Merge remote-tracking branch 'upstream/main' into extract-entry-editor

.github/workflows/cleanup-pr.yml

@@ -29,7 +29,7 @@ jobs:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Delete folder on builds.jabref.org
         if: steps.checksecrets.outputs.secretspresent == 'YES'
-        uses: appleboy/ssh-action@v1.1.0
+        uses: appleboy/ssh-action@v1.2.0
         with:
           script: rm -rf /var/www/builds.jabref.org/www/pull/${{ github.event.pull_request.number }} || true
           host: build-upload.jabref.org

.github/workflows/deployment-arm64.yml

@@ -69,12 +69,12 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].0
+        uses: gittools/actions/gitversion/[email protected].3
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].0
+        uses: gittools/actions/gitversion/[email protected].3
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

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

@@ -85,12 +85,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].0
+        uses: gittools/actions/gitversion/[email protected].3
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].0
+        uses: gittools/actions/gitversion/[email protected].3
 
       # JDK
       - name: 'Set up JDK ${{ matrix.jdk }}'

.github/workflows/deployment.yml

@@ -81,12 +81,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].0
+        uses: gittools/actions/gitversion/[email protected].3
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].0
+        uses: gittools/actions/gitversion/[email protected].3
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

.github/workflows/tests.yml

@@ -109,7 +109,7 @@ jobs:
           submodules: 'false'
           show-progress: 'false'
       - name: markdownlint-cli2-action
-        uses: DavidAnson/markdownlint-cli2-action@v17
+        uses: DavidAnson/markdownlint-cli2-action@v18
         with:
           globs: |
             *.md
@@ -322,7 +322,7 @@ jobs:
           CI: "true"
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
           DBMS: "postgresql"
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         if: (github.ref == 'refs/heads/main') && (steps.checksecrets.outputs.secretspresent == 'YES')
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

CHANGELOG.md

@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added a Markdown export layout. [#12220](https://github.com/JabRef/jabref/pull/12220)
 - We added a "view as BibTeX" option before importing an entry from the citation relation tab. [#11826](https://github.com/JabRef/jabref/issues/11826)
 - We added support finding LaTeX-encoded special characters based on plain Unicode and vice versa. [#11542](https://github.com/JabRef/jabref/pull/11542)
 - When a search hits a file, the file icon of that entry is changed accordingly. [#11542](https://github.com/JabRef/jabref/pull/11542)
@@ -43,8 +44,10 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added automatic browser extension install on Windows for Chrome and Edge. [#6076](https://github.com/JabRef/jabref/issues/6076)
 - We added support to automatically open a `.bib` file in the current/parent folder if no other library is opened. [koppor#377](https://github.com/koppor/jabref/issues/377)
 - We added a search bar for filtering keyboard shortcuts. [#11686](https://github.com/JabRef/jabref/issues/11686)
+- We added new modifiers `camel_case`, `camel_case_n`, `short_title`, and `very_short_title` for the [citation key generator](https://docs.jabref.org/setup/citationkeypatterns). [#11367](https://github.com/JabRef/jabref/issues/11367)
 - By double clicking on a local citation in the Citation Relations Tab you can now jump the linked entry. [#11955](https://github.com/JabRef/jabref/pull/11955)
 - We use the menu icon for background tasks as a progress indicator to visualise an import's progress when dragging and dropping several PDF files into the main table. [#12072](https://github.com/JabRef/jabref/pull/12072)
+- The PDF content importer now supports importing title from upto the second page of the PDF. [#12139](https://github.com/JabRef/jabref/issues/12139)
 
 ### Changed
 
@@ -76,6 +79,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We changed the name of the library-based file directory from 'General File Directory' to 'Library-specific File Directory' per issue. [#571](https://github.com/koppor/jabref/issues/571)
 - We changed the defualt [unwanted charachters](https://docs.jabref.org/setup/citationkeypatterns#removing-unwanted-characters) in the citation key generator and allow a dash (`-`) and colon (`:`) being part of a citation key. [#12144](https://github.com/JabRef/jabref/pull/12144)
 - The CitationKey column is now a default shown column for the entry table. [#10510](https://github.com/JabRef/jabref/issues/10510)
+- We disabled the actions "Open Terminal here" and "Reveal in file explorer" for unsaved libraries. [#11920](https://github.com/JabRef/jabref/issues/11920)
+- JabRef now opens the corresponding directory in the library properties when "Browse" is clicked. [#12223](https://github.com/JabRef/jabref/pull/12223)
 
 ### Fixed
 
@@ -112,6 +117,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the "Do not ask again" checkbox was not working, when asking for permission to use Grobid [koppor#556](https://github.com/koppor/jabref/issues/566).
 - We fixed an issue where we display warning message for moving attached open files. [#10121](https://github.com/JabRef/jabref/issues/10121)
 - We fixed an issue where it was not possible to select selecting content of other user's comments.[#11106](https://github.com/JabRef/jabref/issues/11106)
+- We fixed an issue when handling URLs containing a pipe (`|`) character. [#11876](https://github.com/JabRef/jabref/issues/11876)
 - We fixed an issue where web search preferences "Custom API key" table modifications not discarded. [#11925](https://github.com/JabRef/jabref/issues/11925)
 - We fixed an issue when opening attached files in [extra file columns](https://docs.jabref.org/finding-sorting-and-cleaning-entries/filelinks#adding-additional-columns-to-entry-table-for-file-types). [#12005](https://github.com/JabRef/jabref/issues/12005)
 - We fixed an issue where trying to open a library from a failed mounted directory on Mac would cause an error. [#10548](https://github.com/JabRef/jabref/issues/10548)

build.gradle

@@ -29,7 +29,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.27.0'
+    id 'org.openrewrite.rewrite' version '6.27.2'
 
     id "org.itsallcode.openfasttrace" version "3.0.1"
 }
@@ -265,7 +265,7 @@ dependencies {
 
     // region HTTP clients
     implementation 'org.jsoup:jsoup:1.18.1'
-    implementation 'com.konghq:unirest-java-core:4.4.4'
+    implementation 'com.konghq:unirest-java-core:4.4.5'
     implementation 'com.konghq:unirest-modules-gson:4.4.5'
     implementation 'org.apache.httpcomponents.client5:httpclient5:5.4'
     // endregion
@@ -278,7 +278,7 @@ dependencies {
     // route all requests to java.util.logging to SLF4J (which in turn routes to tinylog)
     implementation 'org.slf4j:jul-to-slf4j:2.0.16'
     // route all requests to log4j to SLF4J
-    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.24.1'
+    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.24.2'
 
     implementation('de.undercouch:citeproc-java:3.1.0') {
         exclude group: 'org.antlr'
@@ -334,23 +334,23 @@ dependencies {
     implementation 'org.yaml:snakeyaml:2.3'
 
     // region AI
-    implementation 'dev.langchain4j:langchain4j:0.35.0'
+    implementation 'dev.langchain4j:langchain4j:0.36.0'
     // Even though we use jvm-openai for LLM connection, we still need this package for tokenization.
-    implementation('dev.langchain4j:langchain4j-open-ai:0.35.0') {
+    implementation('dev.langchain4j:langchain4j-open-ai:0.36.0') {
         exclude group: 'com.squareup.okhttp3'
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
         exclude group: 'org.jetbrains.kotlin'
     }
-    implementation('dev.langchain4j:langchain4j-mistral-ai:0.35.0') {
+    implementation('dev.langchain4j:langchain4j-mistral-ai:0.36.2') {
         exclude group: 'com.squareup.okhttp3'
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
         exclude group: 'org.jetbrains.kotlin'
     }
-    implementation('dev.langchain4j:langchain4j-google-ai-gemini:0.35.0') {
+    implementation('dev.langchain4j:langchain4j-google-ai-gemini:0.36.0') {
         exclude group: 'com.squareup.okhttp3'
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
     }
-    implementation('dev.langchain4j:langchain4j-hugging-face:0.35.0') {
+    implementation('dev.langchain4j:langchain4j-hugging-face:0.36.0') {
         exclude group: 'com.squareup.okhttp3'
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
         exclude group: 'org.jetbrains.kotlin'
@@ -370,17 +370,17 @@ dependencies {
     implementation 'org.jetbrains.kotlin:kotlin-stdlib-jdk8:2.0.21'
     // endregion
 
-    implementation 'commons-io:commons-io:2.17.0'
+    implementation 'commons-io:commons-io:2.18.0'
 
     // Even if "compileOnly" is used, IntelliJ always adds to module-info.java. To avoid issues during committing, we use "implementation" instead of "compileOnly"
     implementation 'io.github.adr:e-adr:2.0.0-SNAPSHOT'
 
-    implementation 'io.zonky.test:embedded-postgres:2.0.7'
+    implementation 'io.zonky.test:embedded-postgres:2.1.0'
     implementation enforcedPlatform('io.zonky.test.postgres:embedded-postgres-binaries-bom:17.0.0')
 
     testImplementation 'io.github.classgraph:classgraph:4.8.177'
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.11.0'
-    testImplementation 'org.junit.platform:junit-platform-launcher:1.10.3'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.11.3'
+    testImplementation 'org.junit.platform:junit-platform-launcher:1.11.3'
 
     testImplementation 'org.mockito:mockito-core:5.14.2'
     testImplementation 'org.xmlunit:xmlunit-core:2.10.0'
@@ -393,14 +393,14 @@ dependencies {
     testImplementation "com.github.javaparser:javaparser-symbol-solver-core:3.26.2"
 
     // recommended by https://github.com/wiremock/wiremock/issues/2149#issuecomment-1835775954
-    testImplementation 'org.wiremock:wiremock-standalone:3.3.1'
+    testImplementation 'org.wiremock:wiremock-standalone:3.9.2'
 
     checkstyle 'com.puppycrawl.tools:checkstyle:10.20.1'
     // xjc needs the runtime as well for the ant task, otherwise it fails
     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:2.19.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.22.0"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")

gradle/wrapper/gradle-wrapper.properties

@@ -1,7 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionSha256Sum=57dafb5c2622c6cc08b993c85b7c06956a2f53536432a30ead46166dbca0f1e9
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.11-bin.zip
+distributionSha256Sum=f397b287023acdba1e9f6fc5ea72d22dd63669d59ed4a289a29b1a76eee151c6
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.11.1-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

src/main/java/org/jabref/gui/actions/ActionHelper.java

@@ -29,6 +29,11 @@ public static BooleanExpression needsDatabase(StateManager stateManager) {
         return stateManager.activeDatabaseProperty().isPresent();
     }
 
+    public static BooleanExpression needsSavedLocalDatabase(StateManager stateManager) {
+        EasyBinding<Boolean> binding = EasyBind.map(stateManager.activeDatabaseProperty(), context -> context.filter(c -> c.getLocation() == DatabaseLocation.LOCAL && c.getDatabasePath().isPresent()).isPresent());
+        return BooleanExpression.booleanExpression(binding);
+    }
+
     public static BooleanExpression needsSharedDatabase(StateManager stateManager) {
         EasyBinding<Boolean> binding = EasyBind.map(stateManager.activeDatabaseProperty(), context -> context.filter(c -> c.getLocation() == DatabaseLocation.SHARED).isPresent());
         return BooleanExpression.booleanExpression(binding);
@@ -49,7 +54,7 @@ public static BooleanExpression needsEntriesSelected(StateManager stateManager)
 
     public static BooleanExpression needsEntriesSelected(int numberOfEntries, StateManager stateManager) {
         return Bindings.createBooleanBinding(() -> stateManager.getSelectedEntries().size() == numberOfEntries,
-                                             stateManager.getSelectedEntries());
+                stateManager.getSelectedEntries());
     }
 
     public static BooleanExpression isFieldSetForSelectedEntry(Field field, StateManager stateManager) {

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

@@ -251,7 +251,7 @@ private void addPreviewPanel() {
 
     public void removePreviewPanelFromThisTab() {
         assert this.getContent() instanceof SplitPane;
-        if (this.getContent() instanceof SplitPane splitPane && splitPane.getItems().contains(previewPanel)) {
+        if (this.getContent() instanceof SplitPane splitPane) {
             splitPane.getItems().remove(previewPanel);
             // Needed to "redraw" the split pane with one item (because JavaFX does not readjust if it is shown)
             // splitPane.setDividerPositions(1.0);
@@ -260,10 +260,10 @@ public void removePreviewPanelFromThisTab() {
 
     @Override
     protected void handleFocus() {
-        LOGGER.error("This is {}", preferences.getPreviewPreferences().showPreviewAsExtraTabProperty().get());
-        LOGGER.error("This is then {}", !preferences.getPreviewPreferences().showPreviewAsExtraTabProperty().get());
+        LOGGER.trace("This is {}", preferences.getPreviewPreferences().showPreviewAsExtraTabProperty().get());
+        LOGGER.trace("This is then {}", !preferences.getPreviewPreferences().showPreviewAsExtraTabProperty().get());
         if (!preferences.getPreviewPreferences().showPreviewAsExtraTabProperty().get()) {
-            LOGGER.error("Focus on preview panel");
+            LOGGER.trace("Focus on preview panel");
 
             // We need to move the preview panel from the non-visible tab to the visible tab
             removePreviewPanelFromOtherTabs();

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/semanticscholar/SemanticScholarFetcher.java

@@ -1,14 +1,14 @@
 package org.jabref.gui.entryeditor.citationrelationtab.semanticscholar;
 
 import java.net.MalformedURLException;
-import java.net.URI;
 import java.net.URL;
 import java.util.List;
 
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.ImporterPreferences;
 import org.jabref.logic.importer.fetcher.CustomizableKeyFetcher;
 import org.jabref.logic.net.URLDownload;
+import org.jabref.logic.util.URLUtil;
 import org.jabref.model.entry.BibEntry;
 
 import com.google.gson.Gson;
@@ -38,7 +38,7 @@ public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
 
         URL citationsUrl;
         try {
-            citationsUrl = URI.create(getAPIUrl("citations", entry)).toURL();
+            citationsUrl = URLUtil.create(getAPIUrl("citations", entry));
         } catch (MalformedURLException e) {
             throw new FetcherException("Malformed URL", e);
         }
@@ -62,7 +62,7 @@ public List<BibEntry> searchCiting(BibEntry entry) throws FetcherException {
 
         URL referencesUrl;
         try {
-            referencesUrl = URI.create(getAPIUrl("references", entry)).toURL();
+            referencesUrl = URLUtil.create(getAPIUrl("references", entry));
         } catch (MalformedURLException e) {
             throw new FetcherException("Malformed URL", e);
         }

src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java

@@ -287,7 +287,7 @@ public Parent getNode() {
 
     @FXML
     private void addNewFile() {
-        dialogService.showCustomDialogAndWait(new LinkedFileEditDialog()).ifPresent(newLinkedFile -> {
+        dialogService.showCustomDialogAndWait(new LinkedFileEditDialog()).filter(file -> !file.isEmpty()).ifPresent(newLinkedFile -> {
             viewModel.addNewLinkedFile(newLinkedFile);
         });
     }