[WIP] Batch Insert entries (#5691)

* Initial changes to remove entry functionality

* Fix logic error in KeyChangeListener

* Fix logic error in BasePanel

* Changes to tests

* Fix typo

* Move remove entry calls to batch version

* Un-propagate for loop in KeyChangeListener

* Finalize changes to SharedEntriesNotPresentEvent

* Fix bug

* Fix other compile errors

* Fix bug and update tests

* Fix tests

* Fix test omission

* Update l10n

* For loop to citationStyle

* Add comment for method not working

* Clarify var name

* Allow single entry for undo

* Replace compound edit undo with normal undo in BasePanel

* Typo

* Simplify loop in DBMSSynchronizer

* Use if instead of stream

* Pluralize Javadoc

* EntryEvent -> EntriesEvent in Javadoc, comments, and var names

* Make imports explicit in BasePanel

* Batch delete to SQL

* Final EntriesRemovedEvent fixes

* Fix checkStyleMain

* More checkStyle fixes

* Initial changes to batch insertEntries calls

* More fixes

* More batching insertEntry

* Move List coercion into DuplicateSearchResult method

* Even more batching insertEntry

* DefaultAuxParser batch insertEntry

* MrDLibImporter batch insertEntry

* Add comment about usage of BasePanel.insertEntry

* Fix typo

* Fix pesky BibDatabaseTest error with setStrings

* Fixed BibDatabase Javadoc

* Finish master merge, start changing DBMS tests

* Add comment

* Final fixes including checkStyle

* Add DBMSProcessor tests

* Fix checkStyleTest

* Finished batching calls to insertEntries

* Minor change for consistency

* Update comments

* Update comment

* Another update comment

* EntryAddedEvent -> EntriesAddedEvnet and removed AllInsertsFinishedEvent

* Fixed some tests, aux parser still failing

* AuxParserTest passes now

* Fix checkstyle

* Make corrections

* Typo

* More streaming

* Add UndoableInsertEntries constructor

* Fix bug

* Get rid of "Integrity Check Failed" info

* Properly close databases in test to avoid database listener errors

* Fix database tests by adding entries after firing EntryAddedEvent

* Remove redundant DBMS connection closure from DBMSSychronizerTest

* Merge test resources from master

* Remove firstEntry hack

* Remove duplicate code from paste() by and pluralize insertEntries() in BasePanel

* Comment fix

* Clarify BasePanel insertEntries JavaDoc

* Rename vars

* Rename vars

* Remove unnecessary TODO and rename EntriesRemovedListener

* Merge fixes

* Remove old comment

* checkStyle fixes

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

@@ -59,7 +59,7 @@
 import org.jabref.gui.undo.CountingUndoManager;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableFieldChange;
-import org.jabref.gui.undo.UndoableInsertEntry;
+import org.jabref.gui.undo.UndoableInsertEntries;
 import org.jabref.gui.undo.UndoableRemoveEntries;
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.worker.SendAsEMailAction;
@@ -80,8 +80,8 @@
 import org.jabref.model.database.KeyCollisionException;
 import org.jabref.model.database.event.BibDatabaseContextChangedEvent;
 import org.jabref.model.database.event.CoarseChangeFilter;
+import org.jabref.model.database.event.EntriesAddedEvent;
 import org.jabref.model.database.event.EntriesRemovedEvent;
-import org.jabref.model.database.event.EntryAddedEvent;
 import org.jabref.model.database.shared.DatabaseLocation;
 import org.jabref.model.database.shared.DatabaseSynchronizer;
 import org.jabref.model.entry.BibEntry;
@@ -168,7 +168,7 @@ public BasePanel(JabRefFrame frame, BasePanelPreferences preferences, BibDatabas
         setupActions();
 
         this.getDatabase().registerListener(new SearchListener());
-        this.getDatabase().registerListener(new EntryRemovedListener());
+        this.getDatabase().registerListener(new EntriesRemovedListener());
 
         // ensure that at each addition of a new entry, the entry is added to the groups interface
         this.bibDatabaseContext.getDatabase().registerListener(new GroupTreeListener());
@@ -605,29 +605,39 @@ public void registerUndoableChanges(List<FieldChange> changes) {
         }
     }
 
+    public void insertEntry(final BibEntry bibEntry) {
+        if (bibEntry != null) {
+            insertEntries(Collections.singletonList(bibEntry));
+        }
+    }
+
     /**
-     * This method is called from JabRefFrame when the user wants to create a new entry.
+     * This method is called from JabRefFrame when the user wants to create a new entry or entries.
+     * It is necessary when the user would expect the added entry or one of the added entries
+     * to be selected in the entry editor
      *
-     * @param bibEntry The new entry.
+     * @param entries The new entries.
      */
-    public void insertEntry(final BibEntry bibEntry) {
-        if (bibEntry != null) {
+
+    public void insertEntries(final List<BibEntry> entries) {
+        if (!entries.isEmpty()) {
             try {
-                bibDatabaseContext.getDatabase().insertEntry(bibEntry);
+                bibDatabaseContext.getDatabase().insertEntries(entries);
 
                 // Set owner and timestamp
-                UpdateField.setAutomaticFields(bibEntry, true, true, Globals.prefs.getUpdateFieldPreferences());
-
-                // Create an UndoableInsertEntry object.
-                getUndoManager().addEdit(new UndoableInsertEntry(bibDatabaseContext.getDatabase(), bibEntry));
+                for (BibEntry entry : entries) {
+                    UpdateField.setAutomaticFields(entry, true, true, Globals.prefs.getUpdateFieldPreferences());
+                }
+                // Create an UndoableInsertEntries object.
+                getUndoManager().addEdit(new UndoableInsertEntries(bibDatabaseContext.getDatabase(), entries));
 
                 markBaseChanged(); // The database just changed.
                 if (Globals.prefs.getBoolean(JabRefPreferences.AUTO_OPEN_FORM)) {
-                    showAndEdit(bibEntry);
+                    showAndEdit(entries.get(0));
                 }
-                clearAndSelect(bibEntry);
+                clearAndSelect(entries.get(0));
             } catch (KeyCollisionException ex) {
-                LOGGER.info("Collision for bibtex key" + bibEntry.getId(), ex);
+                LOGGER.info("Collision for bibtex key" + ex.getId(), ex);
             }
         }
     }
@@ -1111,22 +1121,21 @@ public void searchAndOpen() {
     private class GroupTreeListener {
 
         @Subscribe
-        public void listen(EntryAddedEvent addedEntryEvent) {
-            // if the added entry is an undo don't add it to the current group
-            if (addedEntryEvent.getEntriesEventSource() == EntriesEventSource.UNDO) {
+        public void listen(EntriesAddedEvent addedEntriesEvent) {
+            // if the event is an undo, don't add it to the current group
+            if (addedEntriesEvent.getEntriesEventSource() == EntriesEventSource.UNDO) {
                 return;
             }
 
-            // Automatically add new entry to the selected group (or set of groups)
+            // Automatically add new entries to the selected group (or set of groups)
             if (Globals.prefs.getBoolean(JabRefPreferences.AUTO_ASSIGN_GROUP)) {
-                final List<BibEntry> entries = Collections.singletonList(addedEntryEvent.getBibEntry());
                 Globals.stateManager.getSelectedGroup(bibDatabaseContext).forEach(
-                        selectedGroup -> selectedGroup.addEntriesToGroup(entries));
+                        selectedGroup -> selectedGroup.addEntriesToGroup(addedEntriesEvent.getBibEntries()));
             }
         }
     }
 
-    private class EntryRemovedListener {
+    private class EntriesRemovedListener {
 
         @Subscribe
         public void listen(EntriesRemovedEvent entriesRemovedEvent) {
@@ -1141,8 +1150,8 @@ public void listen(EntriesRemovedEvent entriesRemovedEvent) {
     private class SearchAutoCompleteListener {
 
         @Subscribe
-        public void listen(EntryAddedEvent addedEntryEvent) {
-            DefaultTaskExecutor.runInJavaFXThread(() -> searchAutoCompleter.indexEntry(addedEntryEvent.getBibEntry()));
+        public void listen(EntriesAddedEvent addedEntriesEvent) {
+            DefaultTaskExecutor.runInJavaFXThread(() -> addedEntriesEvent.getBibEntries().forEach(entry -> searchAutoCompleter.indexEntry(entry)));
         }
 
         @Subscribe
@@ -1158,7 +1167,7 @@ public void listen(EntryChangedEvent entryChangedEvent) {
     private class SearchListener {
 
         @Subscribe
-        public void listen(EntryAddedEvent addedEntryEvent) {
+        public void listen(EntriesAddedEvent addedEntryEvent) {
             DefaultTaskExecutor.runInJavaFXThread(() -> frame.getGlobalSearchBar().performSearch());
         }
 

src/main/java/org/jabref/gui/autocompleter/AutoCompleteUpdater.java

@@ -1,6 +1,9 @@
 package org.jabref.gui.autocompleter;
 
-import org.jabref.model.database.event.EntryAddedEvent;
+import java.util.List;
+
+import org.jabref.model.database.event.EntriesAddedEvent;
+import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.event.EntryChangedEvent;
 
 import com.google.common.eventbus.Subscribe;
@@ -17,8 +20,11 @@ public AutoCompleteUpdater(SuggestionProviders suggestionProviders) {
     }
 
     @Subscribe
-    public void listen(EntryAddedEvent addedEntryEvent) {
-        suggestionProviders.indexEntry(addedEntryEvent.getBibEntry());
+    public void listen(EntriesAddedEvent entryAddedEvent) {
+        List<BibEntry> entries = entryAddedEvent.getBibEntries();
+        for (BibEntry entry : entries) {
+            suggestionProviders.indexEntry(entry);
+        }
     }
 
     @Subscribe

src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java

@@ -6,7 +6,7 @@
 import org.jabref.JabRefGUI;
 import org.jabref.gui.preview.PreviewViewer;
 import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableInsertEntry;
+import org.jabref.gui.undo.UndoableInsertEntries;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -26,7 +26,7 @@ public EntryAddChangeViewModel(BibEntry entry) {
     @Override
     public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
         database.getDatabase().insertEntry(entry);
-        undoEdit.addEdit(new UndoableInsertEntry(database.getDatabase(), entry));
+        undoEdit.addEdit(new UndoableInsertEntries(database.getDatabase(), entry));
     }
 
     @Override

src/main/java/org/jabref/gui/collab/EntryChangeViewModel.java

@@ -8,7 +8,7 @@
 import org.jabref.gui.mergeentries.MergeEntries;
 import org.jabref.gui.mergeentries.MergeEntries.DefaultRadioButtonSelectionMode;
 import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableInsertEntry;
+import org.jabref.gui.undo.UndoableInsertEntries;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -43,8 +43,8 @@ public EntryChangeViewModel(BibEntry entry, BibEntry newEntry, BibDatabaseContex
     public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
         database.getDatabase().removeEntry(oldEntry);
         database.getDatabase().insertEntry(mergePanel.getMergeEntry());
-        undoEdit.addEdit(new UndoableInsertEntry(database.getDatabase(), oldEntry));
-        undoEdit.addEdit(new UndoableInsertEntry(database.getDatabase(), mergePanel.getMergeEntry()));
+        undoEdit.addEdit(new UndoableInsertEntries(database.getDatabase(), oldEntry));
+        undoEdit.addEdit(new UndoableInsertEntries(database.getDatabase(), mergePanel.getMergeEntry()));
     }
 
     @Override

src/main/java/org/jabref/gui/duplicationFinder/DuplicateSearch.java

@@ -21,7 +21,7 @@
 import org.jabref.gui.duplicationFinder.DuplicateResolverDialog.DuplicateResolverResult;
 import org.jabref.gui.duplicationFinder.DuplicateResolverDialog.DuplicateResolverType;
 import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableInsertEntry;
+import org.jabref.gui.undo.UndoableInsertEntries;
 import org.jabref.gui.undo.UndoableRemoveEntries;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.DefaultTaskExecutor;
@@ -167,10 +167,8 @@ private void handleDuplicates(DuplicateSearchResult result) {
         }
         // and adding merged entries:
         if (!result.getToAdd().isEmpty()) {
-            for (BibEntry entry : result.getToAdd()) {
-                panel.getDatabase().insertEntry(entry);
-                compoundEdit.addEdit(new UndoableInsertEntry(panel.getDatabase(), entry));
-            }
+            compoundEdit.addEdit(new UndoableInsertEntries(panel.getDatabase(), result.getToAdd()));
+            panel.getDatabase().insertEntries(result.getToAdd());
             panel.markBaseChanged();
         }
 

src/main/java/org/jabref/gui/externalfiles/ImportHandler.java

@@ -12,7 +12,7 @@
 import org.jabref.gui.DialogService;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.undo.UndoableInsertEntry;
+import org.jabref.gui.undo.UndoableInsertEntries;
 import org.jabref.logic.bibtexkeypattern.BibtexKeyGenerator;
 import org.jabref.logic.externalfiles.ExternalFilesContentImporter;
 import org.jabref.logic.importer.ImportFormatPreferences;
@@ -94,7 +94,7 @@ public void importAsNewEntries(List<Path> files) {
             }
 
             importEntries(entriesToAdd);
-            entriesToAdd.forEach(entry -> ce.addEdit(new UndoableInsertEntry(database.getDatabase(), entry)));
+            ce.addEdit(new UndoableInsertEntries(database.getDatabase(), entriesToAdd));
         }
         ce.end();
         undoManager.addEdit(ce);
@@ -109,7 +109,7 @@ private BibEntry createEmptyEntryWithLink(Path file) {
 
     public void importEntries(List<BibEntry> entries) {
         //TODO: Add undo/redo
-        //ce.addEdit(new UndoableInsertEntry(panel.getDatabase(), entry));
+        //undoManager.addEdit(new UndoableInsertEntries(panel.getDatabase(), entries));
 
         database.getDatabase().insertEntries(entries);
 

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

@@ -4,7 +4,6 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.List;
 import java.util.Optional;
 import java.util.stream.Collectors;
@@ -135,9 +134,7 @@ private ParserResult mergeImportResults(List<ImportFormatReader.UnknownFormatImp
                     directParserResult = pr;
                 }
                 // Merge entries:
-                for (BibEntry entry : pr.getDatabase().getEntries()) {
-                    database.insertEntry(entry);
-                }
+                database.insertEntries(pr.getDatabase().getEntries());
 
                 // Merge strings:
                 for (BibtexString bs : pr.getDatabase().getStringValues()) {
@@ -151,16 +148,14 @@ private ParserResult mergeImportResults(List<ImportFormatReader.UnknownFormatImp
             } else {
 
                 ParserResult pr = importResult.parserResult;
-                Collection<BibEntry> entries = pr.getDatabase().getEntries();
+                List<BibEntry> entries = pr.getDatabase().getEntries();
 
                 anythingUseful = anythingUseful | !entries.isEmpty();
 
                 // set timestamp and owner
                 UpdateField.setAutomaticFields(entries, Globals.prefs.getUpdateFieldPreferences()); // set timestamp and owner
 
-                for (BibEntry entry : entries) {
-                    database.insertEntry(entry);
-                }
+                database.insertEntries(entries);
             }
         }
 

src/main/java/org/jabref/gui/importer/actions/AppendDatabaseAction.java

@@ -15,7 +15,7 @@
 import org.jabref.gui.actions.BaseAction;
 import org.jabref.gui.importer.AppendDatabaseDialog;
 import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableInsertEntry;
+import org.jabref.gui.undo.UndoableInsertEntries;
 import org.jabref.gui.undo.UndoableInsertString;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.FileDialogConfiguration;
@@ -59,8 +59,7 @@ private static void mergeFromBibtex(BasePanel panel, ParserResult parserResult,
                                         boolean importStrings, boolean importGroups, boolean importSelectorWords) throws KeyCollisionException {
 
         BibDatabase fromDatabase = parserResult.getDatabase();
-        List<BibEntry> appendedEntries = new ArrayList<>();
-        List<BibEntry> originalEntries = new ArrayList<>();
+        List<BibEntry> entriesToAppend = new ArrayList<>();
         BibDatabase database = panel.getDatabase();
 
         NamedCompound ce = new NamedCompound(Localization.lang("Append library"));
@@ -74,11 +73,10 @@ private static void mergeFromBibtex(BasePanel panel, ParserResult parserResult,
                 BibEntry entry = (BibEntry) originalEntry.clone();
                 UpdateField.setAutomaticFields(entry, overwriteOwner, overwriteTimeStamp,
                         Globals.prefs.getUpdateFieldPreferences());
-                database.insertEntry(entry);
-                appendedEntries.add(entry);
-                originalEntries.add(originalEntry);
-                ce.addEdit(new UndoableInsertEntry(database, entry));
+                entriesToAppend.add(entry);
             }
+            database.insertEntries(entriesToAppend);
+            ce.addEdit(new UndoableInsertEntries(database, entriesToAppend));
         }
 
         if (importStrings) {
@@ -99,7 +97,7 @@ private static void mergeFromBibtex(BasePanel panel, ParserResult parserResult,
                         ExplicitGroup group = new ExplicitGroup("Imported", GroupHierarchyType.INDEPENDENT,
                                 Globals.prefs.getKeywordDelimiter());
                         newGroups.setGroup(group);
-                        group.add(appendedEntries);
+                        group.add(entriesToAppend);
                     } catch (IllegalArgumentException e) {
                         LOGGER.error("Problem appending entries to group", e);
                     }

src/main/java/org/jabref/gui/maintable/MainTable.java

@@ -32,18 +32,14 @@
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.keyboard.KeyBinding;
 import org.jabref.gui.keyboard.KeyBindingRepository;
-import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableInsertEntry;
 import org.jabref.gui.util.ControlHelper;
 import org.jabref.gui.util.CustomLocalDragboard;
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.ViewModelTableRowFactory;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.util.UpdateField;
 import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.database.event.AllInsertsFinishedEvent;
+import org.jabref.model.database.event.EntriesAddedEvent;
 import org.jabref.model.entry.BibEntry;
-import org.jabref.preferences.JabRefPreferences;
 
 import com.google.common.eventbus.Subscribe;
 import org.slf4j.Logger;
@@ -130,8 +126,8 @@ public MainTable(MainTableDataModel model, JabRefFrame frame,
     }
 
     @Subscribe
-    public void listen(AllInsertsFinishedEvent event) {
-        DefaultTaskExecutor.runInJavaFXThread(() -> clearAndSelect(event.getBibEntry()));
+    public void listen(EntriesAddedEvent event) {
+        DefaultTaskExecutor.runInJavaFXThread(() -> clearAndSelect(event.getFirstEntry()));
     }
 
     public void clearAndSelect(BibEntry bibEntry) {
@@ -215,28 +211,8 @@ private void clearAndSelectLast() {
     public void paste() {
         // Find entries in clipboard
         List<BibEntry> entriesToAdd = Globals.clipboardManager.extractData();
-
+        panel.insertEntries(entriesToAdd);
         if (!entriesToAdd.isEmpty()) {
-            // Add new entries
-            NamedCompound ce = new NamedCompound((entriesToAdd.size() > 1 ? Localization.lang("paste entries") : Localization.lang("paste entry")));
-            for (BibEntry entryToAdd : entriesToAdd) {
-                UpdateField.setAutomaticFields(entryToAdd, Globals.prefs.getUpdateFieldPreferences());
-
-                database.getDatabase().insertEntry(entryToAdd);
-
-                ce.addEdit(new UndoableInsertEntry(database.getDatabase(), entryToAdd));
-            }
-            ce.end();
-            undoManager.addEdit(ce);
-
-            // Show editor if user want us to do this
-            BibEntry firstNewEntry = entriesToAdd.get(0);
-            if (Globals.prefs.getBoolean(JabRefPreferences.AUTO_OPEN_FORM)) {
-                panel.showAndEdit(firstNewEntry);
-            }
-
-            // Select and focus first new entry
-            clearAndSelect(firstNewEntry);
             this.requestFocus();
         }
     }