Merge branch 'main' into faq-updates

.github/workflows/pr-comment.yml

@@ -43,7 +43,7 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
       - name: jbang
         if: ${{ steps.read-pr_number.outputs.pr_number != '' }}
-        uses: jbangdev/jbang-action@v0.117.1
+        uses: jbangdev/jbang-action@v0.118.0
         with:
           script: ghprcomment@koppor/ghprcomment
           scriptargs: "-r JabRef/jabref -p ${{ steps.read-pr_number.outputs.pr_number }} -w ${{ github.event.workflow_run.id }}"

.github/workflows/tests.yml

@@ -109,7 +109,7 @@ jobs:
           submodules: 'false'
           show-progress: 'false'
       - name: markdownlint-cli2-action
-        uses: DavidAnson/markdownlint-cli2-action@v16
+        uses: DavidAnson/markdownlint-cli2-action@v17
         with:
           globs: |
             *.md

build.gradle

@@ -270,9 +270,9 @@ dependencies {
     implementation 'org.tinylog:tinylog-impl:2.7.0'
 
     // route all requests to java.util.logging to SLF4J (which in turn routes to tinylog)
-    implementation 'org.slf4j:jul-to-slf4j:2.0.13'
+    implementation 'org.slf4j:jul-to-slf4j:2.0.16'
     // route all requests to log4j to SLF4J
-    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.23.1'
+    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.24.0'
 
     implementation('de.undercouch:citeproc-java:3.1.0') {
         exclude group: 'org.antlr'
@@ -337,7 +337,7 @@ dependencies {
     implementation('dev.langchain4j:langchain4j-google-ai-gemini:0.34.0')
     implementation('dev.langchain4j:langchain4j-hugging-face:0.34.0')
     implementation 'ai.djl:api:0.29.0'
-    implementation 'ai.djl.pytorch:pytorch-model-zoo:0.29.0'
+    implementation 'ai.djl.pytorch:pytorch-model-zoo:0.30.0'
     implementation 'ai.djl.huggingface:tokenizers:0.29.0'
     implementation 'io.github.stefanbratanov:jvm-openai:0.11.0'
     // openai depends on okhttp, which needs kotlin - see https://github.com/square/okhttp/issues/5299 for details
@@ -365,12 +365,12 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:3.0"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.18.0'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.18.1'
     // 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:2.18.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.19.0"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")

docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/trouble-shooting.md

@@ -83,3 +83,9 @@ Another indication is following output
 ```text
 java.lang.UnsupportedClassVersionError: org/javamodularity/moduleplugin/ModuleSystemPlugin has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0
 ```
+
+## Attempts to open preferences panel freezes application
+
+This is likely caused by improper integration of your OS or Desktop Environment with your password prompting program or password manager. Ensure that these are working properly, then restart your machine and attempt to run the program.
+
+For reference, see issue [#11766](https://github.com/JabRef/jabref/issues/11766).

src/main/java/org/jabref/gui/groups/GroupDialogViewModel.java

@@ -26,6 +26,7 @@
 import org.jabref.gui.DialogService;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.icon.IconTheme;
+import org.jabref.gui.importer.actions.SearchGroupsMigrationAction;
 import org.jabref.gui.preferences.GuiPreferences;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.logic.auxparser.DefaultAuxParser;
@@ -319,6 +320,17 @@ public AbstractGroup resultConverter(ButtonType button) {
                         searchGroupSearchTermProperty.getValue().trim(),
                         searchFlagsProperty.getValue());
 
+                if (currentDatabase.getMetaData().getGroupSearchSyntaxVersion().isEmpty()) {
+                    // If the syntax version for search groups is not present, it indicates that the groups
+                    // have not been migrated to the new syntax, or this is the first search group in the library.
+                    // If this is the first search group, set the syntax version to the new version.
+                    // Otherwise, it means that the user did not accept the migration to the new version.
+                    Optional<GroupTreeNode> groups = currentDatabase.getMetaData().getGroups();
+                    if (groups.filter(this::groupOrSubgroupIsSearchGroup).isEmpty()) {
+                        currentDatabase.getMetaData().setGroupSearchSyntaxVersion(SearchGroupsMigrationAction.VERSION_6_0_ALPHA);
+                    }
+                }
+
                 Optional<LuceneManager> luceneManager = stateManager.getLuceneManager(currentDatabase);
                 if (luceneManager.isPresent()) {
                     SearchGroup searchGroup = (SearchGroup) resultingGroup;
@@ -620,4 +632,16 @@ public StringProperty autoGroupPersonsFieldProperty() {
     public StringProperty texGroupFilePathProperty() {
         return texGroupFilePathProperty;
     }
+
+    private boolean groupOrSubgroupIsSearchGroup(GroupTreeNode groupTreeNode) {
+        if (groupTreeNode.getGroup() instanceof SearchGroup) {
+            return true;
+        }
+        for (GroupTreeNode child : groupTreeNode.getChildren()) {
+            if (groupOrSubgroupIsSearchGroup(child)) {
+                return true;
+            }
+        }
+        return false;
+    }
 }

src/main/java/org/jabref/gui/importer/actions/SearchGroupsMigrationAction.java

@@ -13,6 +13,8 @@
 import org.jabref.model.groups.SearchGroup;
 import org.jabref.model.search.SearchFlags;
 
+import org.antlr.v4.runtime.misc.ParseCancellationException;
+
 /**
  * This action checks whether the syntax for SearchGroups is the new one.
  * If not we ask the user whether to migrate.
@@ -54,18 +56,26 @@ public void performAction(ParserResult parserResult, DialogService dialogService
             return;
         }
 
-        parserResult.getMetaData().getGroups().ifPresent(this::migrateGroups);
+        parserResult.getMetaData().getGroups().ifPresent(groupTreeNode -> migrateGroups(groupTreeNode, dialogService));
         parserResult.getMetaData().setGroupSearchSyntaxVersion(VERSION_6_0_ALPHA);
         parserResult.setChangedOnMigration(true);
     }
 
-    private void migrateGroups(GroupTreeNode node) {
+    private void migrateGroups(GroupTreeNode node, DialogService dialogService) {
         if (node.getGroup() instanceof SearchGroup searchGroup) {
-            String luceneSearchExpression = SearchToLuceneMigration.migrateToLuceneSyntax(searchGroup.getSearchExpression(), searchGroup.getSearchFlags().contains(SearchFlags.REGULAR_EXPRESSION));
-            searchGroup.setSearchExpression(luceneSearchExpression);
+            try {
+                String luceneSearchExpression = SearchToLuceneMigration.migrateToLuceneSyntax(searchGroup.getSearchExpression(), searchGroup.getSearchFlags().contains(SearchFlags.REGULAR_EXPRESSION));
+                searchGroup.setSearchExpression(luceneSearchExpression);
+            } catch (ParseCancellationException e) {
+                Optional<String> luceneSearchExpression = dialogService.showInputDialogWithDefaultAndWait(
+                        Localization.lang("Search group migration failed"),
+                        Localization.lang("The search group '%0' could not be migrated. Please enter the new search expression.", searchGroup.getName()),
+                        searchGroup.getSearchExpression());
+                luceneSearchExpression.ifPresent(searchGroup::setSearchExpression);
+            }
         }
         for (GroupTreeNode child : node.getChildren()) {
-            migrateGroups(child);
+            migrateGroups(child, dialogService);
         }
     }
 }

src/main/java/org/jabref/logic/formatter/bibtexfields/HtmlToLatexFormatter.java

@@ -20,8 +20,7 @@ public class HtmlToLatexFormatter extends Formatter implements LayoutFormatter {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(HtmlToLatexFormatter.class);
 
-    private static final int MAX_TAG_LENGTH = 100;
-
+    private static final Pattern REMOVE_TAGS_PATTERN = Pattern.compile("<[^>]{1,100}>");
     private static final Pattern ESCAPED_PATTERN = Pattern.compile("&#([x]*)([0]*)(\\p{XDigit}+);");
     private static final Pattern ESCAPED_PATTERN2 = Pattern.compile("(.)&#([x]*)([0]*)(\\p{XDigit}+);");
     private static final Pattern ESCAPED_PATTERN3 = Pattern.compile("&#([x]*)([0]*)(\\p{XDigit}+);");
@@ -35,29 +34,12 @@ public String format(String text) {
             return result;
         }
 
-        StringBuilder sb = new StringBuilder();
         // Deal with the form <sup>k</sup>and <sub>k</sub>
         result = result.replaceAll("<[ ]?sup>([^<]+)</sup>", "\\\\textsuperscript\\{$1\\}");
         result = result.replaceAll("<[ ]?sub>([^<]+)</sub>", "\\\\textsubscript\\{$1\\}");
-
-        // TODO: maybe rewrite this based on regular expressions instead
         // Note that (at least) the IEEE Xplore fetcher must be fixed as it relies on the current way to
         // remove tags for its image alt-tag to equation converter
-        for (int i = 0; i < result.length(); i++) {
-            int c = result.charAt(i);
-
-            if (c == '<') {
-                int oldI = i;
-                i = readTag(result, i);
-                if (oldI == i) {
-                    // just a single <, which needs to be kept
-                    sb.append('<');
-                }
-            } else {
-                sb.append((char) c);
-            }
-        }
-        result = sb.toString();
+        result = REMOVE_TAGS_PATTERN.matcher(result).replaceAll("");
 
         // Handle text based HTML entities
         Set<String> patterns = HTMLUnicodeConversionMaps.HTML_LATEX_CONVERSION_MAP.keySet();
@@ -122,16 +104,6 @@ public String getExampleInput() {
         return "<strong>JabRef</strong>";
     }
 
-    private int readTag(String text, int position) {
-        // Have just read the < character that starts the tag.
-        int index = text.indexOf('>', position);
-        if ((index > position) && ((index - position) < MAX_TAG_LENGTH)) {
-            return index; // Just skip the tag.
-        } else {
-            return position; // Don't do anything.
-        }
-    }
-
     @Override
     public String getName() {
         return Localization.lang("HTML to LaTeX");

src/main/resources/l10n/JabRef_en.properties

@@ -270,9 +270,11 @@ Dynamically\ group\ entries\ by\ searching\ a\ field\ for\ a\ keyword=Dynamicall
 Each\ line\ must\ be\ of\ the\ following\ form\:\ \'tab\:field1;field2;...;fieldN\'.=Each line must be of the following form\: 'tab\:field1;field2;...;fieldN'.
 
 Search\ groups\ migration\ of\ %0=Search groups migration of %0
-The\ search\ groups\ syntax\ is\ outdated.\ Do\ you\ want\ to\ migrate\ to\ the\ new\ syntax?= The search groups syntax is outdated. Do you want to migrate to the new syntax?
+The\ search\ groups\ syntax\ is\ outdated.\ Do\ you\ want\ to\ migrate\ to\ the\ new\ syntax?=The search groups syntax is outdated. Do you want to migrate to the new syntax?
 Migrate=Migrate
 Keep\ as\ is=Keep as is
+Search\ group\ migration\ failed=Search group migration failed
+The\ search\ group\ '%0'\ could\ not\ be\ migrated.\ Please\ enter\ the\ new\ search\ expression.=The search group '%0' could not be migrated. Please enter the new search expression.
 Edit=Edit
 
 Edit\ file\ type=Edit file type