Add feature to merge .bib files into current bib #13320
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| Original file line number | Diff line number | Diff line change | ||||
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| package org.jabref.gui.mergebibfilesintocurrentbib; | ||||||
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| import java.io.IOException; | ||||||
| import java.nio.file.Files; | ||||||
| import java.nio.file.Path; | ||||||
| import java.util.ArrayList; | ||||||
| import java.util.List; | ||||||
| import java.util.Optional; | ||||||
| import java.util.stream.Collectors; | ||||||
| import java.util.stream.Stream; | ||||||
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| import javax.swing.undo.UndoManager; | ||||||
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| import org.jabref.gui.DialogService; | ||||||
| import org.jabref.gui.StateManager; | ||||||
| import org.jabref.gui.actions.SimpleCommand; | ||||||
| import org.jabref.gui.mergeentries.MergeEntriesAction; | ||||||
| import org.jabref.gui.preferences.GuiPreferences; | ||||||
| import org.jabref.gui.undo.NamedCompound; | ||||||
| import org.jabref.gui.undo.UndoableInsertEntries; | ||||||
| import org.jabref.gui.util.DirectoryDialogConfiguration; | ||||||
| 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.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; | ||||||
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| import org.slf4j.Logger; | ||||||
| import org.slf4j.LoggerFactory; | ||||||
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| import static org.jabref.gui.actions.ActionHelper.needsDatabase; | ||||||
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| public class MergeBibFilesIntoCurrentBibAction extends SimpleCommand { | ||||||
| private static final Logger LOGGER = LoggerFactory.getLogger(MergeBibFilesIntoCurrentBibAction.class); | ||||||
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| private final DialogService dialogService; | ||||||
| private final GuiPreferences preferences; | ||||||
| private final StateManager stateManager; | ||||||
| private final UndoManager undoManager; | ||||||
| private final FileUpdateMonitor fileUpdateMonitor; | ||||||
| private final BibEntryTypesManager entryTypesManager; | ||||||
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| private boolean shouldMergeSameKeyEntries; | ||||||
| private boolean shouldMergeDuplicateEntries; | ||||||
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| private final List<BibEntry> entriesToMerge = new ArrayList<>(); | ||||||
| private final List<List<BibEntry>> duplicatePairsToMerge = new ArrayList<>(); | ||||||
| private final List<List<BibEntry>> sameKeyPairsToMerge = new ArrayList<>(); | ||||||
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| public MergeBibFilesIntoCurrentBibAction(DialogService dialogService, | ||||||
| GuiPreferences preferences, | ||||||
| StateManager stateManager, | ||||||
| UndoManager undoManager, | ||||||
| FileUpdateMonitor fileUpdateMonitor, | ||||||
| BibEntryTypesManager entryTypesManager) { | ||||||
| this.dialogService = dialogService; | ||||||
| this.preferences = preferences; | ||||||
| this.stateManager = stateManager; | ||||||
| this.undoManager = undoManager; | ||||||
| this.fileUpdateMonitor = fileUpdateMonitor; | ||||||
| this.entryTypesManager = entryTypesManager; | ||||||
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| this.executable.bind(needsDatabase(this.stateManager)); | ||||||
| } | ||||||
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| @Override | ||||||
| public void execute() { | ||||||
| Optional<Path> selectedDirectory = getDirectoryToMerge(); | ||||||
| Optional<BibDatabaseContext> context = stateManager.getActiveDatabase(); | ||||||
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| MergeBibFilesIntoCurrentBibPreferences mergeBibFilesIntoCurrentBibPreferences = preferences.getMergeBibFilesIntoCurrentBibPreferences(); | ||||||
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| shouldMergeSameKeyEntries = mergeBibFilesIntoCurrentBibPreferences.shouldMergeSameKeyEntries(); | ||||||
| shouldMergeDuplicateEntries = mergeBibFilesIntoCurrentBibPreferences.shouldMergeDuplicateEntries(); | ||||||
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| if (selectedDirectory.isPresent() && context.isPresent()) { | ||||||
| mergeBibFilesIntoCurrentBib(selectedDirectory.get(), context.get()); | ||||||
| } | ||||||
| } | ||||||
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| private Optional<Path> getDirectoryToMerge() { | ||||||
| DirectoryDialogConfiguration config = new DirectoryDialogConfiguration.Builder() | ||||||
| .withInitialDirectory(preferences.getFilePreferences().getWorkingDirectory()) | ||||||
| .build(); | ||||||
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| return dialogService.showDirectorySelectionDialog(config); | ||||||
| } | ||||||
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| public void mergeBibFilesIntoCurrentBib(Path directory, BibDatabaseContext context) { | ||||||
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| BibDatabase database = context.getDatabase(); | ||||||
| Optional<Path> databasePath = context.getDatabasePath(); | ||||||
| DuplicateCheck duplicateCheck = new DuplicateCheck(entryTypesManager); | ||||||
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| entriesToMerge.clear(); | ||||||
| sameKeyPairsToMerge.clear(); | ||||||
| duplicatePairsToMerge.clear(); | ||||||
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| for (Path path : getAllBibFiles(directory, databasePath.orElseGet(() -> Path.of("")))) { | ||||||
|
There was a problem hiding this comment. Why is the current library ("databasePath") included? I think, one wants to merge into the current one? |
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| ParserResult result; | ||||||
| try { | ||||||
| result = OpenDatabase.loadDatabase(path, preferences.getImportFormatPreferences(), fileUpdateMonitor); | ||||||
| } catch (IOException e) { | ||||||
| LOGGER.error("Could not load file '{}': {}", path, e.getMessage(), e); | ||||||
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There was a problem hiding this comment. It should be a |
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| continue; | ||||||
| } | ||||||
| for (BibEntry toMergeEntry : result.getDatabase().getEntries()) { | ||||||
| processEntry(toMergeEntry, database, duplicateCheck); | ||||||
| } | ||||||
| } | ||||||
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| database.insertEntries(entriesToMerge); | ||||||
| performMerges(); | ||||||
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| NamedCompound compound = new NamedCompound(Localization.lang("Merge BibTeX files into current library")); | ||||||
| compound.addEdit(new UndoableInsertEntries(database, entriesToMerge)); | ||||||
| compound.end(); | ||||||
| undoManager.addEdit(compound); | ||||||
| } | ||||||
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| private void processEntry(BibEntry entry, BibDatabase database, DuplicateCheck duplicateCheck) { | ||||||
| for (BibEntry existingEntry : database.getEntries()) { | ||||||
| if (entry.equals(existingEntry)) { | ||||||
| return; | ||||||
| } else if (entry.getCitationKey().equals(existingEntry.getCitationKey())) { | ||||||
| if (shouldMergeSameKeyEntries) { | ||||||
| sameKeyPairsToMerge.add(List.of(entry, existingEntry)); | ||||||
| } | ||||||
| return; | ||||||
|
Comment on lines
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+133
There was a problem hiding this comment. No - check for Imagine a library with 10k entries - using a hashmap is faster than iterating through all entries. |
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| } else if (duplicateCheck.isDuplicate(entry, existingEntry, BibDatabaseMode.BIBTEX)) { | ||||||
| if (shouldMergeDuplicateEntries) { | ||||||
| duplicatePairsToMerge.add(List.of(entry, existingEntry)); | ||||||
| } | ||||||
| return; | ||||||
| } | ||||||
| } | ||||||
| entriesToMerge.add(entry); | ||||||
| } | ||||||
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| private void performMerges() { | ||||||
| for (List<BibEntry> pair : sameKeyPairsToMerge) { | ||||||
| mergeEntries(pair); | ||||||
| } | ||||||
| for (List<BibEntry> pair : duplicatePairsToMerge) { | ||||||
| mergeEntries(pair); | ||||||
| } | ||||||
| } | ||||||
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| private void mergeEntries(List<BibEntry> entries) { | ||||||
| stateManager.setSelectedEntries(entries); | ||||||
| new MergeEntriesAction(dialogService, stateManager, undoManager, preferences).execute(); | ||||||
| } | ||||||
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| private List<Path> getAllBibFiles(Path directory, Path databasePath) { | ||||||
| if (!checkPathValidity(directory)) { | ||||||
| return List.of(); | ||||||
| } | ||||||
| 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
|
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| } catch (IOException e) { | ||||||
| LOGGER.error("Error finding .bib files in '{}': {}", directory.getFileName(), e.getMessage(), e); | ||||||
| } | ||||||
| return List.of(); | ||||||
| } | ||||||
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| private boolean checkPathValidity(Path directory) { | ||||||
|
There was a problem hiding this comment. Naming nitpick: There was a problem hiding this comment. Already changed it! Thanks! |
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| if (!Files.exists(directory)) { | ||||||
| dialogService.showErrorDialogAndWait(Localization.lang("Chosen folder does not exist:") + " " + directory); | ||||||
| return false; | ||||||
| } | ||||||
| if (!Files.isDirectory(directory)) { | ||||||
| dialogService.showErrorDialogAndWait(Localization.lang("Chosen path is not a folder:") + " " + directory); | ||||||
| return false; | ||||||
| } | ||||||
| if (!Files.isReadable(directory)) { | ||||||
| dialogService.showErrorDialogAndWait(Localization.lang("Chosen folder is not readable:") + " " + directory); | ||||||
| return false; | ||||||
| } | ||||||
| return true; | ||||||
| } | ||||||
| } | ||||||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| package org.jabref.gui.mergebibfilesintocurrentbib; | ||
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| import javafx.beans.property.BooleanProperty; | ||
| import javafx.beans.property.SimpleBooleanProperty; | ||
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| public class MergeBibFilesIntoCurrentBibPreferences { | ||
| private final BooleanProperty shouldMergeSameKeyEntries = new SimpleBooleanProperty(); | ||
| private final BooleanProperty shouldMergeDuplicateEntries = new SimpleBooleanProperty(); | ||
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| public MergeBibFilesIntoCurrentBibPreferences(boolean shouldMergeSameKeyEntries, boolean shouldMergeDuplicateEntries) { | ||
| this.shouldMergeSameKeyEntries.set(shouldMergeSameKeyEntries); | ||
| this.shouldMergeDuplicateEntries.set(shouldMergeDuplicateEntries); | ||
| } | ||
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| public boolean shouldMergeSameKeyEntries() { | ||
| return this.shouldMergeSameKeyEntries.get(); | ||
| } | ||
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| public void setShouldMergeSameKeyEntries(boolean decision) { | ||
| this.shouldMergeSameKeyEntries.set(decision); | ||
| } | ||
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| public BooleanProperty shouldMergeSameKeyEntriesProperty() { | ||
| return this.shouldMergeSameKeyEntries; | ||
| } | ||
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| public boolean shouldMergeDuplicateEntries() { | ||
| return this.shouldMergeDuplicateEntries.get(); | ||
| } | ||
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| public void setShouldMergeDuplicateEntries(boolean decision) { | ||
| this.shouldMergeDuplicateEntries.set(decision); | ||
| } | ||
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| public BooleanProperty shouldMergeDuplicateEntriesProperty() { | ||
| return this.shouldMergeDuplicateEntries; | ||
| } | ||
| } |
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The term 'BIBTEX' in the constant name doesn't follow the convention of using 'Bibtex' in variable/constant names as specified in special instructions.