Merge remote-tracking branch 'upstream/master'

* upstream/master:
  Added a download checkbox to the import dialog (#6381)
  Bump jaxb-xjc from 2.3.2 to 2.3.3 (#6410)
  Bump flexmark-ext-gfm-strikethrough from 0.61.20 to 0.61.24 (#6413)
  Bump byte-buddy-parent from 1.10.9 to 1.10.10 (#6408)
  Bump flexmark-ext-gfm-tasklist from 0.61.20 to 0.61.24 (#6412)
  Bump org.beryx.jlink from 2.17.8 to 2.18.0 (#6411)
  Bump tika-core from 1.24 to 1.24.1 (#6409)
  Bump flexmark from 0.61.20 to 0.61.24 (#6416)
  Bump classgraph from 4.8.77 to 4.8.78 (#6414)
  Restore some missing keyboard shortcuts (#6406)
  Fix StartupWMClass (#6398)

Author: Siedlerchr

CHANGELOG.md

@@ -17,6 +17,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added support for basic markdown in custom formatted previews [#6194](https://github.com/JabRef/jabref/issues/6194)
 - We now show the number of items found and selected to import in the online search dialog. [#6248](https://github.com/JabRef/jabref/pull/6248)
 - We created a new install screen for macOS. [#5759](https://github.com/JabRef/jabref/issues/5759)
+- We implemented an option to download fulltext files while importing. [#6381](https://github.com/JabRef/jabref/pull/6381)
 
 ### Changed
 
@@ -26,6 +27,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We changed the buttons for import/export/show all/reset of preferences to smaller icon buttons in the preferences dialog. [#6130](https://github.com/JabRef/jabref/pull/6130)
 - We moved the functionality "Manage field names & content" from the "Library" menu to the "Edit" menu, because it affects the selected entries and not the whole library
 - We merged the functionality "Append contents from a BibTeX library into the currently viewed library" into the "Import into database" functionality. Fixes [#6049](https://github.com/JabRef/jabref/issues/6049).
+- We changed the directory where fulltext downloads are stored to the directory set in the import-tab in preferences. [#6381](https://github.com/JabRef/jabref/pull/6381)
 - We improved the error message for invalid jstyles. [#6303](https://github.com/JabRef/jabref/issues/6303)
 
 ### Fixed
@@ -102,7 +104,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where adding the addition of a new entry was not completely validated [#6370](https://github.com/JabRef/jabref/issues/6370)
 - We fixed an issue where the blue and red text colors in the Merge entries dialog were not quite visible [#6334](https://github.com/JabRef/jabref/issues/6334)
 - We fixed an issue where underscore character was removed from the file name in the Recent Libraries list in File menu [#6383](https://github.com/JabRef/jabref/issues/6383)
-
+- We fixed an issue where few keyboard shortcuts regarding new entries were missing [#6403](https://github.com/JabRef/jabref/issues/6403)
 ### Removed
 
 - Ampersands are no longer escaped by default in the `bib` file. If you want to keep the current behaviour, you can use the new "Escape Ampersands" formatter as a save action. [#5869](https://github.com/JabRef/jabref/issues/5869)

build.gradle

@@ -16,7 +16,7 @@ plugins {
     id 'com.github.ben-manes.versions' version '0.28.0'
     id 'org.javamodularity.moduleplugin' version '1.5.0'
     id 'org.openjfx.javafxplugin' version '0.0.8'
-    id 'org.beryx.jlink' version '2.17.8'
+    id 'org.beryx.jlink' version '2.18.0'
 
     // nicer test outputs during running and completion
     id 'com.adarshr.test-logger' version '2.0.0'
@@ -112,7 +112,7 @@ dependencies {
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.8'
     implementation 'com.h2database:h2-mvstore:1.4.200'
 
-    implementation group: 'org.apache.tika', name: 'tika-core', version: '1.24'
+    implementation group: 'org.apache.tika', name: 'tika-core', version: '1.24.1'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     implementation 'org.bouncycastle:bcprov-jdk15on:1.65'
@@ -191,16 +191,16 @@ dependencies {
         exclude module: "log4j-core"
     }
 
-    implementation 'com.vladsch.flexmark:flexmark:0.61.20'
-    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.61.20'
-    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.61.20'
+    implementation 'com.vladsch.flexmark:flexmark:0.61.24'
+    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.61.24'
+    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.61.24'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.77'
+    testImplementation 'io.github.classgraph:classgraph:4.8.78'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.6.2'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.6.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.6.2'
 
-    testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.9'
+    testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.10'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
     testImplementation 'org.mockito:mockito-core:3.3.3'
@@ -212,7 +212,7 @@ dependencies {
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
     checkstyle 'com.puppycrawl.tools:checkstyle:8.32'
-    xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.2'
+    xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.3'
     jython 'org.python:jython-standalone:2.7.2'
 }
 

buildres/linux/JabRef.desktop

@@ -9,4 +9,4 @@ Type=Application
 DESKTOP_MIMES
 Categories=DEPLOY_BUNDLE_CATEGORY
 Keywords=bibtex;biblatex;latex;bibliography
-StartupWMClass=org-jabref-JabRefMain
+StartupWMClass=org.jabref.JabRefMain

src/main/java/org/jabref/gui/JabRefFrame.java

@@ -245,6 +245,30 @@ private void initKeyBindings() {
                     case SEARCH:
                         getGlobalSearchBar().focus();
                         break;
+                    case NEW_ARTICLE:
+                        new NewEntryAction(this, StandardEntryType.Article, dialogService, prefs, stateManager).execute();
+                        break;
+                    case NEW_BOOK:
+                        new NewEntryAction(this, StandardEntryType.Book, dialogService, prefs, stateManager).execute();
+                        break;
+                    case NEW_INBOOK:
+                        new NewEntryAction(this, StandardEntryType.InBook, dialogService, prefs, stateManager).execute();
+                        break;
+                    case NEW_MASTERSTHESIS:
+                        new NewEntryAction(this, StandardEntryType.MastersThesis, dialogService, prefs, stateManager).execute();
+                        break;
+                    case NEW_PHDTHESIS:
+                        new NewEntryAction(this, StandardEntryType.PhdThesis, dialogService, prefs, stateManager).execute();
+                        break;
+                    case NEW_PROCEEDINGS:
+                        new NewEntryAction(this, StandardEntryType.Proceedings, dialogService, prefs, stateManager).execute();
+                        break;
+                    case NEW_TECHREPORT:
+                        new NewEntryAction(this, StandardEntryType.TechReport, dialogService, prefs, stateManager).execute();
+                        break;
+                    case NEW_UNPUBLISHED:
+                        new NewEntryAction(this, StandardEntryType.Unpublished, dialogService, prefs, stateManager).execute();
+                        break;
                     default:
                 }
             }

src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java

@@ -38,6 +38,7 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.URLDownload;
 import org.jabref.logic.util.io.FileNameUniqueness;
+import org.jabref.logic.util.io.FileUtil;
 import org.jabref.logic.xmp.XmpPreferences;
 import org.jabref.logic.xmp.XmpUtilWriter;
 import org.jabref.model.database.BibDatabaseContext;
@@ -415,6 +416,7 @@ public void download() {
                 LinkedFile newLinkedFile = LinkedFilesEditorViewModel.fromFile(destination, databaseContext.getFileDirectoriesAsPaths(filePreferences), externalFileTypes);
                 linkedFile.setLink(newLinkedFile.getLink());
                 linkedFile.setFileType(newLinkedFile.getFileType());
+                entry.addFile(0, newLinkedFile);
             });
             downloadProgress.bind(downloadTask.workDonePercentageProperty());
             taskExecutor.execute(downloadTask);
@@ -431,8 +433,9 @@ public BackgroundTask<Path> prepareDownloadTask(Path targetDirectory, URLDownloa
                     String suggestedTypeName = externalFileType.getName();
                     linkedFile.setFileType(suggestedTypeName);
                     String suggestedName = linkedFileHandler.getSuggestedFileName(externalFileType.getExtension());
-                    suggestedName = FileNameUniqueness.getNonOverWritingFileName(targetDirectory, suggestedName);
-                    return targetDirectory.resolve(suggestedName);
+                    String fulltextDir = FileUtil.createDirNameFromPattern(databaseContext.getDatabase(), entry, filePreferences.getFileDirPattern());
+                    suggestedName = FileNameUniqueness.getNonOverWritingFileName(targetDirectory.resolve(fulltextDir), suggestedName);
+                    return targetDirectory.resolve(fulltextDir).resolve(suggestedName);
                 })
                 .then(destination -> new FileDownloadTask(urlDownload.getSource(), destination))
                 .onFailure(exception -> dialogService.showErrorDialogAndWait("Download failed", exception));

src/main/java/org/jabref/gui/importer/ImportEntriesDialog.fxml

@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
 <?import javafx.scene.control.Button?>
+<?import javafx.scene.control.CheckBox?>
 <?import javafx.scene.control.ButtonType?>
 <?import javafx.scene.control.DialogPane?>
 <?import javafx.scene.control.Label?>
@@ -38,6 +39,7 @@
                     <Label fx:id="selectedItems" GridPane.rowIndex="1" GridPane.columnIndex="1"/>
                 </GridPane>
             </HBox>
+            <CheckBox fx:id="downloadLinkedOnlineFiles" text="%Download linked online files"/>
         </VBox>
     </content>
     <ButtonType fx:id="importButton" buttonData="OK_DONE" text="%Import entries"/>

src/main/java/org/jabref/gui/importer/ImportEntriesDialog.java

@@ -12,6 +12,7 @@
 import javafx.scene.Node;
 import javafx.scene.control.Button;
 import javafx.scene.control.ButtonType;
+import javafx.scene.control.CheckBox;
 import javafx.scene.control.Label;
 import javafx.scene.control.ToggleButton;
 import javafx.scene.control.Tooltip;
@@ -50,6 +51,7 @@ public class ImportEntriesDialog extends BaseDialog<Boolean> {
     public ButtonType importButton;
     public Label totalItems;
     public Label selectedItems;
+    public CheckBox downloadLinkedOnlineFiles;
     private final BackgroundTask<ParserResult> task;
     private ImportEntriesViewModel viewModel;
     @Inject private TaskExecutor taskExecutor;
@@ -77,9 +79,11 @@ public ImportEntriesDialog(BibDatabaseContext database, BackgroundTask<ParserRes
         Button btn = (Button) this.getDialogPane().lookupButton(importButton);
         btn.disableProperty().bind(booleanBind);
 
+        downloadLinkedOnlineFiles.setSelected(preferences.getFilePreferences().getDownloadLinkedFiles());
+
         setResultConverter(button -> {
             if (button == importButton) {
-                viewModel.importEntries(entriesListView.getCheckModel().getCheckedItems());
+                viewModel.importEntries(entriesListView.getCheckModel().getCheckedItems(), downloadLinkedOnlineFiles.isSelected());
             } else {
                 dialogService.notify(Localization.lang("Import canceled"));
             }

src/main/java/org/jabref/gui/importer/ImportEntriesViewModel.java

@@ -18,6 +18,7 @@
 import org.jabref.gui.duplicationFinder.DuplicateResolverDialog;
 import org.jabref.gui.externalfiles.ImportHandler;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
+import org.jabref.gui.fieldeditors.LinkedFileViewModel;
 import org.jabref.gui.groups.GroupTreeNodeViewModel;
 import org.jabref.gui.groups.UndoableAddOrRemoveGroup;
 import org.jabref.gui.undo.NamedCompound;
@@ -31,6 +32,7 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibtexString;
+import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.groups.GroupTreeNode;
 import org.jabref.model.metadata.MetaData;
 import org.jabref.model.util.FileUpdateMonitor;
@@ -44,6 +46,7 @@ public class ImportEntriesViewModel extends AbstractViewModel {
     private static final Logger LOGGER = LoggerFactory.getLogger(ImportEntriesViewModel.class);
 
     private final StringProperty message;
+    private final TaskExecutor taskExecutor;
     private final BibDatabaseContext databaseContext;
     private final DialogService dialogService;
     private final UndoManager undoManager;
@@ -58,6 +61,7 @@ public class ImportEntriesViewModel extends AbstractViewModel {
      * @param task     the task executed for parsing the selected files(s).
      */
     public ImportEntriesViewModel(BackgroundTask<ParserResult> task, TaskExecutor taskExecutor, BibDatabaseContext databaseContext, DialogService dialogService, UndoManager undoManager, PreferencesService preferences, StateManager stateManager, FileUpdateMonitor fileUpdateMonitor) {
+        this.taskExecutor = taskExecutor;
         this.databaseContext = databaseContext;
         this.dialogService = dialogService;
         this.undoManager = undoManager;
@@ -99,7 +103,7 @@ public boolean hasDuplicate(BibEntry entry) {
      *
      * @param entriesToImport subset of the entries contained in parserResult
      */
-    public void importEntries(List<BibEntry> entriesToImport) {
+    public void importEntries(List<BibEntry> entriesToImport, boolean downloadFiles) {
         // Check if we are supposed to warn about duplicates.
         // If so, then see if there are duplicates, and warn if yes.
         if (preferences.shouldWarnAboutDuplicatesForImport()) {
@@ -126,6 +130,15 @@ public void importEntries(List<BibEntry> entriesToImport) {
             buildImportHandlerThenImportEntries(entriesToImport);
         }
 
+        if (downloadFiles) {
+            for (BibEntry bibEntry : entriesToImport) {
+                for (LinkedFile linkedFile : bibEntry.getFiles()) {
+                    LinkedFileViewModel linkedFileViewModel = new LinkedFileViewModel(linkedFile, bibEntry, databaseContext, taskExecutor, dialogService, preferences.getXMPPreferences(), preferences.getFilePreferences(), ExternalFileTypes.getInstance());
+                    linkedFileViewModel.download();
+                }
+            }
+        }
+
         NamedCompound namedCompound = new NamedCompound(Localization.lang("Import file"));
         namedCompound.addEdit(new UndoableInsertEntries(databaseContext.getDatabase(), entriesToImport));
 

src/main/java/org/jabref/gui/preferences/ImportTab.fxml

@@ -1,5 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
+<?import javafx.scene.control.CheckBox?>
 <?import javafx.scene.control.ComboBox?>
 <?import javafx.scene.control.Label?>
 <?import javafx.scene.control.TextField?>
@@ -30,5 +31,6 @@
         <Label text="%File directory pattern" GridPane.rowIndex="1"/>
         <TextField fx:id="fileDirPattern" GridPane.columnIndex="1" GridPane.rowIndex="1"
                    prefWidth="300" minWidth="300" maxWidth="300"/>
+        <CheckBox fx:id="downloadLinkedFiles" text="%Download linked online files" GridPane.rowIndex="2"/>
     </GridPane>
 </fx:root>

src/main/java/org/jabref/gui/preferences/ImportTabView.java

@@ -1,6 +1,7 @@
 package org.jabref.gui.preferences;
 
 import javafx.fxml.FXML;
+import javafx.scene.control.CheckBox;
 import javafx.scene.control.ComboBox;
 import javafx.scene.control.TextField;
 
@@ -13,6 +14,7 @@ public class ImportTabView extends AbstractPreferenceTabView<ImportTabViewModel>
 
     @FXML private ComboBox<String> fileNamePattern;
     @FXML private TextField fileDirPattern;
+    @FXML private CheckBox downloadLinkedFiles;
 
     public ImportTabView(JabRefPreferences preferences) {
         this.preferences = preferences;
@@ -28,6 +30,7 @@ public void initialize() {
         fileNamePattern.valueProperty().bindBidirectional(viewModel.fileNamePatternProperty());
         fileNamePattern.itemsProperty().bind(viewModel.defaultFileNamePatternsProperty());
         fileDirPattern.textProperty().bindBidirectional(viewModel.fileDirPatternProperty());
+        downloadLinkedFiles.selectedProperty().bindBidirectional(viewModel.downloadLinkedFilesProperty());
     }
 
     @Override