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Completely rework save operation (#4309)
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* Make FileHistory use Paths instead of strings

* Almost completely rewrite save infrastructure

* Fix build

* Fix tests

* Remove file lock

* Improve comments

* Fix build

* Implement feedback and fix tests

* Fix build
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@tobiasdiez
tobiasdiez committed Sep 13, 2018
1 parent c858a94 commit e83680f
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Showing 41 changed files with 1,035 additions and 1,784 deletions.
26 changes: 13 additions & 13 deletions src/jmh/java/org/jabref/benchmarks/Benchmarks.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,16 +2,15 @@

import java.io.IOException;
import java.io.StringReader;
import java.io.StringWriter;
import java.util.List;
import java.util.Random;
import java.util.stream.Collectors;

import org.jabref.Globals;
import org.jabref.logic.exporter.BibtexDatabaseWriter;
import org.jabref.logic.exporter.SavePreferences;
import org.jabref.logic.exporter.StringSaveSession;
import org.jabref.logic.formatter.bibtexfields.HtmlToLatexFormatter;
import org.jabref.logic.importer.ParseException;
import org.jabref.logic.importer.ParserResult;
import org.jabref.logic.importer.fileformat.BibtexParser;
import org.jabref.logic.layout.format.HTMLChars;
Expand All @@ -37,6 +36,8 @@
import org.openjdk.jmh.annotations.State;
import org.openjdk.jmh.runner.RunnerException;

import static org.mockito.Mockito.mock;

@State(Scope.Thread)
public class Benchmarks {

Expand All @@ -61,11 +62,11 @@ public void init() throws Exception {
entry.setField("rnd", "2" + randomizer.nextInt());
database.insertEntry(entry);
}
BibtexDatabaseWriter<StringSaveSession> databaseWriter = new BibtexDatabaseWriter<>(StringSaveSession::new);
StringSaveSession saveSession = databaseWriter.savePartOfDatabase(
new BibDatabaseContext(database, new MetaData(), new Defaults()), database.getEntries(),
new SavePreferences());
bibtexString = saveSession.getStringValue();
StringWriter outputWriter = new StringWriter();
BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(outputWriter, mock(SavePreferences.class));
databaseWriter.savePartOfDatabase(
new BibDatabaseContext(database, new MetaData(), new Defaults()), database.getEntries());
bibtexString = outputWriter.toString();

latexConversionString = "{A} \\textbf{bold} approach {\\it to} ${{\\Sigma}}{\\Delta}$ modulator \\textsuperscript{2} \\$";

Expand All @@ -80,11 +81,10 @@ public ParserResult parse() throws IOException {

@Benchmark
public String write() throws Exception {
BibtexDatabaseWriter<StringSaveSession> databaseWriter = new BibtexDatabaseWriter<>(StringSaveSession::new);
StringSaveSession saveSession = databaseWriter.savePartOfDatabase(
new BibDatabaseContext(database, new MetaData(), new Defaults()), database.getEntries(),
new SavePreferences());
return saveSession.getStringValue();
StringWriter outputWriter = new StringWriter();
BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(outputWriter, mock(SavePreferences.class));
databaseWriter.savePartOfDatabase(new BibDatabaseContext(database, new MetaData(), new Defaults()), database.getEntries());
return outputWriter.toString();
}

@Benchmark
Expand Down Expand Up @@ -125,7 +125,7 @@ public String htmlToLatexConversion() {
}

@Benchmark
public boolean keywordGroupContains() throws ParseException {
public boolean keywordGroupContains() {
KeywordGroup group = new WordKeywordGroup("testGroup", GroupHierarchyType.INDEPENDENT, "keyword", "testkeyword", false, ',', false);
return group.containsAll(database.getEntries());
}
Expand Down
70 changes: 25 additions & 45 deletions src/main/java/org/jabref/cli/ArgumentProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,14 +16,12 @@
import org.jabref.JabRefException;
import org.jabref.gui.externalfiles.AutoSetLinks;
import org.jabref.logic.bibtexkeypattern.BibtexKeyGenerator;
import org.jabref.logic.exporter.AtomicFileWriter;
import org.jabref.logic.exporter.BibDatabaseWriter;
import org.jabref.logic.exporter.BibtexDatabaseWriter;
import org.jabref.logic.exporter.Exporter;
import org.jabref.logic.exporter.ExporterFactory;
import org.jabref.logic.exporter.FileSaveSession;
import org.jabref.logic.exporter.SaveException;
import org.jabref.logic.exporter.SavePreferences;
import org.jabref.logic.exporter.SaveSession;
import org.jabref.logic.exporter.TemplateExporter;
import org.jabref.logic.importer.FetcherException;
import org.jabref.logic.importer.ImportException;
Expand Down Expand Up @@ -374,27 +372,7 @@ private boolean generateAux(List<ParserResult> loaded, String[] data) {
// write an output, if something could be resolved
if ((newBase != null) && newBase.hasEntries()) {
String subName = StringUtil.getCorrectFileName(data[1], "bib");

try {
System.out.println(Localization.lang("Saving") + ": " + subName);
SavePreferences prefs = Globals.prefs.loadForSaveFromPreferences();
BibDatabaseWriter<SaveSession> databaseWriter = new BibtexDatabaseWriter<>(FileSaveSession::new);
Defaults defaults = new Defaults(Globals.prefs.getDefaultBibDatabaseMode());
SaveSession session = databaseWriter.saveDatabase(new BibDatabaseContext(newBase, defaults), prefs);

// Show just a warning message if encoding did not work for all characters:
if (!session.getWriter().couldEncodeAll()) {
System.err.println(Localization.lang("Warning") + ": "
+ Localization.lang(
"The chosen encoding '%0' could not encode the following characters:",
session.getEncoding().displayName())
+ " " + session.getWriter().getProblemCharacters());
}
session.commit(subName);
} catch (SaveException ex) {
System.err.println(Localization.lang("Could not save file.") + "\n" + ex.getLocalizedMessage());
}

saveDatabase(newBase, subName);
notSavedMsg = true;
}

Expand All @@ -407,34 +385,36 @@ private boolean generateAux(List<ParserResult> loaded, String[] data) {
}
}

private void saveDatabase(BibDatabase newBase, String subName) {
try {
System.out.println(Localization.lang("Saving") + ": " + subName);
SavePreferences prefs = Globals.prefs.loadForSaveFromPreferences();
AtomicFileWriter fileWriter = new AtomicFileWriter(Paths.get(subName), prefs.getEncoding());
BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(fileWriter, prefs);
Defaults defaults = new Defaults(Globals.prefs.getDefaultBibDatabaseMode());
databaseWriter.saveDatabase(new BibDatabaseContext(newBase, defaults));

// Show just a warning message if encoding did not work for all characters:
if (fileWriter.hasEncodingProblems()) {
System.err.println(Localization.lang("Warning") + ": "
+ Localization.lang(
"The chosen encoding '%0' could not encode the following characters:",
prefs.getEncoding().displayName())
+ " " + fileWriter.getEncodingProblems());
}
} catch (IOException ex) {
System.err.println(Localization.lang("Could not save file.") + "\n" + ex.getLocalizedMessage());
}
}

private void exportFile(List<ParserResult> loaded, String[] data) {
if (data.length == 1) {
// This signals that the latest import should be stored in BibTeX
// format to the given file.
if (!loaded.isEmpty()) {
ParserResult pr = loaded.get(loaded.size() - 1);
if (!pr.isInvalid()) {
try {
System.out.println(Localization.lang("Saving") + ": " + data[0]);
SavePreferences prefs = Globals.prefs.loadForSaveFromPreferences();
Defaults defaults = new Defaults(Globals.prefs.getDefaultBibDatabaseMode());
BibDatabaseWriter<SaveSession> databaseWriter = new BibtexDatabaseWriter<>(
FileSaveSession::new);
SaveSession session = databaseWriter.saveDatabase(
new BibDatabaseContext(pr.getDatabase(), pr.getMetaData(), defaults), prefs);

// Show just a warning message if encoding did not work for all characters:
if (!session.getWriter().couldEncodeAll()) {
System.err.println(Localization.lang("Warning") + ": "
+ Localization.lang(
"The chosen encoding '%0' could not encode the following characters:",
session.getEncoding().displayName())
+ " " + session.getWriter().getProblemCharacters());
}
session.commit(data[0]);
} catch (SaveException ex) {
System.err.println(Localization.lang("Could not save file.") + "\n" + ex.getLocalizedMessage());
}
saveDatabase(pr.getDatabase(), data[0]);
}
} else {
System.err.println(Localization.lang("The output option depends on a valid import option."));
Expand Down
153 changes: 4 additions & 149 deletions src/main/java/org/jabref/gui/BasePanel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,6 @@
import java.io.IOException;
import java.io.StringReader;
import java.lang.reflect.InvocationTargetException;
import java.nio.charset.Charset;
import java.nio.charset.UnsupportedCharsetException;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.Collections;
Expand All @@ -17,8 +15,6 @@
import java.util.Set;
import java.util.stream.Collectors;

import javax.swing.JOptionPane;
import javax.swing.JTextArea;
import javax.swing.SwingUtilities;
import javax.swing.undo.CannotRedoException;
import javax.swing.undo.CannotUndoException;
Expand Down Expand Up @@ -73,27 +69,17 @@
import org.jabref.gui.undo.UndoableChangeType;
import org.jabref.gui.undo.UndoableFieldChange;
import org.jabref.gui.undo.UndoableInsertEntry;
import org.jabref.gui.undo.UndoableKeyChange;
import org.jabref.gui.undo.UndoableRemoveEntry;
import org.jabref.gui.util.DefaultTaskExecutor;
import org.jabref.gui.util.FileDialogConfiguration;
import org.jabref.gui.worker.CitationStyleToClipboardWorker;
import org.jabref.gui.worker.SendAsEMailAction;
import org.jabref.logic.bibtexkeypattern.BibtexKeyGenerator;
import org.jabref.logic.citationstyle.CitationStyleCache;
import org.jabref.logic.citationstyle.CitationStyleOutputFormat;
import org.jabref.logic.exporter.BibtexDatabaseWriter;
import org.jabref.logic.exporter.FileSaveSession;
import org.jabref.logic.exporter.SaveException;
import org.jabref.logic.exporter.SavePreferences;
import org.jabref.logic.exporter.SaveSession;
import org.jabref.logic.l10n.Encodings;
import org.jabref.logic.l10n.Localization;
import org.jabref.logic.layout.Layout;
import org.jabref.logic.layout.LayoutHelper;
import org.jabref.logic.pdf.FileAnnotationCache;
import org.jabref.logic.search.SearchQuery;
import org.jabref.logic.util.StandardFileType;
import org.jabref.logic.util.UpdateField;
import org.jabref.logic.util.io.FileFinder;
import org.jabref.logic.util.io.FileFinders;
Expand All @@ -116,13 +102,10 @@
import org.jabref.model.entry.event.EntryEventSource;
import org.jabref.model.entry.specialfields.SpecialField;
import org.jabref.model.entry.specialfields.SpecialFieldValue;
import org.jabref.model.strings.StringUtil;
import org.jabref.preferences.JabRefPreferences;
import org.jabref.preferences.PreviewPreferences;

import com.google.common.eventbus.Subscribe;
import com.jgoodies.forms.builder.FormBuilder;
import com.jgoodies.forms.layout.FormLayout;
import org.fxmisc.easybind.EasyBind;
import org.fxmisc.easybind.Subscription;
import org.slf4j.Logger;
Expand Down Expand Up @@ -298,11 +281,11 @@ private void setupActions() {
actions.put(Actions.EDIT, this::showAndEdit);

// The action for saving a database.
actions.put(Actions.SAVE, saveAction);
actions.put(Actions.SAVE, saveAction::save);

actions.put(Actions.SAVE_AS, saveAction::saveAs);

actions.put(Actions.SAVE_SELECTED_AS_PLAIN, new SaveSelectedAction(SavePreferences.DatabaseSaveType.PLAIN_BIBTEX));
actions.put(Actions.SAVE_SELECTED_AS_PLAIN, saveAction::saveSelectedAsPlain);

// The action for copying selected entries.
actions.put(Actions.COPY, this::copy);
Expand Down Expand Up @@ -670,87 +653,9 @@ public void runCommand(final Actions command) {
}
}

/**
* FIXME: high code duplication with {@link SaveDatabaseAction#saveDatabase(File, boolean, Charset)}
*/
private boolean saveDatabase(File file, boolean selectedOnly, Charset encoding,
SavePreferences.DatabaseSaveType saveType)
throws SaveException {
SaveSession session;
final String SAVE_DATABASE = Localization.lang("Save library");
try {
SavePreferences prefs = Globals.prefs.loadForSaveFromPreferences()
.withEncoding(encoding)
.withSaveType(saveType);

BibtexDatabaseWriter<SaveSession> databaseWriter = new BibtexDatabaseWriter<>(
FileSaveSession::new);
if (selectedOnly) {
session = databaseWriter.savePartOfDatabase(bibDatabaseContext, mainTable.getSelectedEntries(), prefs);
} else {
session = databaseWriter.saveDatabase(bibDatabaseContext, prefs);
}

registerUndoableChanges(session);
}
// FIXME: not sure if this is really thrown anywhere
catch (UnsupportedCharsetException ex) {
frame.getDialogService().showErrorDialogAndWait(Localization.lang("Save library"), Localization.lang("Could not save file.")
+ Localization.lang("Character encoding '%0' is not supported.", encoding.displayName()));
throw new SaveException("rt");
} catch (SaveException ex) {
if (ex.specificEntry()) {
// Error occurred during processing of the entry. Highlight it:
clearAndSelect(ex.getEntry());
showAndEdit(ex.getEntry());
} else {
LOGGER.warn("Could not save", ex);
}

dialogService.showErrorDialogAndWait(SAVE_DATABASE, Localization.lang("Could not save file."), ex);
throw new SaveException("rt");
}

boolean commit = true;
if (!session.getWriter().couldEncodeAll()) {
FormBuilder builder = FormBuilder.create()
.layout(new FormLayout("left:pref, 4dlu, fill:pref", "pref, 4dlu, pref"));
JTextArea ta = new JTextArea(session.getWriter().getProblemCharacters());
ta.setEditable(false);
builder.add(Localization.lang("The chosen encoding '%0' could not encode the following characters:", session.getEncoding().displayName())).xy(1, 1);
builder.add(ta).xy(3, 1);
builder.add(Localization.lang("What do you want to do?")).xy(1, 3);
String tryDiff = Localization.lang("Try different encoding");
int answer = JOptionPane.showOptionDialog(null, builder.getPanel(), SAVE_DATABASE, JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.WARNING_MESSAGE, null, new String[] {Localization.lang("Save"), tryDiff, Localization.lang("Cancel")}, tryDiff);

if (answer == JOptionPane.NO_OPTION) {

// The user wants to use another encoding.
Object choice = JOptionPane.showInputDialog(null, Localization.lang("Select encoding"), SAVE_DATABASE, JOptionPane.QUESTION_MESSAGE, null, Encodings.ENCODINGS_DISPLAYNAMES, encoding);
if (choice == null) {
commit = false;
} else {
Charset newEncoding = Charset.forName((String) choice);
return saveDatabase(file, selectedOnly, newEncoding, saveType);
}
} else if (answer == JOptionPane.CANCEL_OPTION) {
commit = false;
}
}

if (commit) {
session.commit(file.toPath());
this.bibDatabaseContext.getMetaData().setEncoding(encoding); // Make sure to remember which encoding we used.
} else {
session.cancel();
}

return commit;
}

public void registerUndoableChanges(SaveSession session) {
public void registerUndoableChanges(List<FieldChange> changes) {
NamedCompound ce = new NamedCompound(Localization.lang("Save actions"));
for (FieldChange change : session.getFieldChanges()) {
for (FieldChange change : changes) {
ce.addEdit(new UndoableFieldChange(change));
}
ce.end();
Expand Down Expand Up @@ -1207,30 +1112,6 @@ public boolean showDeleteConfirmationDialog(int numberOfEntries) {
}
}

/**
* If the relevant option is set, autogenerate keys for all entries that are lacking keys.
*/
public void autoGenerateKeysBeforeSaving() {
if (Globals.prefs.getBoolean(JabRefPreferences.GENERATE_KEYS_BEFORE_SAVING)) {
NamedCompound ce = new NamedCompound(Localization.lang("Autogenerate BibTeX keys"));

BibtexKeyGenerator keyGenerator = new BibtexKeyGenerator(bibDatabaseContext, Globals.prefs.getBibtexKeyPatternPreferences());
for (BibEntry bes : bibDatabaseContext.getDatabase().getEntries()) {
Optional<String> oldKey = bes.getCiteKeyOptional();
if (StringUtil.isBlank(oldKey)) {
Optional<FieldChange> change = keyGenerator.generateAndSetKey(bes);
change.ifPresent(fieldChange -> ce.addEdit(new UndoableKeyChange(fieldChange)));
}
}

// Store undo information, if any:
if (ce.hasEdits()) {
ce.end();
getUndoManager().addEdit(ce);
}
}
}

/**
* Depending on whether a preview or an entry editor is showing, save the current divider location in the correct preference setting.
*/
Expand Down Expand Up @@ -1597,30 +1478,4 @@ public void action() {
preview.print();
}
}

private class SaveSelectedAction implements BaseAction {

private final SavePreferences.DatabaseSaveType saveType;

public SaveSelectedAction(SavePreferences.DatabaseSaveType saveType) {
this.saveType = saveType;
}

@Override
public void action() throws SaveException {
FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
.withDefaultExtension(StandardFileType.BIBTEX_DB)
.addExtensionFilter(String.format("%1s %2s", "BibTex", Localization.lang("Library")), StandardFileType.BIBTEX_DB)
.withInitialDirectory(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY))
.build();

Optional<Path> chosenFile = dialogService.showFileSaveDialog(fileDialogConfiguration);
if (chosenFile.isPresent()) {
Path path = chosenFile.get();
saveDatabase(path.toFile(), true, Globals.prefs.getDefaultEncoding(), saveType);
frame.getFileHistory().newFile(path.toString());
frame.output(Localization.lang("Saved selected to '%0'.", path.toString()));
}
}
}
}
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