog](https://docs.jabref.org/collect/findunlinkedfiles#link-the-pdfs-to-your-bib-library). [#11439](https://github.com/JabRef/jabref/issues/11439)
 
 ### Changed
 
+- JabRef respects the [configuration for storing files relative to the .bib file](https://docs.jabref.org/finding-sorting-and-cleaning-entries/filelinks#directories-for-files) in more cases. [#11492](https://github.com/JabRef/jabref/pull/11492)
+
 ### Fixed
 
+- We fixed an issue where an exception was thrown after changing "show preview as a tab" in the preferences. [#11509](https://github.com/JabRef/jabref/pull/11509)
+
 ### Removed
 
 

build.gradle

@@ -168,7 +168,7 @@ dependencies {
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.11.0'
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.14.0'
     implementation group: 'org.apache.commons', name: 'commons-text', version: '1.12.0'
-    implementation 'commons-logging:commons-logging:1.3.2'
+    implementation 'commons-logging:commons-logging:1.3.3'
     implementation 'com.h2database:h2-mvstore:2.2.224'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
@@ -198,8 +198,8 @@ dependencies {
     implementation 'org.postgresql:postgresql:42.7.3'
 
     // Support unix socket connection types
-    implementation 'com.kohlschutter.junixsocket:junixsocket-core:2.9.1'
-    implementation 'com.kohlschutter.junixsocket:junixsocket-mysql:2.9.1'
+    implementation 'com.kohlschutter.junixsocket:junixsocket-core:2.10.0'
+    implementation 'com.kohlschutter.junixsocket:junixsocket-mysql:2.10.0'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
@@ -240,7 +240,7 @@ dependencies {
 
     implementation 'org.controlsfx:controlsfx:11.2.1'
 
-    implementation 'org.jsoup:jsoup:1.17.2'
+    implementation 'org.jsoup:jsoup:1.18.1'
     implementation 'com.konghq:unirest-java-core:4.4.0'
     implementation 'com.konghq:unirest-modules-gson:4.4.0'
     implementation 'org.apache.httpcomponents.client5:httpclient5:5.3.1'
@@ -328,7 +328,7 @@ dependencies {
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'
 
-    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.14.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.15.0"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")

docs/code-howtos/faq.md

@@ -7,14 +7,36 @@ parent: Code Howtos
 
 Following is a list of common errors encountered by developers which lead to failing tests, with their common solutions:
 
-* `org.jabref.architecture.MainArchitectureTest` `restrictStandardStreams` <span style="color:red">FAILED</span>
-  * <span style="color:green">Fix</span> : Check if you've used ```System.out.println(...)``` (the standard output stream) to log anything into the console. This is an architectural violation, as you should use the Logger instead for logging. More details on how to log can be found [here](https://devdocs.jabref.org/code-howtos/logging.html).
+* Failing <b>Checkstyle</b> tests:
+  * <span style="color:green">Fix</span>: JabRef follows a pre-defined style of code for uniformity and maintainability that must be adhered to during development. To set up warnings and auto-fixes conforming to these style rules in your IDE, follow [Step 3](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html) of the process to set up a local workspace in the documentation. Ideally, follow all the [set up rules](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/) in the documentation end-to-end to avoid typical set-up errors.<br> <b>Note</b>: The steps provided in the documentation are for IntelliJ, which is the preferred IDE for Java development. The `checkstyle.xml` is also available for VSCode, in the same directory as mentioned in the steps.
 
-* `org.jabref.architecture.MainArchitectureTest` `doNotUseLogicInModel` <span style="color:red">FAILED</span>
-  * <span style="color:green">Fix</span> : One common case when this test fails is when you put any class purely containing business logic at some level inside the ```model``` directory (```org/jabref/model/```). To fix this, shift the class to a subdirectory within the ```logic``` directory (```org/jabref/logic/```).
+* Failing <b>OpenRewrite</b> tests:
+  * <span style="color:green">Fix</span>: [OpenRewrite](https://docs.openrewrite.org/) is an automated refactoring ecosystem for source code. Execute the Gradle task `rewriteRun` from the `rewrite` group of the Gradle Tool window in IntelliJ to apply the automated refactoring and pass the test.<br>
+    ![Executing Gradle task rewriteRun](../images/rewriteRun.png)<br>
 
 * `org.jabref.logic.l10n.LocalizationConsistencyTest` `findMissingLocalizationKeys` <span style="color:red">FAILED</span>
-  * <span style="color:green">Fix</span> : You have probably used Strings that are visible on the UI (to the user) but not wrapped them using ```Localization.lang(...)``` and added them to the [localization properties file](https://github.com/JabRef/jabref/blob/main/src/main/resources/l10n/JabRef_en.properties).
+  * <span style="color:green">Fix</span>: You have probably used Strings that are visible on the UI (to the user) but not wrapped them using `Localization.lang(...)` and added them to the [localization properties file](https://github.com/JabRef/jabref/blob/main/src/main/resources/l10n/JabRef_en.properties).
       Read more about the background and format of localization in JabRef [here](https://devdocs.jabref.org/code-howtos/localization.html).
 
+* `org.jabref.logic.l10n.LocalizationConsistencyTest` `findObsoleteLocalizationKeys` <span style="color:red">FAILED</span>
+  * <span style="color:green">Fix</span>: There are localization keys [localization properties file](https://github.com/JabRef/jabref/blob/main/src/main/resources/l10n/JabRef_en.properties) that are not used in the code, probably due to the removal of existing code. Navigate to the unused key-value pairs in the file and remove them. You can always click on the details of the failing test to pinpoint which keys are unused.
+    Read more about the background and format of localization in JabRef [here](https://devdocs.jabref.org/code-howtos/localization.html).
+
+* `org.jabref.logic.citationstyle.CitationStyle` `discoverCitationStyles` <span style="color:red">ERROR: Could not find any citation style. Tried with /ieee.csl.</span>
+  * <span style="color:green">Fix</span>: Check the directory `src/main/resources/csl-styles`. If it is missing or empty, run `git submodule update`. Now, check inside if `ieee.csl` exists. If it does not, run `git reset --hard` <b>inside that directory</b>.
+
+* `java.lang.IllegalArgumentException`: Unable to load locale en-US<br> <span style="color:red">ERROR: Could not generate BibEntry citation. The CSL engine could not create a preview for your item.</span>
+  * <span style="color:green">Fix</span>: Check the directory `src/main/resources/csl-locales`. If it is missing or empty, run `git submodule update`. If still not fixed, run `git reset --hard` <b>inside that directory</b>.
+
+* `org.jabref.architecture.MainArchitectureTest` `restrictStandardStreams` <span style="color:red">FAILED</span>
+  * <span style="color:green">Fix</span>: Check if you've used `System.out.println(...)` (the standard output stream) to log anything into the console. This is an architectural violation, as you should use the Logger instead for logging. More details on how to log can be found [here](https://devdocs.jabref.org/code-howtos/logging.html).
+
+* `org.jabref.architecture.MainArchitectureTest` `doNotUseLogicInModel` <span style="color:red">FAILED</span>
+  * <span style="color:green">Fix</span>: One common case when this test fails is when you put any class purely containing business logic inside the `model` package (i.e., inside the directory `org/jabref/model/`). To fix this, shift the class to a sub-package within the `logic` package (i.e., the directory`org/jabref/logic/`). An efficient way to do this is to use IntelliJ's built-in refactoring capabilities - right-click on the file, go to "Refactor" and use "Move Class". The import statement for all the classes using this class will be automatically adjusted according to the new location.<br>
+    ![Moving a file using refactor](../images/refactor-moving.png)<br>
+
+* `ANTLR Tool version 4.12.0 used for code generation does not match the current runtime version 4.13.1`
+  * <span style="color:green">Fix</span>: Execute the Gradle task `clean` from the `build` group of the Gradle Tool Window in IntelliJ:<br>
+    ![Executing Gradle task clean](../images/clean.png)<br>
+
 <!-- markdownlint-disable-file MD033 -->

gradle/wrapper/gradle-wrapper.properties

@@ -1,7 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionSha256Sum=a4b4158601f8636cdeeab09bd76afb640030bb5b144aafe261a5e8af027dc612
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.8-bin.zip
+distributionSha256Sum=d725d707bfabd4dfdc958c624003b3c80accc03f7037b5122c4b1d0ef15cecab
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.9-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

gradlew

@@ -15,6 +15,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+# SPDX-License-Identifier: Apache-2.0
+#
 
 ##############################################################################
 #
@@ -84,7 +86,8 @@ done
 # shellcheck disable=SC2034
 APP_BASE_NAME=${0##*/}
 # Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
-APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
+APP_HOME=$( cd -P "${APP_HOME:-./}" > /dev/null && printf '%s
+' "$PWD" ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum

gradlew.bat

@@ -13,6 +13,8 @@
 @rem See the License for the specific language governing permissions and
 @rem limitations under the License.
 @rem
+@rem SPDX-License-Identifier: Apache-2.0
+@rem
 
 @if "%DEBUG%"=="" @echo off
 @rem ##########################################################################

src/main/java/org/jabref/architecture/AllowedToUseClassGetResource.java

@@ -0,0 +1,11 @@
+package org.jabref.architecture;
+
+/**
+ * Annotation to indicate that this logic class can use class.getResource().
+ * Mostly, because {@link java.nio.file.Path} is not used.
+ * See <a href="graal#7682">https://github.com/oracle/graal/issues/7682</a> for a longer discussion.
+ */
+public @interface AllowedToUseClassGetResource {
+    // The rationale
+    String value();
+}

src/main/java/org/jabref/architecture/AllowedToUseSwing.java

@@ -4,7 +4,6 @@
  * Annotation to indicate that this logic class can access swing
  */
 public @interface AllowedToUseSwing {
-
     // The rationale
     String value();
 }

src/main/java/org/jabref/gui/entryeditor/EntryEditor.java

@@ -147,8 +147,6 @@ public EntryEditor(LibraryTab libraryTab, UndoAction undoAction, RedoAction redo
                 activeTab.notifyAboutFocus(currentlyEditedEntry);
             }
         });
-        EasyBind.listen(preferencesService.getPreviewPreferences().showPreviewAsExtraTabProperty(),
-                (obs, oldValue, newValue) -> adaptVisibleTabs());
     }
 
     private void setupDragAndDrop(LibraryTab libraryTab) {
@@ -386,6 +384,9 @@ public void setCurrentlyEditedEntry(BibEntry currentlyEditedEntry) {
             getSelectedTab().notifyAboutFocus(currentlyEditedEntry);
         });
 
+        EasyBind.listen(preferencesService.getPreviewPreferences().showPreviewAsExtraTabProperty(),
+                (obs, oldValue, newValue) -> adaptVisibleTabs());
+
         adaptVisibleTabs();
         setupToolBar();
 

src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java

@@ -6,7 +6,6 @@
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
-import java.util.stream.Collectors;
 
 import org.jabref.gui.externalfiletype.ExternalFileType;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
@@ -52,6 +51,7 @@ public List<IOException> getFileExceptions() {
     }
 
     private static final Logger LOGGER = LoggerFactory.getLogger(AutoSetFileLinksUtil.class);
+
     private final List<Path> directories;
     private final AutoLinkPreferences autoLinkPreferences;
     private final FilePreferences filePreferences;
@@ -106,7 +106,9 @@ public LinkFilesResult linkAssociatedFiles(List<BibEntry> entries, NamedCompound
     public List<LinkedFile> findAssociatedNotLinkedFiles(BibEntry entry) throws IOException {
         List<LinkedFile> linkedFiles = new ArrayList<>();
 
-        List<String> extensions = filePreferences.getExternalFileTypes().stream().map(ExternalFileType::getExtension).collect(Collectors.toList());
+        List<String> extensions = filePreferences.getExternalFileTypes().stream().map(ExternalFileType::getExtension).toList();
+
+        LOGGER.debug("Searching for extensions {} in directories {}", extensions, directories);
 
         // Run the search operation
         FileFinder fileFinder = FileFinders.constructFromConfiguration(autoLinkPreferences);
@@ -134,6 +136,7 @@ public List<LinkedFile> findAssociatedNotLinkedFiles(BibEntry entry) throws IOEx
                 Path relativeFilePath = FileUtil.relativize(foundFile, directories);
                 LinkedFile linkedFile = new LinkedFile("", relativeFilePath, strType);
                 linkedFiles.add(linkedFile);
+                LOGGER.debug("Found file {} for entry {}", linkedFile, entry.getCitationKey());
             }
         }
 

src/main/java/org/jabref/gui/externalfiles/DateRange.java

@@ -11,11 +11,19 @@ public enum DateRange {
 
     private final String dateRange;
 
-    DateRange(String dateRange) { 
+    DateRange(String dateRange) {
        this.dateRange = dateRange;
     }
 
+    public static DateRange parse(String name) {
+        try {
+            return DateRange.valueOf(name);
+        } catch (IllegalArgumentException e) {
+            return ALL_TIME;
+        }
+    }
+
     public String getDateRange() {
-        return dateRange; 
-    } 
+        return dateRange;
+    }
 }

src/main/java/org/jabref/gui/externalfiles/ExternalFileSorter.java

@@ -13,6 +13,14 @@ public enum ExternalFileSorter {
         this.sorter = sorter;
     }
 
+    public static ExternalFileSorter parse(String name) {
+        try {
+            return ExternalFileSorter.valueOf(name);
+        } catch (IllegalArgumentException e) {
+            return DEFAULT;
+        }
+    }
+
     public String getSorter() {
         return sorter;
     }

src/main/java/org/jabref/gui/externalfiles/FileExtensionViewModel.java

@@ -15,16 +15,22 @@
 
 public class FileExtensionViewModel {
 
+    private final String name;
     private final String description;
     private final List<String> extensions;
     private final FilePreferences filePreferences;
 
     FileExtensionViewModel(FileType fileType, FilePreferences filePreferences) {
+        this.name = fileType.getName();
         this.description = Localization.lang("%0 file", fileType.getName());
         this.extensions = fileType.getExtensionsWithAsteriskAndDot();
         this.filePreferences = filePreferences;
     }
 
+    public String getName() {
+        return this.name;
+    }
+
     public String getDescription() {
         return this.description + extensions.stream().collect(Collectors.joining(", ", " (", ")"));
     }