Merge remote-tracking branch 'upstream/main' into fix-rpm-uninstall

* upstream/main: [OO] Major performance improvements & fixes (#12221) move check for invalid characters to linked files editor (#12219) Update Gradle Wrapper from 8.11 to 8.11.1 (#12218)
JabRef · Nov 25, 2024 · 26d1968 · 26d1968
2 parents 7eac59b + de81430
commit 26d1968
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diff --git a/gradle/wrapper/gradle-wrapper.properties b/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

diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java b/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);
         });
     }

diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java
@@ -4,7 +4,6 @@
 import java.net.MalformedURLException;
 import java.net.URI;
 import java.net.URL;
-import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
@@ -32,15 +31,13 @@
 import org.jabref.gui.linkedfile.AttachFileFromURLAction;
 import org.jabref.gui.preferences.GuiPreferences;
 import org.jabref.gui.util.BindingsHelper;
-import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.logic.bibtex.FileFieldWriter;
 import org.jabref.logic.importer.FulltextFetchers;
 import org.jabref.logic.importer.util.FileFieldParser;
 import org.jabref.logic.integrity.FieldCheckers;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.BackgroundTask;
 import org.jabref.logic.util.TaskExecutor;
-import org.jabref.logic.util.io.FileNameCleaner;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -107,19 +104,6 @@ public static LinkedFile fromFile(Path file, List<Path> fileDirectories, Externa
         return new LinkedFile("", relativePath, suggestedFileType.getName());
     }
 
-    public LinkedFileViewModel fromFile(Path file, ExternalApplicationsPreferences externalApplicationsPreferences) {
-        List<Path> fileDirectories = databaseContext.getFileDirectories(preferences.getFilePreferences());
-
-        LinkedFile linkedFile = fromFile(file, fileDirectories, externalApplicationsPreferences);
-        return new LinkedFileViewModel(
-                linkedFile,
-                entry,
-                databaseContext,
-                taskExecutor,
-                dialogService,
-                preferences);
-    }
-
     private List<LinkedFileViewModel> parseToFileViewModel(String stringValue) {
         return FileFieldParser.parse(stringValue).stream()
                               .map(linkedFile -> new LinkedFileViewModel(
@@ -140,41 +124,6 @@ public ListProperty<LinkedFileViewModel> filesProperty() {
         return files;
     }
 
-    public void addNewFile() {
-        Path workingDirectory = databaseContext.getFirstExistingFileDir(preferences.getFilePreferences())
-                                               .orElse(preferences.getFilePreferences().getWorkingDirectory());
-
-        FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                .withInitialDirectory(workingDirectory)
-                .build();
-
-        List<Path> fileDirectories = databaseContext.getFileDirectories(preferences.getFilePreferences());
-        List<Path> selectedFiles = dialogService.showFileOpenDialogAndGetMultipleFiles(fileDialogConfiguration);
-
-        for (Path fileToAdd : selectedFiles) {
-            if (FileUtil.detectBadFileName(fileToAdd.toString())) {
-                String newFilename = FileNameCleaner.cleanFileName(fileToAdd.getFileName().toString());
-
-                boolean correctButtonPressed = dialogService.showConfirmationDialogAndWait(Localization.lang("File \"%0\" cannot be added!", fileToAdd.getFileName()),
-                        Localization.lang("Illegal characters in the file name detected.\nFile will be renamed to \"%0\" and added.", newFilename),
-                        Localization.lang("Rename and add"));
-
-                if (correctButtonPressed) {
-                    Path correctPath = fileToAdd.resolveSibling(newFilename);
-                    try {
-                        Files.move(fileToAdd, correctPath);
-                        addNewLinkedFile(correctPath, fileDirectories);
-                    } catch (IOException ex) {
-                        LOGGER.error("Error moving file", ex);
-                        dialogService.showErrorDialogAndWait(ex);
-                    }
-                }
-            } else {
-                addNewLinkedFile(fileToAdd, fileDirectories);
-            }
-        }
-    }
-
     public void addNewLinkedFile(LinkedFile linkedFile) {
         files.add(new LinkedFileViewModel(
                 linkedFile,
@@ -185,22 +134,17 @@ public void addNewLinkedFile(LinkedFile linkedFile) {
                 preferences));
     }
 
-    private void addNewLinkedFile(Path correctPath, List<Path> fileDirectories) {
-        LinkedFile newLinkedFile = fromFile(correctPath, fileDirectories, preferences.getExternalApplicationsPreferences());
-        addNewLinkedFile(newLinkedFile);
-    }
-
     @Override
     public void bindToEntry(BibEntry entry) {
         super.bindToEntry(entry);
 
-        if ((entry != null) && preferences.getEntryEditorPreferences().autoLinkFilesEnabled()) {
+        if (preferences.getEntryEditorPreferences().autoLinkFilesEnabled()) {
             LOGGER.debug("Auto-linking files for entry {}", entry);
             BackgroundTask<List<LinkedFileViewModel>> findAssociatedNotLinkedFiles = BackgroundTask
                     .wrap(() -> findAssociatedNotLinkedFiles(entry))
                     .onSuccess(list -> {
                         if (!list.isEmpty()) {
-                            LOGGER.debug("Found non-associated files:", list);
+                            LOGGER.debug("Found non-associated files: {}", list);
                             files.addAll(list);
                         }
                     });

diff --git a/src/main/java/org/jabref/gui/linkedfile/LinkedFileEditDialogViewModel.java b/src/main/java/org/jabref/gui/linkedfile/LinkedFileEditDialogViewModel.java
@@ -1,7 +1,9 @@
 package org.jabref.gui.linkedfile;
 
+import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URI;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.Optional;
 import java.util.regex.Pattern;
@@ -22,15 +24,22 @@
 import org.jabref.gui.frame.ExternalApplicationsPreferences;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.logic.FilePreferences;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.util.io.FileNameCleaner;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.LinkedFile;
 
+import com.google.common.annotations.VisibleForTesting;
 import com.tobiasdiez.easybind.EasyBind;
 import com.tobiasdiez.easybind.optional.ObservableOptionalValue;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class LinkedFileEditDialogViewModel extends AbstractViewModel {
 
+    private static final Logger LOGGER = LoggerFactory.getLogger(LinkedFileEditDialogViewModel.class);
+
     private static final Pattern REMOTE_LINK_PATTERN = Pattern.compile("[a-z]+://.*");
     private final StringProperty link = new SimpleStringProperty("");
     private final StringProperty description = new SimpleStringProperty("");
@@ -86,13 +95,31 @@ public void openBrowseDialog() {
                 .withInitialFileName(fileName)
                 .build();
 
-        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(path -> {
-            // Store the directory for next time:
-            filePreferences.setWorkingDirectory(path);
-            link.set(relativize(path));
+        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(this::checkForBadFileNameAndAdd);
+    }
 
-            setExternalFileTypeByExtension(link.getValueSafe());
-        });
+    @VisibleForTesting
+    void checkForBadFileNameAndAdd(Path fileToAdd) {
+        if (FileUtil.detectBadFileName(fileToAdd.toString())) {
+            String newFilename = FileNameCleaner.cleanFileName(fileToAdd.getFileName().toString());
+
+            boolean correctButtonPressed = dialogService.showConfirmationDialogAndWait(Localization.lang("File \"%0\" cannot be added!", fileToAdd.getFileName()),
+                    Localization.lang("Illegal characters in the file name detected.\nFile will be renamed to \"%0\" and added.", newFilename),
+                    Localization.lang("Rename and add"));
+
+            if (correctButtonPressed) {
+                Path correctPath = fileToAdd.resolveSibling(newFilename);
+                try {
+                    Files.move(fileToAdd, correctPath);
+                    link.set(relativize(correctPath));
+                    filePreferences.setWorkingDirectory(correctPath);
+                    setExternalFileTypeByExtension(link.getValueSafe());
+                } catch (IOException ex) {
+                    LOGGER.error("Error moving file", ex);
+                    dialogService.showErrorDialogAndWait(ex);
+                }
+            }
+        }
     }
 
     public void setValues(LinkedFile linkedFile) {

diff --git a/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLCitationOOAdapter.java b/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLCitationOOAdapter.java
@@ -69,7 +69,6 @@ public void insertCitation(XTextCursor cursor, CitationStyle selectedStyle, List
 
         OOText ooText = OOFormat.setLocaleNone(OOText.fromString(formattedCitation));
         insertReferences(cursor, entries, ooText, selectedStyle.isNumericStyle());
-        cursor.collapseToEnd();
     }
 
     /**
@@ -119,7 +118,6 @@ public void insertInTextCitation(XTextCursor cursor, CitationStyle selectedStyle
             }
             OOText ooText = OOFormat.setLocaleNone(OOText.fromString(finalText));
             insertReferences(cursor, List.of(currentEntry), ooText, selectedStyle.isNumericStyle());
-            cursor.collapseToEnd();
         }
     }
 
@@ -131,9 +129,6 @@ public void insertEmpty(XTextCursor cursor, CitationStyle selectedStyle, List<Bi
             throws CreationException, Exception {
         OOText emptyOOText = OOFormat.setLocaleNone(OOText.fromString(""));
         insertReferences(cursor, entries, emptyOOText, selectedStyle.isNumericStyle());
-
-        // Move the cursor to the end of the inserted text - although no need as we don't insert any text, but a good practice
-        cursor.collapseToEnd();
     }
 
     /**
@@ -165,11 +160,6 @@ public void insertBibliography(XTextCursor cursor, CitationStyle selectedStyle,
                 OOText ooText = OOFormat.setLocaleNone(OOText.fromString(formattedCitation));
 
                 OOTextIntoOO.write(document, cursor, ooText);
-                    // Select the paragraph break
-                    cursor.goLeft((short) 1, true);
-
-                    // Delete the selected content (paragraph break)
-                    cursor.setString("");
             }
         } else {
             // Ordering will be according to citeproc item data provider (default)
@@ -180,7 +170,6 @@ public void insertBibliography(XTextCursor cursor, CitationStyle selectedStyle,
                 OOText ooText = OOFormat.setLocaleNone(OOText.fromString(formattedCitation));
                 OOTextIntoOO.write(document, cursor, ooText);
             }
-            cursor.collapseToEnd();
         }
     }
 
@@ -208,12 +197,8 @@ private void insertReferences(XTextCursor cursor, List<BibEntry> entries, OOText
         CSLReferenceMark mark = markManager.createReferenceMark(entries);
         mark.insertReferenceIntoOO(document, cursor, ooText, !preceedingSpaceExists, false);
 
-        // Move the cursor to the end of the inserted text
-        cursor.collapseToEnd();
-
         markManager.setUpdateRequired(isNumericStyle);
         readAndUpdateExistingMarks();
-        cursor.collapseToEnd();
     }
 
     /**

diff --git a/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLFormatUtils.java b/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLFormatUtils.java
@@ -72,6 +72,15 @@ public static String transformHTML(String html) {
         // Clean up any remaining span tags
         html = html.replaceAll("</?span[^>]*>", "");
 
+        // Convert line breaks to paragraph breaks
+        html = html.replaceAll("[\n\r]+", "<p></p>");
+
+        // Remove leading paragraph tags (preserving any whitespaces after them for indentation)
+        html = html.replaceAll("^\\s*<p>\\s*</p>", "");
+
+        // Remove extra trailing paragraph tags when there are multiple (keeping one)
+        html = html.replaceAll("(?:<p>\\s*</p>\\s*){2,}$", "<p></p>");
+
         return html;
     }
 
@@ -113,9 +122,9 @@ public static String generateAlphanumericCitation(List<BibEntry> entries, BibDat
 
     /**
      * Method to update citation number of a bibliographic entry (to be inserted in the list of references).
-     * By default, citeproc-java ({@link org.jabref.logic.citationstyle.CitationStyleGenerator#generateBibliography(List, String, CitationStyleOutputFormat, BibDatabaseContext, BibEntryTypesManager) generateBibliography} always start the numbering of a list of citations with "1".
-     * If a citation doesn't correspond to the first cited entry, the number should be changed to the relevant current citation number.
-     * If an entries has been cited before, the colder number should be reused.
+     * By default, citeproc-java ({@link org.jabref.logic.citationstyle.CitationStyleGenerator#generateBibliography(List, String, CitationStyleOutputFormat, BibDatabaseContext, BibEntryTypesManager) generateBibliography} always starts the numbering of a list of citations with "1".
+     * If a citation doesn't correspond to the first cited entry, the number should be changed to the appropriate current citation number.
+     * The numbers should be globally unique. If an entry has been cited before, the older citation number corresponding to it should be reused.
      * The number can be enclosed in different formats, such as "1", "1.", "1)", "(1)" or "[1]".
      * <p>
      * <b>Precondition:</b> Use ONLY with numeric citation styles.</p>

diff --git a/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLUpdateBibliography.java b/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLUpdateBibliography.java
@@ -101,9 +101,7 @@ private void populateCSLBibTextSection(XTextDocument doc,
 
         // Use CSLCitationOOAdapter to insert the bibliography
         cslAdapter.insertBibliography(cursor, citationStyle, entries, bibDatabaseContext, bibEntryTypesManager);
-        LOGGER.debug("Bibliography inserted using CSLCitationOOAdapter");
 
-        cursor.collapseToEnd();
         LOGGER.debug("CSL bibliography section population completed");
     }
 }
diff --git a/src/main/java/org/jabref/logic/util/io/FileUtil.java b/src/main/java/org/jabref/logic/util/io/FileUtil.java
@@ -576,13 +576,10 @@ public static String shortenFileName(String fileName, Integer maxLength) {
         numCharsBeforeEllipsis = Math.min(numCharsBeforeEllipsis, name.length());
         numCharsAfterEllipsis = Math.min(numCharsAfterEllipsis, name.length() - numCharsBeforeEllipsis);
 
-        StringBuilder result = new StringBuilder();
-        result.append(name, 0, numCharsBeforeEllipsis)
-              .append(ELLIPSIS)
-              .append(name.substring(name.length() - numCharsAfterEllipsis))
-              .append(extension);
-
-        return result.toString();
+        return name.substring(0, numCharsBeforeEllipsis) +
+               ELLIPSIS +
+               name.substring(name.length() - numCharsAfterEllipsis) +
+               extension;
     }
 
     public static boolean isCharLegal(char c) {

diff --git a/src/test/java/org/jabref/gui/linkedfile/LinkedFileEditDialogViewModelTest.java b/src/test/java/org/jabref/gui/linkedfile/LinkedFileEditDialogViewModelTest.java
@@ -0,0 +1,55 @@
+package org.jabref.gui.linkedfile;
+
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.TreeSet;
+
+import javafx.collections.FXCollections;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.externalfiletype.ExternalFileTypes;
+import org.jabref.gui.frame.ExternalApplicationsPreferences;
+import org.jabref.gui.preferences.GuiPreferences;
+import org.jabref.logic.FilePreferences;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.LinkedFile;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+import org.mockito.Answers;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+class LinkedFileEditDialogViewModelTest {
+    private final GuiPreferences preferences = mock(GuiPreferences.class, Answers.RETURNS_DEEP_STUBS);
+    private final FilePreferences filePreferences = mock(FilePreferences.class, Answers.RETURNS_DEEP_STUBS);
+    private final BibDatabaseContext bibDatabaseContext = mock(BibDatabaseContext.class);
+    private final DialogService dialogService = mock(DialogService.class);
+    private final ExternalApplicationsPreferences externalApplicationsPreferences = mock(ExternalApplicationsPreferences.class);
+
+    @BeforeEach
+    void setup() {
+        when(externalApplicationsPreferences.getExternalFileTypes()).thenReturn(FXCollections.observableSet(new TreeSet<>(ExternalFileTypes.getDefaultExternalFileTypes())));
+        when(preferences.getExternalApplicationsPreferences()).thenReturn(externalApplicationsPreferences);
+        when(preferences.getFilePreferences()).thenReturn(filePreferences);
+    }
+
+    @Test
+    void badFilenameCharWillBeReplacedByUnderscore(@TempDir Path tempDir) throws Exception {
+
+        Path invalidFile = tempDir.resolve("?invalid.pdf");
+        Files.createFile(invalidFile);
+        when(dialogService.showConfirmationDialogAndWait(any(), any(), any())).thenReturn(true);
+
+        LinkedFileEditDialogViewModel viewModel = new LinkedFileEditDialogViewModel(new LinkedFile("", "", ""), bibDatabaseContext, dialogService, externalApplicationsPreferences, filePreferences);
+
+        viewModel.checkForBadFileNameAndAdd(invalidFile);
+
+        LinkedFile expectedFile = new LinkedFile("", tempDir.resolve("_invalid.pdf").toString(), "PDF");
+        assertEquals(expectedFile, viewModel.getNewLinkedFile());
+    }
+}