Add cites field to bib entries for citation relation

CHANGELOG.md

@@ -11,9 +11,12 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- When importing entries form the "Citation relations" tab, the field [cites](https://docs.jabref.org/advanced/entryeditor/entrylinks) is now filled according to the relationship between the entries. [#10572](https://github.com/JabRef/jabref/pull/10752)
+
 ### Changed
 
 - The Custom export format now uses the custom DOI base URI in the preferences for the `DOICheck`, if activated [forum#4084](https://discourse.jabref.org/t/export-html-disregards-custom-doi-base-uri/4084)
+- We changed the order of the lists in the "Citation relations" tab. `Cites` are now on the left and `Cited by` on the right [#10572](https://github.com/JabRef/jabref/pull/10752)
 
 ### Fixed
 

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

@@ -285,7 +285,7 @@ private List<EntryEditorTab> createTabs() {
         entryEditorTabs.add(new FileAnnotationTab(libraryTab.getAnnotationCache()));
         entryEditorTabs.add(new RelatedArticlesTab(entryEditorPreferences, preferencesService, dialogService, taskExecutor));
         entryEditorTabs.add(new CitationRelationsTab(entryEditorPreferences, dialogService, databaseContext,
-                undoManager, stateManager, fileMonitor, preferencesService, libraryTab));
+                undoManager, stateManager, fileMonitor, preferencesService, libraryTab, taskExecutor));
 
         sourceTab = new SourceTab(
                 databaseContext,

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationItem.java

@@ -5,20 +5,7 @@
 /**
  * Class to hold a BibEntry and a boolean value whether it is already in the current database or not.
  */
-public class CitationRelationItem {
-    private final BibEntry entry;
-    private final boolean isLocal;
-
-    public CitationRelationItem(BibEntry entry, boolean isLocal) {
-        this.entry = entry;
-        this.isLocal = isLocal;
-    }
-
-    public BibEntry getEntry() {
-        return entry;
-    }
-
-    public boolean isLocal() {
-        return isLocal;
-    }
+public record CitationRelationItem(
+        BibEntry entry,
+        boolean isLocal) {
 }

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java

@@ -32,10 +32,10 @@
 import org.jabref.gui.entryeditor.EntryEditorTab;
 import org.jabref.gui.entryeditor.citationrelationtab.semanticscholar.CitationFetcher;
 import org.jabref.gui.entryeditor.citationrelationtab.semanticscholar.SemanticScholarFetcher;
-import org.jabref.gui.externalfiles.ImportHandler;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.NoSelectionModel;
+import org.jabref.gui.util.TaskExecutor;
 import org.jabref.gui.util.ViewModelListCellFactory;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
@@ -66,12 +66,14 @@ public class CitationRelationsTab extends EntryEditorTab {
     private final FileUpdateMonitor fileUpdateMonitor;
     private final PreferencesService preferencesService;
     private final LibraryTab libraryTab;
+    private final TaskExecutor taskExecutor;
     private final BibEntryRelationsRepository bibEntryRelationsRepository;
+    private final CitationsRelationsTabViewModel citationsRelationsTabViewModel;
 
     public CitationRelationsTab(EntryEditorPreferences preferences, DialogService dialogService,
                                 BibDatabaseContext databaseContext, UndoManager undoManager,
                                 StateManager stateManager, FileUpdateMonitor fileUpdateMonitor,
-                                PreferencesService preferencesService, LibraryTab lTab) {
+                                PreferencesService preferencesService, LibraryTab lTab, TaskExecutor taskExecutor) {
         this.preferences = preferences;
         this.dialogService = dialogService;
         this.databaseContext = databaseContext;
@@ -80,11 +82,13 @@ public CitationRelationsTab(EntryEditorPreferences preferences, DialogService di
         this.fileUpdateMonitor = fileUpdateMonitor;
         this.preferencesService = preferencesService;
         this.libraryTab = lTab;
+        this.taskExecutor = taskExecutor;
         setText(Localization.lang("Citation relations"));
         setTooltip(new Tooltip(Localization.lang("Show articles related by citation")));
 
         this.bibEntryRelationsRepository = new BibEntryRelationsRepository(new SemanticScholarFetcher(preferencesService.getImporterPreferences()),
                 new BibEntryRelationsCache());
+        citationsRelationsTabViewModel = new CitationsRelationsTabViewModel(databaseContext, preferencesService, undoManager, stateManager, dialogService, fileUpdateMonitor, Globals.TASK_EXECUTOR);
     }
 
     /**
@@ -107,7 +111,7 @@ private SplitPane getPaneAndStartSearch(BibEntry entry) {
         citedByHBox.setPrefHeight(40);
 
         // Create Heading Lab
-        Label citingLabel = new Label(Localization.lang("Citing"));
+        Label citingLabel = new Label(Localization.lang("Cites"));
         styleLabel(citingLabel);
         Label citedByLabel = new Label(Localization.lang("Cited By"));
         styleLabel(citedByLabel);
@@ -160,20 +164,19 @@ private SplitPane getPaneAndStartSearch(BibEntry entry) {
 
         refreshCitingButton.setOnMouseClicked(event -> {
             searchForRelations(entry, citingListView, abortCitingButton,
-                    refreshCitingButton, CitationFetcher.SearchType.CITING, importCitingButton, citingProgress, true);
+                    refreshCitingButton, CitationFetcher.SearchType.CITES, importCitingButton, citingProgress, true);
         });
 
         refreshCitedByButton.setOnMouseClicked(event -> searchForRelations(entry, citedByListView, abortCitedButton,
                 refreshCitedByButton, CitationFetcher.SearchType.CITED_BY, importCitedByButton, citedByProgress, true));
 
         // Create SplitPane to hold all nodes above
-        SplitPane container = new SplitPane(citedByVBox, citingVBox);
-
-        styleFetchedListView(citingListView);
+        SplitPane container = new SplitPane(citingVBox, citedByVBox);
         styleFetchedListView(citedByListView);
+        styleFetchedListView(citingListView);
 
         searchForRelations(entry, citingListView, abortCitingButton, refreshCitingButton,
-                CitationFetcher.SearchType.CITING, importCitingButton, citingProgress, false);
+                CitationFetcher.SearchType.CITES, importCitingButton, citingProgress, false);
 
         searchForRelations(entry, citedByListView, abortCitedButton, refreshCitedByButton,
                 CitationFetcher.SearchType.CITED_BY, importCitedByButton, citedByProgress, false);
@@ -193,7 +196,7 @@ private void styleFetchedListView(CheckListView<CitationRelationItem> listView)
 
                     HBox separator = new HBox();
                     HBox.setHgrow(separator, Priority.SOMETIMES);
-                    Node entryNode = BibEntryView.getEntryNode(entry.getEntry());
+                    Node entryNode = BibEntryView.getEntryNode(entry.entry());
                     HBox.setHgrow(entryNode, Priority.ALWAYS);
                     HBox hContainer = new HBox();
                     hContainer.prefWidthProperty().bind(listView.widthProperty().subtract(25));
@@ -203,8 +206,8 @@ private void styleFetchedListView(CheckListView<CitationRelationItem> listView)
                         jumpTo.setTooltip(new Tooltip(Localization.lang("Jump to entry in database")));
                         jumpTo.getStyleClass().add("addEntryButton");
                         jumpTo.setOnMouseClicked(event -> {
-                            libraryTab.showAndEdit(entry.getEntry());
-                            libraryTab.clearAndSelect(entry.getEntry());
+                            libraryTab.showAndEdit(entry.entry());
+                            libraryTab.clearAndSelect(entry.entry());
                             citingTask.cancel();
                             citedByTask.cancel();
                         });
@@ -285,7 +288,7 @@ protected void bindToEntry(BibEntry entry) {
      *
      * @param entry         BibEntry currently selected in Jabref Database
      * @param listView      ListView to use
-     * @param abortButton         Button to stop the search
+     * @param abortButton   Button to stop the search
      * @param refreshButton refresh Button to use
      * @param searchType    type of search (CITING / CITEDBY)
      */
@@ -305,15 +308,15 @@ private void searchForRelations(BibEntry entry, CheckListView<CitationRelationIt
 
         listView.setItems(observableList);
 
-        if (citingTask != null && !citingTask.isCanceled() && searchType == CitationFetcher.SearchType.CITING) {
+        if (citingTask != null && !citingTask.isCanceled() && searchType == CitationFetcher.SearchType.CITES) {
             citingTask.cancel();
         } else if (citedByTask != null && !citedByTask.isCanceled() && searchType == CitationFetcher.SearchType.CITED_BY) {
             citedByTask.cancel();
         }
 
         BackgroundTask<List<BibEntry>> task;
 
-        if (searchType == CitationFetcher.SearchType.CITING) {
+        if (searchType == CitationFetcher.SearchType.CITES) {
             task = BackgroundTask.wrap(() -> {
                 if (shouldRefresh) {
                     bibEntryRelationsRepository.forceRefreshReferences(entry);
@@ -332,18 +335,18 @@ private void searchForRelations(BibEntry entry, CheckListView<CitationRelationIt
         }
 
         task.onRunning(() -> prepareToSearchForRelations(abortButton, refreshButton, importButton, progress, task))
-                .onSuccess(fetchedList -> onSearchForRelationsSucceed(entry, listView, abortButton, refreshButton,
-                        searchType, importButton, progress, fetchedList, observableList))
-                .onFailure(exception -> {
-                    LOGGER.error("Error while fetching citing Articles", exception);
-                    hideNodes(abortButton, progress, importButton);
-                    listView.setPlaceholder(new Label(Localization.lang("Error while fetching citing entries: %0",
-                            exception.getMessage())));
-
-                    refreshButton.setVisible(true);
-                    dialogService.notify(exception.getMessage());
-                })
-                .executeWith(Globals.TASK_EXECUTOR);
+            .onSuccess(fetchedList -> onSearchForRelationsSucceed(entry, listView, abortButton, refreshButton,
+                    searchType, importButton, progress, fetchedList, observableList))
+            .onFailure(exception -> {
+                LOGGER.error("Error while fetching citing Articles", exception);
+                hideNodes(abortButton, progress, importButton);
+                listView.setPlaceholder(new Label(Localization.lang("Error while fetching citing entries: %0",
+                        exception.getMessage())));
+
+                refreshButton.setVisible(true);
+                dialogService.notify(exception.getMessage());
+            })
+            .executeWith(taskExecutor);
     }
 
     private void onSearchForRelationsSucceed(BibEntry entry, CheckListView<CitationRelationItem> listView,
@@ -354,7 +357,7 @@ private void onSearchForRelationsSucceed(BibEntry entry, CheckListView<CitationR
         hideNodes(abortButton, progress);
 
         observableList.setAll(fetchedList.stream().map(entr -> new CitationRelationItem(entr, false))
-                .collect(Collectors.toList()));
+                                         .collect(Collectors.toList()));
 
         if (!observableList.isEmpty()) {
             listView.refresh();
@@ -396,19 +399,11 @@ private void showNodes(Node... nodes) {
      *
      * @param entriesToImport entries to import
      */
-    private void importEntries(List<CitationRelationItem> entriesToImport, CitationFetcher.SearchType searchType, BibEntry entry) {
+    private void importEntries(List<CitationRelationItem> entriesToImport, CitationFetcher.SearchType searchType, BibEntry existingEntry) {
         citingTask.cancel();
         citedByTask.cancel();
-        List<BibEntry> entries = entriesToImport.stream().map(CitationRelationItem::getEntry).collect(Collectors.toList());
-        ImportHandler importHandler = new ImportHandler(
-                databaseContext,
-                preferencesService,
-                fileUpdateMonitor,
-                undoManager,
-                stateManager,
-                dialogService,
-                Globals.TASK_EXECUTOR);
-        importHandler.importEntries(entries);
+
+        citationsRelationsTabViewModel.importEntries(entriesToImport, searchType, existingEntry);
 
         dialogService.notify(Localization.lang("Number of entries successfully imported") + ": " + entriesToImport.size());
     }

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationsRelationsTabViewModel.java

@@ -0,0 +1,115 @@
+package org.jabref.gui.entryeditor.citationrelationtab;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import javax.swing.undo.UndoManager;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.StateManager;
+import org.jabref.gui.entryeditor.citationrelationtab.semanticscholar.CitationFetcher;
+import org.jabref.gui.externalfiles.ImportHandler;
+import org.jabref.gui.util.TaskExecutor;
+import org.jabref.logic.citationkeypattern.CitationKeyGenerator;
+import org.jabref.logic.citationkeypattern.CitationKeyPatternPreferences;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.field.StandardField;
+import org.jabref.model.util.FileUpdateMonitor;
+import org.jabref.preferences.PreferencesService;
+
+public class CitationsRelationsTabViewModel {
+
+    private final BibDatabaseContext databaseContext;
+    private final PreferencesService preferencesService;
+    private final UndoManager undoManager;
+    private final StateManager stateManager;
+    private final DialogService dialogService;
+    private final FileUpdateMonitor fileUpdateMonitor;
+    private final TaskExecutor taskExecutor;
+
+    public CitationsRelationsTabViewModel(BibDatabaseContext databaseContext, PreferencesService preferencesService, UndoManager undoManager, StateManager stateManager, DialogService dialogService, FileUpdateMonitor fileUpdateMonitor, TaskExecutor taskExecutor) {
+        this.databaseContext = databaseContext;
+        this.preferencesService = preferencesService;
+        this.undoManager = undoManager;
+        this.stateManager = stateManager;
+        this.dialogService = dialogService;
+        this.fileUpdateMonitor = fileUpdateMonitor;
+        this.taskExecutor = taskExecutor;
+    }
+
+    public void importEntries(List<CitationRelationItem> entriesToImport, CitationFetcher.SearchType searchType, BibEntry existingEntry) {
+        List<BibEntry> entries = entriesToImport.stream().map(CitationRelationItem::entry).toList();
+
+        ImportHandler importHandler = new ImportHandler(
+                databaseContext,
+                preferencesService,
+                fileUpdateMonitor,
+                undoManager,
+                stateManager,
+                dialogService,
+                taskExecutor);
+
+        switch (searchType) {
+            case CITES -> importCites(entries, existingEntry, importHandler);
+            case CITED_BY -> importCitedBy(entries, existingEntry, importHandler);
+        }
+    }
+
+    private void importCites(List<BibEntry> entries, BibEntry existingEntry, ImportHandler importHandler) {
+        CitationKeyPatternPreferences citationKeyPatternPreferences = preferencesService.getCitationKeyPatternPreferences();
+        CitationKeyGenerator generator = new CitationKeyGenerator(databaseContext, citationKeyPatternPreferences);
+        boolean generateNewKeyOnImport = preferencesService.getImporterPreferences().generateNewKeyOnImportProperty().get();
+
+        List<String> citeKeys = getExistingEntriesFromCiteField(existingEntry);
+        citeKeys.removeIf(String::isEmpty);
+        for (BibEntry entryToCite : entries) {
+            if (generateNewKeyOnImport || entryToCite.getCitationKey().isEmpty()) {
+                String key = generator.generateKey(entryToCite);
+                entryToCite.setCitationKey(key);
+                addToKeyToList(citeKeys, key);
+            } else {
+                addToKeyToList(citeKeys, entryToCite.getCitationKey().get());
+            }
+        }
+        existingEntry.setField(StandardField.CITES, toCommaSeparatedString(citeKeys));
+        importHandler.importEntries(entries);
+    }
+
+    private void importCitedBy(List<BibEntry> entries, BibEntry existingEntry, ImportHandler importHandler) {
+        CitationKeyPatternPreferences citationKeyPatternPreferences = preferencesService.getCitationKeyPatternPreferences();
+        CitationKeyGenerator generator = new CitationKeyGenerator(databaseContext, citationKeyPatternPreferences);
+        boolean generateNewKeyOnImport = preferencesService.getImporterPreferences().generateNewKeyOnImportProperty().get();
+
+        for (BibEntry entryThatCitesOurExistingEntry : entries) {
+            List<String> existingCites = getExistingEntriesFromCiteField(entryThatCitesOurExistingEntry);
+            existingCites.removeIf(String::isEmpty);
+            String key;
+            if (generateNewKeyOnImport || entryThatCitesOurExistingEntry.getCitationKey().isEmpty()) {
+                key = generator.generateKey(entryThatCitesOurExistingEntry);
+                entryThatCitesOurExistingEntry.setCitationKey(key);
+            } else {
+                key = existingEntry.getCitationKey().get();
+            }
+            addToKeyToList(existingCites, key);
+            entryThatCitesOurExistingEntry.setField(StandardField.CITES, toCommaSeparatedString(existingCites));
+        }
+
+        importHandler.importEntries(entries);
+    }
+
+    private void addToKeyToList(List<String> list, String key) {
+        if (!list.contains(key)) {
+            list.add(key);
+        }
+    }
+
+    private List<String> getExistingEntriesFromCiteField(BibEntry entry) {
+        return Arrays.stream(entry.getField(StandardField.CITES).orElse("").split(",")).collect(Collectors.toList());
+    }
+
+    private String toCommaSeparatedString(List<String> citeentries) {
+        return String.join(",", citeentries);
+    }
+}

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

@@ -1,5 +1,8 @@
 package org.jabref.gui.entryeditor.citationrelationtab.semanticscholar;
 
+/**
+ * Used for GSON
+ */
 public class AuthorResponse {
     private String authorId;
     private String name;

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

@@ -1,5 +1,8 @@
 package org.jabref.gui.entryeditor.citationrelationtab.semanticscholar;
 
+/**
+ * Used for GSON
+ */
 public class CitationDataItem {
     private PaperDetails citingPaper;
 

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

@@ -14,7 +14,7 @@ public interface CitationFetcher {
      * Possible search methods
      */
     enum SearchType {
-        CITING("reference"),
+        CITES("reference"),
         CITED_BY("citation");
 
         public final String label;

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

@@ -2,6 +2,9 @@
 
 import java.util.List;
 
+/**
+ * Used for GSON
+ */
 public class CitationsResponse {
     private int offset;
     private int next;