Merge remote-tracking branch 'upstream/main' into restapi

* upstream/main: (26 commits) Remove bibtexml.xsd (We don't support BibTeXML any more) Rewrite code of MedlineImporter (#9673) Rename variable and add more documentation Fix checkstyle Add hanling of "field = {content\}" Add link to PR Add link to PR. JabRef writes a new backup file only if there is a change. Add debug output to log.txt Refine logging howto Change log level for non-found files during PDF indexing Initial ImportHandlerTest Streamline AppDirs paths add a clear history button in sub-menu Removed redundant list add for en.properties add Localization.lang for string correct changelog add test for getLastSearchHistory and change HashLinkedSet to ArrayList fix the checkstlye ...
JabRef · Mar 18, 2023 · ba80857 · ba80857
2 parents cf14659 + a0cb4be
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 ### Added
 
 - We added a field showing the BibTeX/biblatex source for added and deleted entries in the "External Changes Resolver" dialog. [#9509](https://github.com/JabRef/jabref/issues/9509)
+- We added a search history list in the search field's right click menu [#7906](https://github.com/JabRef/jabref/issues/7906)
 - We added a full text fetcher for IACR eprints. [#9651](https://github.com/JabRef/jabref/pull/9651)
 - We added "Attach file from URL" to right-click context menu to download and store a file with the reference library. [#9646](https://github.com/JabRef/jabref/issues/9646)
 - We enabled updating an existing entry with data from InspireHEP. [#9351](https://github.com/JabRef/jabref/issues/9351)
@@ -23,8 +24,16 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 ### Changed
 
 - 'Get full text' now also checks the file url. [#568](https://github.com/koppor/jabref/issues/568)
+- `log.txt` now contains an entry if a BibTeX entry could not be parsed.
+- JabRef writes a new backup file only if there is a change. Before, JabRef created a backup upon start. [#9679](https://github.com/JabRef/jabref/pull/9679)
+- We modified the `Add Group` dialog to use the most recently selected group hierarchical context. [#9141](https://github.com/JabRef/jabref/issues/9141)
 - We refined the 'main directory not found' error message. [#9625](https://github.com/JabRef/jabref/pull/9625)
-- We modified the `Add Group` dialog to use the most recently selected group hierarchical context [#9141](https://github.com/JabRef/jabref/issues/9141)
+- JabRef writes a new backup file only if there is a change. Before, JabRef created a backup upon start. [#9679](https://github.com/JabRef/jabref/pull/9679)
+- Backups of libraries are not stored per JabRef version, but collected together.
+- We streamlined the paths for logs and backups: The parent path fragement is always `logs` or `backups`.
+- `log.txt` now contains debug messages. Debugging needs to be enabled explicitly. [#9678](https://github.com/JabRef/jabref/pull/9678)
+- `log.txt` does not contain entries for non-found files during PDF indexing. [#9678](https://github.com/JabRef/jabref/pull/9678)
+- We improved the Medline importer to correctly import ISO dates for `revised`. [#9536](https://github.com/JabRef/jabref/issues/9536)
 
 
 
@@ -37,6 +46,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where the command line export using `--exportMatches` flag does not create an output bib file [#9581](https://github.com/JabRef/jabref/issues/9581)
 - We fixed an issue where custom field in the custom entry types could not be set to mulitline [#9609](https://github.com/JabRef/jabref/issues/9609)
 - We fixed an issue where the Office XML exporter did not resolve BibTeX-Strings when exporting entries [forum#3741](https://discourse.jabref.org/t/exporting-bibtex-constant-strings-to-ms-office-2007-xml/3741)
+- JabRef is now more relaxed when parsing field content: In case a field content ended with `\`, the combination `\}` was treated as plain `}`. [#9668](https://github.com/JabRef/jabref/issues/9668)
 
 
 ### Removed

diff --git a/build.gradle b/build.gradle
@@ -271,8 +271,6 @@ processResources {
 
 task generateSource(dependsOn: ["generateBstGrammarSource",
                                 "generateSearchGrammarSource",
-                                "generateMedlineSource",
-                                "generateBibtexmlSource",
                                 "generateEndnoteSource",
                                 "generateModsSource",
                                 "generateCitaviSource"]) {
@@ -302,24 +300,6 @@ tasks.register("generateSearchGrammarSource", JavaExec) {
     args  = ["-o","src-gen/main/java/org/jabref/search" , "-visitor", "-no-listener", "-package", "org.jabref.search", "$projectDir/src/main/antlr4/org/jabref/search/Search.g4"]
 }
 
-task generateMedlineSource(type: XjcTask) {
-    group = 'JabRef'
-    description = "Generates java files for the medline importer."
-
-    schemaFile = "src/main/resources/xjc/medline/medline.xsd"
-    outputDirectory = "src-gen/main/java"
-    javaPackage = "org.jabref.logic.importer.fileformat.medline"
-}
-
-task generateBibtexmlSource(type: XjcTask) {
-    group = 'JabRef'
-    description = "Generates java files for the bibtexml importer."
-
-    schemaFile = "src/main/resources/xjc/bibtexml/bibtexml.xsd"
-    outputDirectory = "src-gen/main/java/"
-    javaPackage = "org.jabref.logic.importer.fileformat.bibtexml"
-}
-
 task generateEndnoteSource(type: XjcTask) {
     group = 'JabRef'
     description = "Generates java files for the endnote importer."

diff --git a/docs/code-howtos/logging.md b/docs/code-howtos/logging.md
@@ -5,20 +5,44 @@ parent: Code Howtos
 
 JabRef uses the logging facade [SLF4j](https://www.slf4j.org). All log messages are passed internally to [tinylog](https://tinylog.org/v2/) which handles any filtering, formatting and writing of log messages.
 
-* Obtaining a logger for a class:
+Obtaining a logger for a class:
 
-    ```java
-    private static final Logger LOGGER = LoggerFactory.getLogger(<ClassName>.class);
-    ```
+```java
+private static final Logger LOGGER = LoggerFactory.getLogger(<ClassName>.class);
+```
 
-* If the logging event is caused by an exception, please add the exception to the log message as:
+Please always use `LOGGER.debug` for debugging.
 
-    ```java
-      catch (SomeException e) {
-         LOGGER.warn("Warning text.", e);
-         ...
-      }
-    ```
+Example:
+
+```java
+String example = "example";
+LOGGER.debug("Some state {}", example);
+```
+
+Enable logging in `tinylog.properties`:
+
+```properties
+level@org.jabref.example.ExampleClass = debug
+```
+
+If the logging event is caused by an exception, please add the exception to the log message as:
+
+```java
+  catch (SomeException e) {
+     LOGGER.warn("Warning text.", e);
+     ...
+  }
+```
+
+When running tests, `tinylog-test.properties` is used.
+It is located under `src/test/resources`. As default, only `info` is logged.
+When developing, it makes sense to use `debug` as log level.
+One can change the log level per class using the pattern `level@class=debug` is set to `debug`.
+In the `.properties` file, this is done for `org.jabref.model.entry.BibEntry`.
+
+## Further reading
+
+SLF4J also support parameterized logging, e.g. if you want to print out multiple arguments in a log statement use a pair of curly braces (`{}`). 
+Head to <https://www.slf4j.org/faq.html#logging_performance> for examples.
 
-* SLF4J also support parameterized logging, e.g. if you want to print out multiple arguments in a log statement use a pair of curly braces. [Examples](https://www.slf4j.org/faq.html#logging\_performance)
-* When running tests, `tinylog-test.properties` is used. It is located under `src/test/resources`. As default, only `info` is logged. When developing, it makes sense to use `debug` as log level. One can change the log level per class using the pattern `level@class=debug` is set to `debug`. In the `.properties` file, this is done for `org.jabref.model.entry.BibEntry`.
diff --git a/src/main/java/org/jabref/cli/Launcher.java b/src/main/java/org/jabref/cli/Launcher.java
@@ -24,6 +24,7 @@
 import org.jabref.logic.remote.client.RemoteClient;
 import org.jabref.logic.shared.restserver.rest.Root;
 import org.jabref.logic.util.BuildInfo;
+import org.jabref.logic.util.OS;
 import org.jabref.migrations.PreferencesMigrations;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
@@ -118,10 +119,12 @@ static void startServer() {
      * the log configuration programmatically anymore.
      */
     private static void addLogToDisk() {
-        Path directory = Path.of(AppDirsFactory.getInstance().getUserLogDir(
-                "jabref",
-                new BuildInfo().version.toString(),
-                "org.jabref"));
+        Path directory = Path.of(AppDirsFactory.getInstance()
+                                               .getUserDataDir(
+                OS.APP_DIR_APP_NAME,
+                "logs",
+                OS.APP_DIR_APP_AUTHOR))
+                .resolve(new BuildInfo().version.toString());
         try {
             Files.createDirectories(directory);
         } catch (IOException e) {
@@ -133,7 +136,7 @@ private static void addLogToDisk() {
         // https://tinylog.org/v2/configuration/#shared-file-writer
         Map<String, String> configuration = Map.of(
                 "writerFile", "shared file",
-                "writerFile.level", "info",
+                "writerFile.level", "debug",
                 "writerFile.file", directory.resolve("log.txt").toString(),
                 "writerFile.charset", "UTF-8");
 

diff --git a/src/main/java/org/jabref/gui/ClipBoardManager.java b/src/main/java/org/jabref/gui/ClipBoardManager.java
@@ -87,7 +87,7 @@ public static String getContents() {
         return result;
     }
 
-    public Optional<String> getBibTeXEntriesFromClipbaord() {
+    public Optional<String> getBibTeXEntriesFromClipboard() {
         return Optional.ofNullable(clipboard.getContent(DragAndDropDataFormats.ENTRIES)).map(String.class::cast);
     }
 

diff --git a/src/main/java/org/jabref/gui/StateManager.java b/src/main/java/org/jabref/gui/StateManager.java
@@ -71,6 +71,8 @@ public class StateManager {
 
     private final ObjectProperty<LastAutomaticFieldEditorEdit> lastAutomaticFieldEditorEdit = new SimpleObjectProperty<>();
 
+    private final ObservableList<String> searchHistory = FXCollections.observableArrayList();
+
     public StateManager() {
         activeGroups.bind(Bindings.valueAt(selectedGroups, activeDatabase.orElseOpt(null)));
     }
@@ -212,4 +214,25 @@ public List<String> collectAllDatabasePaths() {
                                   () -> list.add("")));
         return list;
     }
+
+    public void addSearchHistory(String search) {
+        searchHistory.remove(search);
+        searchHistory.add(search);
+    }
+
+    public ObservableList<String> getWholeSearchHistory() {
+        return searchHistory;
+    }
+
+    public List<String> getLastSearchHistory(int size) {
+        int sizeSearches = searchHistory.size();
+        if (size < sizeSearches) {
+            return searchHistory.subList(sizeSearches - size, sizeSearches);
+        }
+        return searchHistory;
+    }
+
+    public void clearSearchHistory() {
+        searchHistory.clear();
+    }
 }
diff --git a/src/main/java/org/jabref/gui/backup/BackupResolverDialog.java b/src/main/java/org/jabref/gui/backup/BackupResolverDialog.java
@@ -32,7 +32,7 @@ public BackupResolverDialog(Path originalPath) {
         getDialogPane().setMinHeight(180);
         getDialogPane().getButtonTypes().setAll(RESTORE_FROM_BACKUP, REVIEW_BACKUP, IGNORE_BACKUP);
 
-        Optional<Path> backupPathOpt = BackupFileUtil.getPathOfLatestExisingBackupFile(originalPath, BackupFileType.BACKUP);
+        Optional<Path> backupPathOpt = BackupFileUtil.getPathOfLatestExistingBackupFile(originalPath, BackupFileType.BACKUP);
         String backupFilename = backupPathOpt.map(Path::getFileName).map(Path::toString).orElse(Localization.lang("File not found"));
         String content = new StringBuilder()
                 .append(Localization.lang("A backup file for '%0' was found at [%1]",

diff --git a/src/main/java/org/jabref/gui/dialogs/BackupUIManager.java b/src/main/java/org/jabref/gui/dialogs/BackupUIManager.java
@@ -63,7 +63,7 @@ private static Optional<ParserResult> showReviewBackupDialog(DialogService dialo
             // This will be modified by using the `DatabaseChangesResolverDialog`.
             BibDatabaseContext originalDatabase = originalParserResult.getDatabaseContext();
 
-            Path backupPath = BackupFileUtil.getPathOfLatestExisingBackupFile(originalPath, BackupFileType.BACKUP).orElseThrow();
+            Path backupPath = BackupFileUtil.getPathOfLatestExistingBackupFile(originalPath, BackupFileType.BACKUP).orElseThrow();
             BibDatabaseContext backupDatabase = OpenDatabase.loadDatabase(backupPath, importFormatPreferences, new DummyFileUpdateMonitor()).getDatabaseContext();
 
             DatabaseChangeResolverFactory changeResolverFactory = new DatabaseChangeResolverFactory(dialogService, originalDatabase, preferencesService.getBibEntryPreferences());

diff --git a/src/main/java/org/jabref/gui/edit/EditAction.java b/src/main/java/org/jabref/gui/edit/EditAction.java
@@ -1,5 +1,6 @@
 package org.jabref.gui.edit;
 
+import javafx.scene.control.TextField;
 import javafx.scene.control.TextInputControl;
 import javafx.scene.web.WebView;
 
@@ -22,6 +23,7 @@ public class EditAction extends SimpleCommand {
     private static final Logger LOGGER = LoggerFactory.getLogger(EditAction.class);
 
     private final JabRefFrame frame;
+    private TextField text;
     private final StandardActions action;
     private final StateManager stateManager;
 
@@ -52,8 +54,12 @@ public void execute() {
                 // DELETE_ENTRY in text field should do forward delete
                 switch (action) {
                     case COPY -> textInput.copy();
+                    case UNDO -> textInput.undo();
+                    case REDO -> textInput.redo();
                     case CUT -> textInput.cut();
                     case PASTE -> textInput.paste();
+                    case DELETE -> textInput.clear();
+                    case SELECT_ALL -> textInput.selectAll();
                     case DELETE_ENTRY -> textInput.deleteNextChar();
                     default -> throw new IllegalStateException("Only cut/copy/paste supported in TextInputControl but got " + action);
                 }

diff --git a/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java b/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java
@@ -258,7 +258,7 @@ private void generateKeys(List<BibEntry> entries) {
     }
 
     public List<BibEntry> handleBibTeXData(String entries) {
-        BibtexParser parser = new BibtexParser(preferencesService.getImportFormatPreferences(), Globals.getFileUpdateMonitor());
+        BibtexParser parser = new BibtexParser(preferencesService.getImportFormatPreferences(), fileUpdateMonitor);
         try {
             return parser.parseEntries(new ByteArrayInputStream(entries.getBytes(StandardCharsets.UTF_8)));
         } catch (ParseException ex) {

diff --git a/src/main/java/org/jabref/gui/maintable/MainTable.java b/src/main/java/org/jabref/gui/maintable/MainTable.java
@@ -322,9 +322,9 @@ private void clearAndSelectLast() {
 
     public void paste() {
         List<BibEntry> entriesToAdd;
-            entriesToAdd = this.clipBoardManager.getBibTeXEntriesFromClipbaord()
+            entriesToAdd = this.clipBoardManager.getBibTeXEntriesFromClipboard()
             .map(importHandler::handleBibTeXData)
-            .orElseGet(this::handleNonBibteXStringData);
+            .orElseGet(this::handleNonBibTeXStringData);
 
         for (BibEntry entry : entriesToAdd) {
             importHandler.importEntryWithDuplicateCheck(database, entry);
@@ -334,7 +334,7 @@ public void paste() {
         }
     }
 
-    private List<BibEntry> handleNonBibteXStringData() {
+    private List<BibEntry> handleNonBibTeXStringData() {
         String data = ClipBoardManager.getContents();
         List<BibEntry> entries = new ArrayList<>();
         try {

diff --git a/src/main/java/org/jabref/gui/search/GlobalSearchBar.java b/src/main/java/org/jabref/gui/search/GlobalSearchBar.java
@@ -14,6 +14,8 @@
 import javafx.beans.binding.BooleanBinding;
 import javafx.beans.property.BooleanProperty;
 import javafx.beans.property.SimpleBooleanProperty;
+import javafx.collections.ListChangeListener;
+import javafx.collections.ObservableList;
 import javafx.css.PseudoClass;
 import javafx.event.Event;
 import javafx.geometry.Insets;
@@ -138,6 +140,19 @@ public GlobalSearchBar(JabRefFrame frame, StateManager stateManager, Preferences
             }
         });
 
+        searchField.setContextMenu(SearchFieldRightClickMenu.create(
+                keyBindingRepository,
+                stateManager,
+                searchField));
+
+        ObservableList<String> search = stateManager.getWholeSearchHistory();
+        search.addListener((ListChangeListener.Change<? extends String> change) -> {
+            searchField.setContextMenu(SearchFieldRightClickMenu.create(
+                    keyBindingRepository,
+                    stateManager,
+                    searchField));
+        });
+
         ClipBoardManager.addX11Support(searchField);
 
         regularExpressionButton = IconTheme.JabRefIcons.REG_EX.asToggleButton();
@@ -292,6 +307,7 @@ public void performSearch() {
             informUserAboutInvalidSearchQuery();
             return;
         }
+        this.stateManager.addSearchHistory(searchField.textProperty().get());
         stateManager.setSearchQuery(searchQuery);
     }
 

diff --git a/src/main/java/org/jabref/gui/search/SearchFieldRightClickMenu.java b/src/main/java/org/jabref/gui/search/SearchFieldRightClickMenu.java
@@ -0,0 +1,72 @@
+package org.jabref.gui.search;
+
+import javafx.scene.control.ContextMenu;
+import javafx.scene.control.Menu;
+import javafx.scene.control.MenuItem;
+import javafx.scene.control.SeparatorMenuItem;
+
+import org.jabref.gui.StateManager;
+import org.jabref.gui.actions.ActionFactory;
+import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.gui.actions.StandardActions;
+import org.jabref.gui.edit.EditAction;
+import org.jabref.gui.keyboard.KeyBindingRepository;
+import org.jabref.logic.l10n.Localization;
+
+import org.controlsfx.control.textfield.CustomTextField;
+
+public class SearchFieldRightClickMenu {
+    public static ContextMenu create(KeyBindingRepository keyBindingRepository,
+                                     StateManager stateManager,
+                                     CustomTextField searchField) {
+        ActionFactory factory = new ActionFactory(keyBindingRepository);
+        ContextMenu contextMenu = new ContextMenu();
+
+        contextMenu.getItems().addAll(
+                factory.createMenuItem(StandardActions.UNDO, new EditAction(StandardActions.UNDO, null, stateManager)),
+                factory.createMenuItem(StandardActions.REDO, new EditAction(StandardActions.REDO, null, stateManager)),
+                factory.createMenuItem(StandardActions.CUT, new EditAction(StandardActions.CUT, null, stateManager)),
+                factory.createMenuItem(StandardActions.COPY, new EditAction(StandardActions.COPY, null, stateManager)),
+                factory.createMenuItem(StandardActions.PASTE, new EditAction(StandardActions.PASTE, null, stateManager)),
+                factory.createMenuItem(StandardActions.DELETE, new EditAction(StandardActions.DELETE, null, stateManager)),
+
+                new SeparatorMenuItem(),
+
+                factory.createMenuItem(StandardActions.SELECT_ALL, new EditAction(StandardActions.SELECT_ALL, null, stateManager)),
+                createSearchFromHistorySubMenu(factory, stateManager, searchField)
+        );
+
+        return contextMenu;
+    }
+
+    private static Menu createSearchFromHistorySubMenu(ActionFactory factory,
+                                                       StateManager stateManager,
+                                                       CustomTextField searchField) {
+        Menu searchFromHistorySubMenu = factory.createMenu(() -> Localization.lang("Search from history..."));
+
+        int num = stateManager.getLastSearchHistory(10).size();
+        if (num == 0) {
+            MenuItem item = new MenuItem(Localization.lang("your search history is empty"));
+            searchFromHistorySubMenu.getItems().addAll(item);
+        } else {
+            for (int i = 0; i < num; i++) {
+                int finalI = i;
+                MenuItem item = factory.createMenuItem(() -> stateManager.getLastSearchHistory(10).get(finalI), new SimpleCommand() {
+                    @Override
+                    public void execute() {
+                        searchField.setText(stateManager.getLastSearchHistory(10).get(finalI));
+                    }
+                });
+                searchFromHistorySubMenu.getItems().addAll(item);
+            }
+            MenuItem clear = factory.createMenuItem(() -> Localization.lang("Clear history"), new SimpleCommand() {
+                @Override
+                public void execute() {
+                    stateManager.clearSearchHistory();
+                }
+            });
+            searchFromHistorySubMenu.getItems().addAll(new SeparatorMenuItem(), clear);
+        }
+        return searchFromHistorySubMenu;
+    }
+}