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Towards hierarchical keywords (#1950)
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* Small code cleanup in SpecialFieldsUtils

* Refactor code related to keywords

* Move StringUtil to model and remove EntryUtil

* Add a few more tests

* Change keyword delemiter in groups to Character

* Optimize imports

* Removed unused keyword separator in shareddb ui manager

* Fix build errors

* Fix failing architecture tests

* Reformat imports

* Small renamings

* Move from Inheritance to composition in KeywordList

* Fix tests

* ArXiv accepts import format preferences instead of keyword delimiter

* Fix binding

* Fix arXiv tests
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@tobiasdiez
tobiasdiez authored Sep 24, 2016
1 parent 03a1e46 commit 6ae86ae
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Showing 86 changed files with 1,104 additions and 672 deletions.
2 changes: 1 addition & 1 deletion src/databaseTest/java/net/sf/jabref/shared/DBMSSynchronizerTest.java
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Expand Up @@ -46,7 +46,7 @@ public void setUp() throws SQLException, DatabaseNotSupportedException {
BibDatabaseContext context = new BibDatabaseContext(bibDatabase);


dbmsSynchronizer = new DBMSSynchronizer(context, ", ");
dbmsSynchronizer = new DBMSSynchronizer(context, ',');
dbmsProcessor = DBMSProcessor.getProcessorInstance(dbmsConnection);

bibDatabase.registerListener(dbmsSynchronizer);
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4 changes: 2 additions & 2 deletions src/databaseTest/java/net/sf/jabref/shared/SynchronizationTestSimulator.java
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Expand Up @@ -37,10 +37,10 @@ public class SynchronizationTestSimulator {
public void setUp() throws SQLException, DatabaseNotSupportedException {
this.dbmsConnection = TestConnector.getTestDBMSConnection(dbmsType);

clientContextA = new BibDatabaseContext(new Defaults(BibDatabaseMode.BIBTEX), DatabaseLocation.SHARED, ", ");
clientContextA = new BibDatabaseContext(new Defaults(BibDatabaseMode.BIBTEX), DatabaseLocation.SHARED, ',');
clientContextA.getDBMSSynchronizer().openSharedDatabase(dbmsConnection);

clientContextB = new BibDatabaseContext(new Defaults(BibDatabaseMode.BIBTEX), DatabaseLocation.SHARED, ", ");
clientContextB = new BibDatabaseContext(new Defaults(BibDatabaseMode.BIBTEX), DatabaseLocation.SHARED, ',');
clientContextB.getDBMSSynchronizer().openSharedDatabase(dbmsConnection);
eventListenerB = new SynchronizationTestEventListener();
clientContextB.getDBMSSynchronizer().registerListener(eventListenerB);
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4 changes: 2 additions & 2 deletions src/integrationTest/java/net/sf/jabref/gui/ParameterizedMenuNewEntryTest.java
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Expand Up @@ -3,7 +3,7 @@
import java.util.Arrays;
import java.util.Collection;

import net.sf.jabref.model.entry.EntryUtil;
import net.sf.jabref.model.strings.StringUtil;

import org.assertj.swing.fixture.JTableFixture;
import org.junit.Ignore;
Expand Down Expand Up @@ -31,7 +31,7 @@ public void addEntryOfGivenType() {
JTableFixture entryTable = mainFrame.table();

entryTable.requireRowCount(0);
mainFrame.menuItemWithPath("BibTeX", "New entry by type...", EntryUtil.capitalizeFirst(entryType)).click();
mainFrame.menuItemWithPath("BibTeX", "New entry by type...", StringUtil.capitalizeFirst(entryType)).click();
entryTable.requireRowCount(1);
}

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2 changes: 1 addition & 1 deletion src/jmh/java/net/sf/jabref/benchmarks/Benchmarks.java
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Expand Up @@ -125,7 +125,7 @@ public String htmlToLatexConversion() {
@Benchmark
public boolean keywordGroupContains() throws ParseException {
KeywordGroup group = new KeywordGroup("testGroup", "keyword", "testkeyword", false, false,
GroupHierarchyType.INDEPENDENT, ", ");
GroupHierarchyType.INDEPENDENT, ',');
return group.containsAll(database.getEntries());
}

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4 changes: 1 addition & 3 deletions src/main/java/net/sf/jabref/JabRefGUI.java
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Expand Up @@ -200,10 +200,8 @@ private void openWindow() {
boolean isSharedDatabaseEdited = Globals.prefs.getBoolean(JabRefPreferences.SHARED_DATABASE_LAST_EDITED);
if (isSharedDatabaseEdited) {
boolean isFocused = Globals.prefs.getBoolean(JabRefPreferences.SHARED_DATABASE_LAST_FOCUSED);
String keywordSeparator = Globals.prefs.get(JabRefPreferences.KEYWORD_SEPARATOR);

try {
new SharedDatabaseUIManager(mainFrame, keywordSeparator).openLastSharedDatabaseTab(isFocused);
new SharedDatabaseUIManager(mainFrame).openLastSharedDatabaseTab(isFocused);
} catch (SQLException | DatabaseNotSupportedException e) {
LOGGER.info("Failed to restore shared database. Use connection dialog to connect.");
new OpenSharedDatabaseDialog(mainFrame).setVisible(true);
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3 changes: 2 additions & 1 deletion src/main/java/net/sf/jabref/gui/BasePanel.java
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Expand Up @@ -2397,7 +2397,8 @@ public Optional<String> searchAndOpen() {
Map<BibEntry, List<File>> result;
if (Globals.prefs.getBoolean(JabRefPreferences.AUTOLINK_USE_REG_EXP_SEARCH_KEY)) {
String regExp = Globals.prefs.get(JabRefPreferences.REG_EXP_SEARCH_EXPRESSION_KEY);
result = RegExpFileSearch.findFilesForSet(entries, extensions, dirs, regExp);
result = RegExpFileSearch.findFilesForSet(entries, extensions, dirs, regExp,
Globals.prefs.getKeywordDelimiter());
} else {
boolean autoLinkExactKeyOnly = Globals.prefs.getBoolean(JabRefPreferences.AUTOLINK_EXACT_KEY_ONLY);
result = FileUtil.findAssociatedFiles(entries, extensions, dirs, autoLinkExactKeyOnly);
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12 changes: 6 additions & 6 deletions src/main/java/net/sf/jabref/gui/EntryCustomizationDialog.java
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Expand Up @@ -38,8 +38,8 @@
import net.sf.jabref.model.entry.BibEntry;
import net.sf.jabref.model.entry.CustomEntryType;
import net.sf.jabref.model.entry.EntryType;
import net.sf.jabref.model.entry.EntryUtil;
import net.sf.jabref.model.entry.InternalBibtexFields;
import net.sf.jabref.model.strings.StringUtil;

import com.jgoodies.forms.builder.ButtonBarBuilder;

Expand Down Expand Up @@ -259,7 +259,7 @@ private void applyChanges() {

if (defaulted.contains(stringListEntry.getKey())) {
// This type should be reverted to its default setup.
String nm = EntryUtil.capitalizeFirst(stringListEntry.getKey());
String nm = StringUtil.capitalizeFirst(stringListEntry.getKey());
EntryTypes.removeType(nm, bibDatabaseMode);

updateTypesForEntries(nm);
Expand All @@ -284,8 +284,8 @@ private void applyChanges() {

if (changesMade) {
CustomEntryType typ = biblatexMode ?
new CustomEntryType(EntryUtil.capitalizeFirst(stringListEntry.getKey()), reqStr, optStr, opt2Str) :
new CustomEntryType(EntryUtil.capitalizeFirst(stringListEntry.getKey()), reqStr, optStr);
new CustomEntryType(StringUtil.capitalizeFirst(stringListEntry.getKey()), reqStr, optStr, opt2Str) :
new CustomEntryType(StringUtil.capitalizeFirst(stringListEntry.getKey()), reqStr, optStr);

EntryTypes.addOrModifyCustomEntryType(typ);
updateTypesForEntries(typ.getName());
Expand Down Expand Up @@ -319,14 +319,14 @@ private void typeDeletion(String name) {
+ "type will be declared "
+ "typeless. Continue?"),
Localization.lang("Delete custom format") +
" '" + EntryUtil.capitalizeFirst(name) + '\'', JOptionPane.YES_NO_OPTION,
" '" + StringUtil.capitalizeFirst(name) + '\'', JOptionPane.YES_NO_OPTION,
JOptionPane.WARNING_MESSAGE);
if (reply != JOptionPane.YES_OPTION) {
return;
}
}
EntryTypes.removeType(name, bibDatabaseMode);
updateTypesForEntries(EntryUtil.capitalizeFirst(name));
updateTypesForEntries(StringUtil.capitalizeFirst(name));
changed.remove(name);
reqLists.remove(name);
optLists.remove(name);
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112 changes: 55 additions & 57 deletions src/main/java/net/sf/jabref/gui/actions/ManageKeywordsAction.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,8 @@
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.TreeSet;

import javax.swing.AbstractAction;
import javax.swing.Action;
Expand Down Expand Up @@ -40,7 +37,9 @@
import net.sf.jabref.model.FieldChange;
import net.sf.jabref.model.entry.BibEntry;
import net.sf.jabref.model.entry.FieldName;
import net.sf.jabref.preferences.JabRefPreferences;
import net.sf.jabref.model.entry.Keyword;
import net.sf.jabref.model.entry.KeywordList;
import net.sf.jabref.model.strings.StringUtil;
import net.sf.jabref.specialfields.Printed;
import net.sf.jabref.specialfields.Priority;
import net.sf.jabref.specialfields.Quality;
Expand All @@ -64,14 +63,14 @@ public class ManageKeywordsAction extends MnemonicAwareAction {
private JDialog diag;


private DefaultListModel<String> keywordListModel;
private DefaultListModel<Keyword> keywordListModel;

private JRadioButton intersectKeywords;
private JRadioButton mergeKeywords;

private boolean canceled;

private final Set<String> sortedKeywordsOfAllEntriesBeforeUpdateByUser = new TreeSet<>();
private final KeywordList sortedKeywordsOfAllEntriesBeforeUpdateByUser = new KeywordList();


public ManageKeywordsAction(JabRefFrame frame) {
Expand All @@ -87,7 +86,7 @@ private void createDialog() {
JTextField keyword = new JTextField();

keywordListModel = new DefaultListModel<>();
JList<String> keywordList = new JList<>(keywordListModel);
JList<Keyword> keywordList = new JList<>(keywordListModel);
keywordList.setVisibleRowCount(8);
JScrollPane kPane = new JScrollPane(keywordList);

Expand Down Expand Up @@ -149,9 +148,9 @@ public void actionPerformed(ActionEvent e) {

final ActionListener removeActionListenter = arg0 -> {
// keywordList.getSelectedIndices(); does not work, therefore we operate on the values
List<String> values = keywordList.getSelectedValuesList();
List<Keyword> values = keywordList.getSelectedValuesList();

for (String val : values) {
for (Keyword val : values) {
keywordListModel.removeElement(val);
}
};
Expand Down Expand Up @@ -213,29 +212,33 @@ public void keyPressed(KeyEvent e) {
diag.getContentPane().add(bb.getPanel(), BorderLayout.SOUTH);
}

private void addButtonActionListener(JTextField keyword) {
String text = keyword.getText().trim();
if (!text.isEmpty()) {
if (keywordListModel.isEmpty()) {
keywordListModel.addElement(text);
private void addButtonActionListener(JTextField keywordTextField) {
if (StringUtil.isBlank(keywordTextField.getText())) {
return; // nothing to add
}


Keyword newKeyword = new Keyword(keywordTextField.getText().trim());
if (keywordListModel.isEmpty()) {
keywordListModel.addElement(newKeyword);
} else {
int idx = 0;
Keyword element = keywordListModel.getElementAt(idx);
while ((idx < keywordListModel.size()) && (element.compareTo(newKeyword) < 0)) {
idx++;
}
if (idx == keywordListModel.size()) {
// list is empty or word is greater than last word in list
keywordListModel.addElement(newKeyword);
} else if (element.compareTo(newKeyword) == 0) {
// nothing to do, word already in table
} else {
int idx = 0;
String element = keywordListModel.getElementAt(idx);
while ((idx < keywordListModel.size()) && (element.compareTo(text) < 0)) {
idx++;
}
if (idx == keywordListModel.size()) {
// list is empty or word is greater than last word in list
keywordListModel.addElement(text);
} else if (element.compareTo(text) == 0) {
// nothing to do, word already in table
} else {
keywordListModel.add(idx, text);
}
keywordListModel.add(idx, newKeyword);
}
keyword.setText(null);
keyword.requestFocusInWindow();
}
keywordTextField.setText(null);
keywordTextField.requestFocusInWindow();

}

@Override
Expand Down Expand Up @@ -263,19 +266,19 @@ public void actionPerformed(ActionEvent e) {
return;
}

Set<String> keywordsToAdd = new HashSet<>();
Set<String> userSelectedKeywords = new HashSet<>();
KeywordList keywordsToAdd = new KeywordList();
KeywordList userSelectedKeywords = new KeywordList();
// build keywordsToAdd and userSelectedKeywords in parallel
for (Enumeration<String> keywords = keywordListModel.elements(); keywords.hasMoreElements();) {
String keyword = keywords.nextElement();
for (Enumeration<Keyword> keywords = keywordListModel.elements(); keywords.hasMoreElements();) {
Keyword keyword = keywords.nextElement();
userSelectedKeywords.add(keyword);
if (!sortedKeywordsOfAllEntriesBeforeUpdateByUser.contains(keyword)) {
keywordsToAdd.add(keyword);
}
}

Set<String> keywordsToRemove = new HashSet<>();
for (String kword : sortedKeywordsOfAllEntriesBeforeUpdateByUser) {
KeywordList keywordsToRemove = new KeywordList();
for (Keyword kword : sortedKeywordsOfAllEntriesBeforeUpdateByUser) {
if (!userSelectedKeywords.contains(kword)) {
keywordsToRemove.add(kword);
}
Expand All @@ -295,19 +298,18 @@ public void actionPerformed(ActionEvent e) {
bp.markBaseChanged();
}

private NamedCompound updateKeywords(List<BibEntry> entries, Set<String> keywordsToAdd,
Set<String> keywordsToRemove) {
private NamedCompound updateKeywords(List<BibEntry> entries, KeywordList keywordsToAdd,
KeywordList keywordsToRemove) {
NamedCompound ce = new NamedCompound(Localization.lang("Update keywords"));
for (BibEntry entry : entries) {
Set<String> keywords = entry.getKeywords();
KeywordList keywords = entry.getKeywords(Globals.prefs.getKeywordDelimiter());

// update keywords
keywords.removeAll(keywordsToRemove);
keywords.addAll(keywordsToAdd);

// put keywords back
Optional<FieldChange> change = entry.putKeywords(keywords,
Globals.prefs.get(JabRefPreferences.KEYWORD_SEPARATOR));
Optional<FieldChange> change = entry.putKeywords(keywords, Globals.prefs.getKeywordDelimiter());
if (change.isPresent()) {
ce.addEdit(new UndoableFieldChange(change.get()));
}
Expand All @@ -320,61 +322,57 @@ private NamedCompound updateKeywords(List<BibEntry> entries, Set<String> keyword
return ce;
}

private void synchronizeSpecialFields(Set<String> keywordsToAdd, Set<String> keywordsToRemove) {
private void synchronizeSpecialFields(KeywordList keywordsToAdd, KeywordList keywordsToRemove) {
// we need to check whether a special field is added
// for each field:
// check if something is added
// if yes, add all keywords of that special fields to the keywords to be removed

Set<String> clone;
KeywordList clone;

// Priority
clone = createClone(keywordsToAdd);
clone = keywordsToAdd.createClone();
clone.retainAll(Priority.getInstance().getKeyWords());
if (!clone.isEmpty()) {
keywordsToRemove.addAll(Priority.getInstance().getKeyWords());
}

// Quality
clone = createClone(keywordsToAdd);
clone = keywordsToAdd.createClone();
clone.retainAll(Quality.getInstance().getKeyWords());
if (!clone.isEmpty()) {
keywordsToRemove.addAll(Quality.getInstance().getKeyWords());
}

// Rank
clone = createClone(keywordsToAdd);
clone = keywordsToAdd.createClone();
clone.retainAll(Rank.getInstance().getKeyWords());
if (!clone.isEmpty()) {
keywordsToRemove.addAll(Rank.getInstance().getKeyWords());
}

// Relevance
clone = createClone(keywordsToAdd);
clone = keywordsToAdd.createClone();
clone.retainAll(Relevance.getInstance().getKeyWords());
if (!clone.isEmpty()) {
keywordsToRemove.addAll(Relevance.getInstance().getKeyWords());
}

// Read status
clone = createClone(keywordsToAdd);
clone = keywordsToAdd.createClone();
clone.retainAll(ReadStatus.getInstance().getKeyWords());
if (!clone.isEmpty()) {
keywordsToRemove.addAll(ReadStatus.getInstance().getKeyWords());
}

// Printed
clone = createClone(keywordsToAdd);
clone = keywordsToAdd.createClone();
clone.retainAll(Printed.getInstance().getKeyWords());
if (!clone.isEmpty()) {
keywordsToRemove.addAll(Printed.getInstance().getKeyWords());
}
}

private static Set<String> createClone(Set<String> keywordsToAdd) {
return new HashSet<>(keywordsToAdd);
}

private void fillKeyWordList() {
BasePanel bp = frame.getCurrentBasePanel();
List<BibEntry> entries = bp.getSelectedEntries();
Expand All @@ -385,27 +383,27 @@ private void fillKeyWordList() {

if (mergeKeywords.isSelected()) {
for (BibEntry entry : entries) {
Set<String> separatedKeywords = entry.getKeywords();
KeywordList separatedKeywords = entry.getKeywords(Globals.prefs.getKeywordDelimiter());
sortedKeywordsOfAllEntriesBeforeUpdateByUser.addAll(separatedKeywords);
}
} else {
assert intersectKeywords.isSelected();

// all keywords from first entry have to be added
BibEntry firstEntry = entries.get(0);
Set<String> separatedKeywords = firstEntry.getKeywords();
KeywordList separatedKeywords = firstEntry.getKeywords(Globals.prefs.getKeywordDelimiter());
sortedKeywordsOfAllEntriesBeforeUpdateByUser.addAll(separatedKeywords);

// for the remaining entries, intersection has to be used
// this approach ensures that one empty keyword list leads to an empty set of common keywords
for (int i = 1; i < entries.size(); i++) {
BibEntry entry = entries.get(i);
separatedKeywords = entry.getKeywords();
separatedKeywords = entry.getKeywords(Globals.prefs.getKeywordDelimiter());
sortedKeywordsOfAllEntriesBeforeUpdateByUser.retainAll(separatedKeywords);
}
}
for (String s : sortedKeywordsOfAllEntriesBeforeUpdateByUser) {
keywordListModel.addElement(s);
for (Keyword keyword : sortedKeywordsOfAllEntriesBeforeUpdateByUser) {
keywordListModel.addElement(keyword);
}
}

Expand Down
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