Merge branch 'main' into vector-api

.github/workflows/deployment-arm64.yml

@@ -66,12 +66,12 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v2.0.0
+        uses: gittools/actions/gitversion/setup@v3.0.0
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v2.0.0
+        uses: gittools/actions/gitversion/execute@v3.0.0
       - 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@v2.0.0
+        uses: gittools/actions/gitversion/setup@v3.0.0
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v2.0.0
+        uses: gittools/actions/gitversion/execute@v3.0.0
 
       # 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@v2.0.0
+        uses: gittools/actions/gitversion/setup@v3.0.0
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v2.0.0
+        uses: gittools/actions/gitversion/execute@v3.0.0
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

CHANGELOG.md

@@ -12,6 +12,8 @@ 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. [#2146](https://github.com/JabRef/jabref/issues/2146), [#8893](https://github.com/JabRef/jabref/issues/8893)
+- We added Tools > New library based on references in PDF file... to create a new library based on the references section in a PDF file. [#11522](https://github.com/JabRef/jabref/pull/11522)
+- When converting the references section of a paper (PDF file), more than the last page is treated. [#11522](https://github.com/JabRef/jabref/pull/11522)
 - 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)
 

build.gradle

@@ -119,9 +119,9 @@ sourceSets {
 
 repositories {
     mavenCentral()
-    maven { url 'https://oss.sonatype.org/content/groups/public' }
     maven { url 'https://s01.oss.sonatype.org/content/repositories/snapshots/' }
     maven { url 'https://jitpack.io' }
+    maven { url 'https://oss.sonatype.org/content/groups/public' }
     maven { url 'https://sandec.jfrog.io/artifactory/repo' }
 }
 
@@ -169,7 +169,7 @@ dependencies {
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.15.0'
     implementation group: 'org.apache.commons', name: 'commons-text', version: '1.12.0'
     implementation 'commons-logging:commons-logging:1.3.3'
-    implementation 'com.h2database:h2-mvstore:2.2.224'
+    implementation 'com.h2database:h2-mvstore:2.3.230'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     implementation 'org.bouncycastle:bcprov-jdk18on:1.78.1'
@@ -221,7 +221,7 @@ dependencies {
     implementation 'org.kordamp.ikonli:ikonli-materialdesign2-pack:12.3.1'
     implementation 'com.github.sialcasa.mvvmFX:mvvmfx-validation:f195849ca9' //jitpack
     implementation 'de.saxsys:mvvmfx:1.8.0'
-    implementation('com.tobiasdiez:easybind:2.2.1-SNAPSHOT') {
+    implementation('org.jabref:easybind:2.2.1-SNAPSHOT') {
         exclude group: 'org.openjfx'
     }
     implementation 'org.fxmisc.flowless:flowless:0.7.3'
@@ -241,8 +241,8 @@ dependencies {
     implementation 'org.controlsfx:controlsfx:11.2.1'
 
     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 'com.konghq:unirest-java-core:4.4.4'
+    implementation 'com.konghq:unirest-modules-gson:4.4.4'
     implementation 'org.apache.httpcomponents.client5:httpclient5:5.3.1'
 
     implementation 'org.slf4j:slf4j-api:2.0.13'

rewrite.yml

@@ -169,7 +169,7 @@ recipeList:
 #  - org.openrewrite.staticanalysis.RemoveUnusedLocalVariables
 #  - org.openrewrite.staticanalysis.RemoveUnusedPrivateFields
 #  - org.openrewrite.staticanalysis.RenameLocalVariablesToCamelCase
-  - org.openrewrite.staticanalysis.RenameMethodsNamedHashcodeEqualOrTostring
+  - org.openrewrite.staticanalysis.RenameMethodsNamedHashcodeEqualOrToString
   - org.openrewrite.staticanalysis.ReplaceRedundantFormatWithPrintf
   - org.openrewrite.staticanalysis.ReplaceStringBuilderWithString
   - org.openrewrite.staticanalysis.ReplaceWeekYearWithYear

settings.gradle

@@ -5,7 +5,7 @@ pluginManagement {
             // Updated solution at https://github.com/foodiestudio/convention-plugins?tab=readme-ov-file#convention-plugins
             if (requested.id.id.startsWith("com.github.koppor")) {
                 // This is https://github.com/java9-modularity/gradle-modules-plugin/pull/282
-                useModule("com.github.koppor:gradle-modules-plugin:jitpack-SNAPSHOT")
+                useModule("com.github.koppor:gradle-modules-plugin:1.8.15-cmd-1")
             }
         }
     }

src/main/java/org/jabref/architecture/ApacheCommonsLang3Allowed.java → src/main/java/org/jabref/architecture/AllowedToUseApacheCommonsLang3.java

@@ -4,7 +4,7 @@
  * Annotation to indicate that usage of ApacheCommonsLang3 is explicitly allowed.
  * The intention is to fully switch to Google Guava and only use Apache Commons Lang3 if there is no other possibility
  */
-public @interface ApacheCommonsLang3Allowed {
+public @interface AllowedToUseApacheCommonsLang3 {
 
     // The rationale
     String value();

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

@@ -93,6 +93,8 @@ public enum StandardActions implements Action {
 
     PARSE_LATEX(Localization.lang("Search for citations in LaTeX files..."), IconTheme.JabRefIcons.LATEX_CITATIONS),
     NEW_SUB_LIBRARY_FROM_AUX(Localization.lang("New sublibrary based on AUX file") + "...", Localization.lang("New BibTeX sublibrary") + Localization.lang("This feature generates a new library based on which entries are needed in an existing LaTeX document."), IconTheme.JabRefIcons.NEW),
+    NEW_LIBRARY_FROM_PDF_ONLINE(Localization.lang("New library based on references in PDF file... (online)"), Localization.lang("This feature generates a new library based on the list of references in a PDF file. Thereby, it uses GROBID's functionality."), IconTheme.JabRefIcons.NEW),
+    NEW_LIBRARY_FROM_PDF_OFFLINE(Localization.lang("New library based on references in PDF file... (offline)"), Localization.lang("This feature generates a new library based on the list of references in a PDF file. Thereby, it uses JabRef's build-in functionality.."), IconTheme.JabRefIcons.NEW),
     WRITE_METADATA_TO_PDF(Localization.lang("Write metadata to PDF files"), Localization.lang("Will write metadata to the PDFs linked from selected entries."), KeyBinding.WRITE_METADATA_TO_PDF),
 
     START_NEW_STUDY(Localization.lang("Start new systematic literature review")),

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

@@ -44,6 +44,7 @@
 import org.jabref.gui.util.ViewModelListCellFactory;
 import org.jabref.gui.util.ViewModelTreeCellFactory;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.PreferencesService;
@@ -104,6 +105,7 @@ public UnlinkedFilesDialogView() {
             if (button == ButtonType.CANCEL) {
                 viewModel.cancelTasks();
             }
+            saveConfiguration();
             return null;
         });
 
@@ -236,7 +238,7 @@ private void loadSavedConfiguration() {
                                                                 .stream()
                                                                 .filter(item -> Objects.equals(item.getName(), unlinkedFilesDialogPreferences.getUnlinkedFilesSelectedExtension()))
                                                                 .findFirst()
-                                                                .orElseThrow();
+                                                                .orElseGet(() -> new FileExtensionViewModel(StandardFileType.ANY_FILE, preferencesService.getFilePreferences()));
         fileTypeCombo.getSelectionModel().select(selectedExtension);
         fileDateCombo.getSelectionModel().select(unlinkedFilesDialogPreferences.getUnlinkedFilesSelectedDateRange());
         fileSortCombo.getSelectionModel().select(unlinkedFilesDialogPreferences.getUnlinkedFilesSelectedSort());
@@ -256,7 +258,6 @@ void browseFileDirectory() {
     @FXML
     void scanFiles() {
         viewModel.startSearch();
-        saveConfiguration();
     }
 
     @FXML

src/main/java/org/jabref/gui/frame/MainMenu.java

@@ -51,6 +51,7 @@
 import org.jabref.gui.journals.AbbreviateAction;
 import org.jabref.gui.libraryproperties.LibraryPropertiesAction;
 import org.jabref.gui.linkedfile.RedownloadMissingFilesAction;
+import org.jabref.gui.maintable.NewLibraryFromPdfAction;
 import org.jabref.gui.mergeentries.MergeEntriesAction;
 import org.jabref.gui.preferences.ShowPreferencesAction;
 import org.jabref.gui.preview.CopyCitationAction;
@@ -80,6 +81,8 @@
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.PreferencesService;
 
+import com.tobiasdiez.easybind.EasyBind;
+
 public class MainMenu extends MenuBar {
     private final JabRefFrame frame;
     private final FileHistoryMenu fileHistoryMenu;
@@ -273,9 +276,17 @@ private void createMenu() {
         final MenuItem pushToApplicationMenuItem = factory.createMenuItem(pushToApplicationCommand.getAction(), pushToApplicationCommand);
         pushToApplicationCommand.registerReconfigurable(pushToApplicationMenuItem);
 
+        NewLibraryFromPdfAction newLibraryFromPdfAction = new NewLibraryFromPdfAction(frame, stateManager, dialogService, preferencesService, taskExecutor);
+        // Action used twice, because it distinguishes internally between online and offline
+        // We want the UI to show "online" and "offline" explicitly
+        MenuItem newLibraryFromPdfMenuItemOnline = factory.createMenuItem(StandardActions.NEW_LIBRARY_FROM_PDF_ONLINE, newLibraryFromPdfAction);
+        MenuItem newLibraryFromPdfMenuItemOffline = factory.createMenuItem(StandardActions.NEW_LIBRARY_FROM_PDF_OFFLINE, newLibraryFromPdfAction);
+
         tools.getItems().addAll(
                 factory.createMenuItem(StandardActions.PARSE_LATEX, new ParseLatexAction(stateManager)),
                 factory.createMenuItem(StandardActions.NEW_SUB_LIBRARY_FROM_AUX, new NewSubLibraryAction(frame, stateManager, dialogService)),
+                newLibraryFromPdfMenuItemOnline,
+                newLibraryFromPdfMenuItemOffline,
 
                 new SeparatorMenuItem(),
 
@@ -303,6 +314,9 @@ private void createMenu() {
 
                 factory.createMenuItem(StandardActions.REDOWNLOAD_MISSING_FILES, new RedownloadMissingFilesAction(stateManager, dialogService, preferencesService.getFilePreferences(), taskExecutor))
         );
+
+        EasyBind.subscribe(preferencesService.getGrobidPreferences().grobidEnabledProperty(), newLibraryFromPdfMenuItemOnline::setVisible);
+
         SidePaneType webSearchPane = SidePaneType.WEB_SEARCH;
         SidePaneType groupsPane = SidePaneType.GROUPS;
         SidePaneType openOfficePane = SidePaneType.OPEN_OFFICE;

src/main/java/org/jabref/gui/maintable/ExtractReferencesAction.java

@@ -15,7 +15,6 @@
 import org.jabref.gui.actions.SimpleCommand;
 import org.jabref.gui.importer.ImportEntriesDialog;
 import org.jabref.gui.util.BackgroundTask;
-import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.fileformat.BibliographyFromPdfImporter;
 import org.jabref.logic.importer.util.GrobidService;
@@ -33,30 +32,28 @@
 /**
  * SIDE EFFECT: Sets the "cites" field of the entry having the linked files
  *
- * Mode choice A: online or offline
- * Mode choice B: complete entry or single file (the latter is not implemented)
+ * <ul>
+ *   <li>Mode choice A: online or offline</li>
+ *   <li>Mode choice B: complete entry or single file (the latter is not implemented)</li>
+ * </ul>
  *
- * The different modes should be implemented as sub classes. However, this was too complicated, thus we use variables at the constructor to parameterize this class.
+ * The mode is selected by the preferences whether to use Grobid or not.
  */
 public class ExtractReferencesAction extends SimpleCommand {
     private final int FILES_LIMIT = 10;
 
-    private final boolean online;
     private final DialogService dialogService;
     private final StateManager stateManager;
     private final PreferencesService preferencesService;
     private final BibEntry entry;
     private final LinkedFile linkedFile;
-    private final TaskExecutor taskExecutor;
 
     private final BibliographyFromPdfImporter bibliographyFromPdfImporter;
 
-    public ExtractReferencesAction(boolean online,
-                                   DialogService dialogService,
+    public ExtractReferencesAction(DialogService dialogService,
                                    StateManager stateManager,
-                                   PreferencesService preferencesService,
-                                   TaskExecutor taskExecutor) {
-        this(online, dialogService, stateManager, preferencesService, null, null, taskExecutor);
+                                   PreferencesService preferencesService) {
+        this(dialogService, stateManager, preferencesService, null, null);
     }
 
     /**
@@ -65,20 +62,16 @@ public ExtractReferencesAction(boolean online,
      * @param entry the entry to handle (can be null)
      * @param linkedFile the linked file (can be null)
      */
-    private ExtractReferencesAction(boolean online,
-                                    @NonNull DialogService dialogService,
+    private ExtractReferencesAction(@NonNull DialogService dialogService,
                                     @NonNull StateManager stateManager,
                                     @NonNull PreferencesService preferencesService,
                                     @Nullable BibEntry entry,
-                                    @Nullable LinkedFile linkedFile,
-                                    @NonNull TaskExecutor taskExecutor) {
-        this.online = online;
+                                    @Nullable LinkedFile linkedFile) {
         this.dialogService = dialogService;
         this.stateManager = stateManager;
         this.preferencesService = preferencesService;
         this.entry = entry;
         this.linkedFile = linkedFile;
-        this.taskExecutor = taskExecutor;
         bibliographyFromPdfImporter = new BibliographyFromPdfImporter(preferencesService.getCitationKeyPatternPreferences());
 
         if (this.linkedFile == null) {
@@ -98,15 +91,14 @@ public void execute() {
 
     private void extractReferences() {
         stateManager.getActiveDatabase().ifPresent(databaseContext -> {
-            assert online == this.preferencesService.getGrobidPreferences().isGrobidEnabled();
-
             List<BibEntry> selectedEntries;
             if (entry == null) {
                 selectedEntries = stateManager.getSelectedEntries();
             } else {
                 selectedEntries = List.of(entry);
             }
 
+            boolean online = this.preferencesService.getGrobidPreferences().isGrobidEnabled();
             Callable<ParserResult> parserResultCallable;
             if (online) {
                 Optional<Callable<ParserResult>> parserResultCallableOnline = getParserResultCallableOnline(databaseContext, selectedEntries);
@@ -166,9 +158,21 @@ private void extractReferences(Iterator<Path> fileListIterator, ParserResult res
             result.getDatabase().insertEntries(bibliographyFromPdfImporter.importDatabase(fileListIterator.next()).getDatabase().getEntries());
         }
 
+        String cites = getCites(result.getDatabase().getEntries(), currentEntry);
+        currentEntry.setField(StandardField.CITES, cites);
+    }
+
+    /**
+     * Creates the field content for the "cites" field. The field contains the citation keys of the imported entries.
+     *
+     * TODO: Move this part to logic somehow
+     *
+     * @param currentEntry used to create citation keys if the importer did not provide one from the imported entry
+     */
+    private static String getCites(List<BibEntry> entries, BibEntry currentEntry) {
         StringJoiner cites = new StringJoiner(",");
         int count = 0;
-        for (BibEntry importedEntry : result.getDatabase().getEntries()) {
+        for (BibEntry importedEntry : entries) {
             count++;
             Optional<String> citationKey = importedEntry.getCitationKey();
             String citationKeyToAdd;
@@ -195,7 +199,7 @@ private void extractReferences(Iterator<Path> fileListIterator, ParserResult res
             }
             cites.add(citationKeyToAdd);
         }
-        currentEntry.setField(StandardField.CITES, cites.toString());
+        return cites.toString();
     }
 
     private Optional<Callable<ParserResult>> getParserResultCallableOnline(BibDatabaseContext databaseContext, List<BibEntry> selectedEntries) {