Add feature to merge .bib files into current bib #13320
+710
−0
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change | ||||
|---|---|---|---|---|---|---|
| @@ -0,0 +1,231 @@ | ||||||
| package org.jabref.gui.mergebibfilesintocurrentbib; | ||||||
|
|
||||||
| import java.io.IOException; | ||||||
| import java.nio.file.Files; | ||||||
| import java.nio.file.Path; | ||||||
| import java.sql.SQLException; | ||||||
| import java.util.ArrayList; | ||||||
| import java.util.List; | ||||||
| import java.util.Optional; | ||||||
| import java.util.stream.Collectors; | ||||||
| import java.util.stream.Stream; | ||||||
|
|
||||||
| import javax.swing.undo.UndoManager; | ||||||
|
|
||||||
| import org.jabref.gui.ClipBoardManager; | ||||||
| import org.jabref.gui.DialogService; | ||||||
| import org.jabref.gui.LibraryTabContainer; | ||||||
| import org.jabref.gui.StateManager; | ||||||
| import org.jabref.gui.actions.SimpleCommand; | ||||||
| import org.jabref.gui.autosaveandbackup.BackupManager; | ||||||
| import org.jabref.gui.dialogs.BackupUIManager; | ||||||
| import org.jabref.gui.mergeentries.MergeEntriesAction; | ||||||
| import org.jabref.gui.preferences.GuiPreferences; | ||||||
| import org.jabref.gui.shared.SharedDatabaseUIManager; | ||||||
| import org.jabref.gui.undo.NamedCompound; | ||||||
| import org.jabref.gui.undo.UndoableInsertEntries; | ||||||
| import org.jabref.gui.util.DirectoryDialogConfiguration; | ||||||
| import org.jabref.gui.util.UiTaskExecutor; | ||||||
| import org.jabref.logic.ai.AiService; | ||||||
| import org.jabref.logic.database.DuplicateCheck; | ||||||
| import org.jabref.logic.importer.OpenDatabase; | ||||||
| import org.jabref.logic.importer.ParserResult; | ||||||
| import org.jabref.logic.l10n.Localization; | ||||||
| import org.jabref.logic.shared.DatabaseNotSupportedException; | ||||||
| import org.jabref.logic.shared.exception.InvalidDBMSConnectionPropertiesException; | ||||||
| import org.jabref.logic.shared.exception.NotASharedDatabaseException; | ||||||
| import org.jabref.logic.util.TaskExecutor; | ||||||
| import org.jabref.model.database.BibDatabase; | ||||||
| import org.jabref.model.database.BibDatabaseContext; | ||||||
| import org.jabref.model.database.BibDatabaseMode; | ||||||
| import org.jabref.model.entry.BibEntry; | ||||||
| import org.jabref.model.entry.BibEntryTypesManager; | ||||||
| import org.jabref.model.util.FileUpdateMonitor; | ||||||
|
|
||||||
| import org.slf4j.Logger; | ||||||
| import org.slf4j.LoggerFactory; | ||||||
|
|
||||||
| import static org.jabref.gui.actions.ActionHelper.needsDatabase; | ||||||
|
|
||||||
| public class MergeBibFilesIntoCurrentBibAction extends SimpleCommand { | ||||||
| private static final Logger LOGGER = LoggerFactory.getLogger(MergeBibFilesIntoCurrentBibAction.class); | ||||||
|
|
||||||
| private final LibraryTabContainer tabContainer; | ||||||
| private final DialogService dialogService; | ||||||
| private final GuiPreferences preferences; | ||||||
| private final StateManager stateManager; | ||||||
| private final UndoManager undoManager; | ||||||
| private final FileUpdateMonitor fileUpdateMonitor; | ||||||
| private final AiService aiService; | ||||||
| private final BibEntryTypesManager entryTypesManager; | ||||||
| private final ClipBoardManager clipBoardManager; | ||||||
| private final TaskExecutor taskExecutor; | ||||||
|
|
||||||
| private boolean shouldMergeSameKeyEntries; | ||||||
| private boolean shouldMergeDuplicateEntries; | ||||||
|
|
||||||
| public MergeBibFilesIntoCurrentBibAction(LibraryTabContainer tabContainer, | ||||||
| DialogService dialogService, | ||||||
| GuiPreferences preferences, | ||||||
| StateManager stateManager, | ||||||
| UndoManager undoManager, | ||||||
| FileUpdateMonitor fileUpdateMonitor, | ||||||
| AiService aiService, | ||||||
| BibEntryTypesManager entryTypesManager, | ||||||
| ClipBoardManager clipBoardManager, | ||||||
| TaskExecutor taskExecutor) { | ||||||
| this.tabContainer = tabContainer; | ||||||
| this.dialogService = dialogService; | ||||||
| this.preferences = preferences; | ||||||
| this.stateManager = stateManager; | ||||||
| this.undoManager = undoManager; | ||||||
| this.fileUpdateMonitor = fileUpdateMonitor; | ||||||
| this.aiService = aiService; | ||||||
| this.entryTypesManager = entryTypesManager; | ||||||
| this.clipBoardManager = clipBoardManager; | ||||||
| this.taskExecutor = taskExecutor; | ||||||
|
|
||||||
| this.executable.bind(needsDatabase(this.stateManager)); | ||||||
| } | ||||||
|
|
||||||
| @Override | ||||||
| public void execute() { | ||||||
| Optional<Path> selectedDirectory = getDirectoryToMerge(); | ||||||
| Optional<BibDatabaseContext> context = stateManager.getActiveDatabase(); | ||||||
|
|
||||||
| MergeBibFilesIntoCurrentBibPreferences mergeBibFilesIntoCurrentBibPreferences = preferences.getMergeBibFilesIntoCurrentBibPreferences(); | ||||||
|
|
||||||
| shouldMergeSameKeyEntries = mergeBibFilesIntoCurrentBibPreferences.shouldMergeSameKeyEntries(); | ||||||
| shouldMergeDuplicateEntries = mergeBibFilesIntoCurrentBibPreferences.shouldMergeDuplicateEntries(); | ||||||
|
|
||||||
| if (selectedDirectory.isPresent() && context.isPresent()) { | ||||||
| mergeBibFilesIntoCurrentBib(selectedDirectory.get(), context.get()); | ||||||
| } | ||||||
| } | ||||||
|
|
||||||
| public Optional<Path> getDirectoryToMerge() { | ||||||
| DirectoryDialogConfiguration config = new DirectoryDialogConfiguration.Builder() | ||||||
| .withInitialDirectory(preferences.getFilePreferences().getWorkingDirectory()) | ||||||
| .build(); | ||||||
|
|
||||||
| return dialogService.showDirectorySelectionDialog(config); | ||||||
| } | ||||||
|
|
||||||
| public void mergeBibFilesIntoCurrentBib(Path directory, BibDatabaseContext context) { | ||||||
| List<BibEntry> newEntries = new ArrayList<>(); | ||||||
| List<BibEntry> selectedEntries; | ||||||
|
|
||||||
| BibDatabase database = context.getDatabase(); | ||||||
| Optional<Path> databasePath = context.getDatabasePath(); | ||||||
|
|
||||||
| BibEntryTypesManager entryTypesManager = new BibEntryTypesManager(); | ||||||
|
|
||||||
| DuplicateCheck dupCheck = new DuplicateCheck(entryTypesManager); | ||||||
|
|
||||||
| for (Path p : getAllBibFiles(directory, databasePath.orElseGet(() -> Path.of("")))) { | ||||||
|
|
||||||
| ParserResult result = loadDatabase(p); | ||||||
|
|
||||||
| for (BibEntry toMergeEntry : result.getDatabase().getEntries()) { | ||||||
| boolean validNewEntry = true; | ||||||
| for (BibEntry e : database.getEntries()) { | ||||||
|
|
||||||
| if (toMergeEntry.equals(e)) { | ||||||
| validNewEntry = false; | ||||||
| break; | ||||||
| } else if (toMergeEntry.getCitationKey().equals(e.getCitationKey())) { | ||||||
| validNewEntry = false; | ||||||
|
|
||||||
| if (shouldMergeSameKeyEntries) { | ||||||
| selectedEntries = new ArrayList<>(); | ||||||
| selectedEntries.add(toMergeEntry); | ||||||
| selectedEntries.add(e); | ||||||
| stateManager.setSelectedEntries(selectedEntries); | ||||||
|
There was a problem hiding this comment. changes to the ui should only happen at the very end of the action. |
||||||
| new MergeEntriesAction(dialogService, stateManager, undoManager, preferences).execute(); | ||||||
| } | ||||||
| break; | ||||||
| } else if (dupCheck.isDuplicate(toMergeEntry, e, BibDatabaseMode.BIBTEX)) { | ||||||
| validNewEntry = false; | ||||||
|
|
||||||
| if (shouldMergeDuplicateEntries) { | ||||||
| selectedEntries = new ArrayList<>(); | ||||||
| selectedEntries.add(toMergeEntry); | ||||||
| selectedEntries.add(e); | ||||||
| stateManager.setSelectedEntries(selectedEntries); | ||||||
| new MergeEntriesAction(dialogService, stateManager, undoManager, preferences).execute(); | ||||||
| } | ||||||
| break; | ||||||
| } | ||||||
| } | ||||||
|
|
||||||
| if (validNewEntry) { | ||||||
| newEntries.add(toMergeEntry); | ||||||
| database.insertEntry(toMergeEntry); | ||||||
| } | ||||||
| } | ||||||
| } | ||||||
| NamedCompound ce = new NamedCompound(Localization.lang("Merge BibTeX files into current library")); | ||||||
|
|
||||||
| ce.addEdit(new UndoableInsertEntries(database, newEntries)); | ||||||
| ce.end(); | ||||||
|
|
||||||
| undoManager.addEdit(ce); | ||||||
| } | ||||||
|
|
||||||
| public List<Path> getAllBibFiles(Path directory, Path databasePath) { | ||||||
| try (Stream<Path> stream = Files.find( | ||||||
| directory, | ||||||
| Integer.MAX_VALUE, | ||||||
| (path, _) -> path.getFileName().toString().endsWith(".bib") && | ||||||
| !path.equals(databasePath) | ||||||
| )) { | ||||||
| return stream.collect(Collectors.toList()); | ||||||
|
There was a problem hiding this comment.
Suggested change
|
||||||
| } catch (IOException e) { | ||||||
| LOGGER.error("Error finding .bib files in '{}'", directory.getFileName(), e); | ||||||
| } | ||||||
|
There was a problem hiding this comment. I think the exception is thrown if the Files.find method cannot open or read the path, so I think there should be check for if the path is valid or not to have correct and helpful feedback to the user (including a message). |
||||||
| return List.of(); | ||||||
| } | ||||||
|
|
||||||
| public ParserResult loadDatabase(Path file) { | ||||||
|
There was a problem hiding this comment. Why don't you reuse existing methods? Looks like code duplication to me. |
||||||
| Path fileToLoad = file.toAbsolutePath(); | ||||||
|
|
||||||
| preferences.getFilePreferences().setWorkingDirectory(fileToLoad.getParent()); | ||||||
| Path backupDir = preferences.getFilePreferences().getBackupDirectory(); | ||||||
|
|
||||||
| ParserResult parserResult = null; | ||||||
| if (BackupManager.backupFileDiffers(fileToLoad, backupDir)) { | ||||||
| parserResult = BackupUIManager.showRestoreBackupDialog(dialogService, fileToLoad, preferences, fileUpdateMonitor, undoManager, stateManager) | ||||||
| .orElse(null); | ||||||
| } | ||||||
|
|
||||||
| try { | ||||||
| if (parserResult == null) { | ||||||
| parserResult = OpenDatabase.loadDatabase(fileToLoad, | ||||||
| preferences.getImportFormatPreferences(), | ||||||
| fileUpdateMonitor); | ||||||
| } | ||||||
|
|
||||||
| if (parserResult.hasWarnings()) { | ||||||
| String content = Localization.lang("Please check your library file for wrong syntax.") | ||||||
| + "\n\n" + parserResult.getErrorMessage(); | ||||||
| UiTaskExecutor.runInJavaFXThread(() -> | ||||||
| dialogService.showWarningDialogAndWait(Localization.lang("Open library error"), content)); | ||||||
| } | ||||||
| } catch (IOException e) { | ||||||
| parserResult = ParserResult.fromError(e); | ||||||
| LOGGER.error("Error opening file '{}'", fileToLoad, e); | ||||||
| } | ||||||
|
|
||||||
| if (parserResult.getDatabase().isShared()) { | ||||||
| try { | ||||||
| new SharedDatabaseUIManager(tabContainer, dialogService, preferences, aiService, stateManager, entryTypesManager, | ||||||
| fileUpdateMonitor, undoManager, clipBoardManager, taskExecutor) | ||||||
| .openSharedDatabaseFromParserResult(parserResult); | ||||||
| } catch (SQLException | | ||||||
| DatabaseNotSupportedException | | ||||||
| InvalidDBMSConnectionPropertiesException | | ||||||
| NotASharedDatabaseException e) { | ||||||
| parserResult.getDatabaseContext().clearDatabasePath(); | ||||||
| parserResult.getDatabase().clearSharedDatabaseID(); | ||||||
| LOGGER.error("Connection error", e); | ||||||
| } | ||||||
| } | ||||||
| return parserResult; | ||||||
| } | ||||||
| } | ||||||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| package org.jabref.gui.mergebibfilesintocurrentbib; | ||
|
|
||
| import javafx.beans.property.BooleanProperty; | ||
| import javafx.beans.property.SimpleBooleanProperty; | ||
|
|
||
| public class MergeBibFilesIntoCurrentBibPreferences { | ||
| private final BooleanProperty shouldMergeSameKeyEntries = new SimpleBooleanProperty(); | ||
| private final BooleanProperty shouldMergeDuplicateEntries = new SimpleBooleanProperty(); | ||
|
|
||
| public MergeBibFilesIntoCurrentBibPreferences(boolean shouldMergeSameKeyEntries, boolean shouldMergeDuplicateEntries) { | ||
| this.shouldMergeSameKeyEntries.set(shouldMergeSameKeyEntries); | ||
| this.shouldMergeDuplicateEntries.set(shouldMergeDuplicateEntries); | ||
| } | ||
|
|
||
| public boolean shouldMergeSameKeyEntries() { | ||
| return this.shouldMergeSameKeyEntries.get(); | ||
| } | ||
|
|
||
| public void setShouldMergeSameKeyEntries(boolean decision) { | ||
| this.shouldMergeSameKeyEntries.set(decision); | ||
| } | ||
|
|
||
| public BooleanProperty shouldMergeSameKeyEntriesProperty() { | ||
| return this.shouldMergeSameKeyEntries; | ||
| } | ||
|
|
||
| public boolean shouldMergeDuplicateEntries() { | ||
| return this.shouldMergeDuplicateEntries.get(); | ||
| } | ||
|
|
||
| public void setShouldMergeDuplicateEntries(boolean decision) { | ||
| this.shouldMergeDuplicateEntries.set(decision); | ||
| } | ||
|
|
||
| public BooleanProperty shouldMergeDuplicateEntriesProperty() { | ||
| return this.shouldMergeDuplicateEntries; | ||
| } | ||
| } |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Uh oh!
There was an error while loading. Please reload this page.