Merge branch 'rewrite-journal-abbrevation-repository-12571' of github.com:LoayTarek5/jabref into rewrite-journal-abbrevation-repository-12571

Author: LoayTarek5

.github/workflows/link-issue.yml

@@ -113,20 +113,36 @@ jobs:
 
           echo "Updating issue '${{ needs.determine_issue_number.outputs.issue_number }}'"
 
-          # Check if good first/second/.. issue
-          # If yes, copy label to GitHub PR for transparency
+
+          # Copy over labels from issue to PR if they match good first/second/third/forth issue or component:* labels
+
           LABELS=$(gh api repos/${{ github.repository }}/issues/${{ needs.determine_issue_number.outputs.issue_number }}/labels --jq '.[].name')
+
+          # Check for good first/second/.. issue label
           LABEL=$(echo "$LABELS" | grep -E '^good (first|second|third|forth) issue$' || true)
-          if [ -n "$LABEL" ]; then
-            echo "✅ Found label: $LABEL"
+
+          # Check for component:* labels (can be multiple)
+          COMPONENT_LABELS=$(echo "$LABELS" | grep -E '^component:' || true)
+
+          if [ -n "$LABEL" ] || [ -n "$COMPONENT_LABELS" ]; then
             SILENT=false
-            # Apply label
-            gh issue edit "${{ github.event.pull_request.number }}" --add-label "$LABEL"
+            if [ -n "$LABEL" ]; then
+              echo "✅ Found label: $LABEL"
+              gh pr edit "${{ github.event.pull_request.number }}" --add-label "$LABEL"
+            fi
+            if [ -n "$COMPONENT_LABELS" ]; then
+              echo "✅ Found component labels:"
+              while IFS= read -r COMPONENT_LABEL; do
+                echo "   - $COMPONENT_LABEL"
+                gh pr edit "${{ github.event.pull_request.number }}" --add-label "$COMPONENT_LABEL"
+              done <<< "$COMPONENT_LABELS"
+            fi
           else
             echo "🚫 Silent fail if not possible to add assignee"
             SILENT=true
           fi
 
+
           # "gh issue edit" cannot be used - workaround found at https://github.com/cli/cli/issues/9620#issuecomment-2703135049
 
           ASSIGNEES=$(gh api /repos/JabRef/jabref/issues/${{ needs.determine_issue_number.outputs.issue_number }} --jq '[.assignees[].login]')

.github/workflows/tests-code.yml

@@ -57,6 +57,7 @@ jobs:
 
   dependencyscopes:
     name: Dependency Scopes
+    # too slow on ubuntu-slim
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
@@ -70,7 +71,8 @@ jobs:
 
   openrewrite:
     name: OpenRewrite
-    runs-on: ubuntu-slim
+    # too slow on ubuntu-slim
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout source
         uses: actions/checkout@v6
@@ -314,7 +316,8 @@ jobs:
           files: |
             jablib/src/main/java/org/jabref/logic/citationstyle/CSLStyleUtils.java
             jablib/src/test/java/org/jabref/logic/citationstyle/CSLStyleUtilsTest.java
-
+            jablib/src/main/java/org/jabref/logic/exporter/AcademicPagesExporter.java
+            jablib/src/test/java/org/jabref/logic/exporter/AcademicPagesExporterTest.java
       - uses: ./.github/actions/setup-gradle
         if: steps.changed-windows-related-files.outputs.any_changed == 'true'
       - name: Run jablib tests

CHANGELOG.md

@@ -9,10 +9,10 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ## [Unreleased]
 
-- We added `--key-patterns` option to CLI parameters to allows users to set a citation key's pattern for a specific entry type. [#14707](https://github.com/JabRef/jabref/issues/14707)
-
 ### Added
 
+- We added `--key-patterns` option to CLI parameters to allows users to set a citation key's pattern for a specific entry type. [#14707](https://github.com/JabRef/jabref/issues/14707)
+- We added a CLI option `--field-formatters` to the `convert` and `generate-bib-from-aux` commands to apply field formatters during export. [#11520](https://github.com/JabRef/jabref/issues/11520)
 - We added a preference to skip the import dialog for entries received from browser extensions, allowing direct import into the current library. The import dialog is shown by default; users can enable direct import in Preferences.
 - We added support for dragging entries from the "Citation relations" tab to other libraries. [#15135](https://github.com/JabRef/jabref/issues/15135)
 - We added a fetcher selection dropdown to the citation count field in the General tab, allowing users to choose between Semantic Scholar, OpenAlex, OpenCitations, and scite.ai as the source. The selected fetcher is now persisted across restarts and can also be configured in the Entry Editor preferences. [#15134](https://github.com/JabRef/jabref/issues/15134)
@@ -32,6 +32,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
     ⚠️ JabRef will recreate the index in a new folder for new files and this will take a long time for a huge library.
     Moreover, switching back and forth JabRef versions and meanwhile adding PDFs also requires rebuilding the index now and then.
     [#15220](https://github.com/JabRef/jabref/pull/15220)
+- We enabled drag and drop of Windows shortcut (`.lnk`) files to open libraries. [#15036](https://github.com/JabRef/jabref/issues/15036)
 - We refined the "Select files to import" page in "Search for unlinked local files" dialog to give the users the choice of linking the file to a related entry or import it to a new entry. [#13689](https://github.com/JabRef/jabref/issues/13689)
 
 ### Fixed

build-logic/src/main/kotlin/org.jabref.gradle.base.dependency-rules.gradle.kts

@@ -22,6 +22,7 @@ jvmDependencyConflicts {
     conflictResolution {
         select("org.gradlex:jna", "net.java.dev.jna:jna-jpms")
         select("org.gradlex:jna-platform", "net.java.dev.jna:jna-platform-jpms")
+        select("org.jabref:mslinks", "com.github.vatbub:mslinks")
     }
 }
 

gradle.properties

@@ -1,3 +1,6 @@
+# Activate this if you work on the build itself
+# org.gradle.logging.level=info
+
 org.gradle.vfs.watch=true
 
 # -Xmx6g
@@ -10,18 +13,17 @@ org.gradle.jvmargs=-Xmx6g -Dorg.kordamp.banner=false
 
 # hint by https://docs.gradle.org/current/userguide/performance.html#enable_configuration_cache
 org.gradle.configuration-cache=true
+
 org.gradle.configuration-cache.parallel=true
 
 # hint by https://docs.gradle.org/current/userguide/performance.html#enable_the_build_cache
 org.gradle.caching=true
 
-# Activate this if you work on the build itself
-# org.gradle.logging.level=info
-
-org.gradle.configureondemand=true
-
 # hint by https://docs.gradle.org/current/userguide/performance.html#sec:enable_parallel_execution
 org.gradle.parallel=true
 
+# Causes issues when .kts files change
+org.gradle.configureondemand=false
+
 # Tweak Java Toolchains
 org.gradle.java.installations.auto-download=true

gradle/modules.properties

@@ -8,7 +8,7 @@ info.picocli.codegen=info.picocli:picocli-codegen
 io.github.darvil.terminal.textformatter=io.github.darvil82:terminal-text-formatter
 io.github.eadr=io.github.adr:e-adr
 jul.to.slf4j=org.slf4j:jul-to-slf4j
-mslinks=com.github.vatbub:mslinks
+mslinks=org.jabref:mslinks
 org.apache.logging.log4j.to.slf4j=org.apache.logging.log4j:log4j-to-slf4j
 org.glassfish.jersey.container.grizzly2.http=org.glassfish.jersey.containers:jersey-container-grizzly2-http
 org.glassfish.jersey.core.common=org.glassfish.jersey.core:jersey-common

jabgui/src/main/java/org/jabref/gui/frame/FrameDndHandler.java

@@ -241,10 +241,14 @@ private List<Path> getBibFiles(Dragboard dragboard) {
         if (!dragboard.hasFiles()) {
             return List.of();
         } else {
-            return dragboard.getFiles().stream().map(File::toPath).filter(FileUtil::isBibFile).collect(Collectors.toList());
+            return dragboard.getFiles().stream().map(File::toPath).filter(this::isAcceptedFile).collect(Collectors.toList());
         }
     }
 
+    private boolean isAcceptedFile(Path path) {
+        return FileUtil.isBibFile(FileUtil.resolveIfShortcut(path));
+    }
+
     private boolean hasGroups(Dragboard dragboard) {
         return !getGroups(dragboard).isEmpty();
     }

jabgui/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java

@@ -8,6 +8,7 @@
 import java.util.Iterator;
 import java.util.List;
 import java.util.Optional;
+import java.util.stream.Collectors;
 
 import javax.swing.undo.UndoManager;
 
@@ -37,6 +38,7 @@
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.logic.util.io.FileHistory;
+import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.util.FileUpdateMonitor;
 
@@ -163,12 +165,19 @@ public void openFile(Path file) {
     ///
     /// @param filesToOpen the filesToOpen, may be null or not existing
     public void openFiles(List<Path> filesToOpen) {
+        // Resolve any shortcuts to their targets and filter to only .bib files.
+        // The resulting list must remain modifiable for downstream processing (iterator.remove() calls below).
+        List<Path> resolvedFiles = filesToOpen.stream()
+                                              .map(FileUtil::resolveIfShortcut)
+                                              .filter(FileUtil::isBibFile)
+                                              .collect(Collectors.toList());
+
         LibraryTab toRaise = null;
-        int initialCount = filesToOpen.size();
+        int initialCount = resolvedFiles.size();
         int removed = 0;
 
         // Check if any of the files are already open:
-        for (Iterator<Path> iterator = filesToOpen.iterator(); iterator.hasNext(); ) {
+        for (Iterator<Path> iterator = resolvedFiles.iterator(); iterator.hasNext(); ) {
             Path file = iterator.next();
             for (LibraryTab libraryTab : tabContainer.getLibraryTabs()) {
                 if ((libraryTab.getBibDatabaseContext().getDatabasePath().isPresent())
@@ -188,10 +197,10 @@ public void openFiles(List<Path> filesToOpen) {
 
         // Run the actual open in a thread to prevent the program
         // locking until the file is loaded.
-        if (!filesToOpen.isEmpty()) {
+        if (!resolvedFiles.isEmpty()) {
             assert fileUpdateMonitor != null;
             FileHistory fileHistory = preferences.getLastFilesOpenedPreferences().getFileHistory();
-            filesToOpen.forEach(theFile -> {
+            resolvedFiles.forEach(theFile -> {
                 // This method will execute the concrete file opening and loading in a background thread
                 openTheFile(theFile);
                 fileHistory.newFile(theFile);

jabgui/src/main/java/org/jabref/gui/maintable/MainTable.java

@@ -61,6 +61,7 @@
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.TaskExecutor;
+import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibEntryTypesManager;
@@ -537,7 +538,10 @@ private void handleOnDragDropped(TableRow<BibEntryTableViewModel> row, BibEntryT
         boolean success = false;
 
         if (event.getDragboard().hasFiles()) {
-            List<Path> files = event.getDragboard().getFiles().stream().map(File::toPath).collect(Collectors.toList());
+            List<Path> files = event.getDragboard().getFiles().stream()
+                                    .map(File::toPath)
+                                    .map(FileUtil::resolveIfShortcut)
+                                    .collect(Collectors.toList());
 
             // Depending on the pressed modifier, move/copy/link files to drop target
             // Modifiers do not work on macOS: https://bugs.openjdk.org/browse/JDK-8264172
@@ -568,7 +572,10 @@ private void handleOnDragDroppedTableView(DragEvent event) {
         boolean success = false;
 
         if (event.getDragboard().hasFiles()) {
-            List<Path> files = event.getDragboard().getFiles().stream().map(File::toPath).toList();
+            List<Path> files = event.getDragboard().getFiles().stream()
+                                    .map(File::toPath)
+                                    .map(FileUtil::resolveIfShortcut)
+                                    .toList();
             importHandler
                     .importFilesInBackground(files, event.getTransferMode())
                     .executeWith(taskExecutor);

jabkit/src/main/java/org/jabref/toolkit/commands/Convert.java

@@ -8,6 +8,7 @@
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 
+import org.jabref.logic.cleanup.FieldFormatterCleanupMapper;
 import org.jabref.logic.exporter.Exporter;
 import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.exporter.SaveException;
@@ -50,6 +51,9 @@ class Convert implements Runnable {
     @Option(names = {"--output-format"}, description = "Output format")
     private String outputFormat = "bibtex";
 
+    @Option(names = {"--field-formatters"}, description = "Field Formatter")
+    private String fieldFormatters;
+
     @Override
     public void run() {
         Optional<ParserResult> parserResult = JabKit.importFile(inputFile, inputFormat, jabKit.cliPreferences, sharedOptions.porcelain);
@@ -63,6 +67,8 @@ public void run() {
             return;
         }
 
+        FieldFormatterCleanupMapper.applyFormatters(fieldFormatters, parserResult.get().getDatabase().getEntries());
+
         if (!sharedOptions.porcelain) {
             System.out.println(Localization.lang("Converting '%0' to '%1'.", inputFile, outputFormat));
         }