Add "Look up DOIs" to Quality menu

CHANGELOG.md

@@ -47,7 +47,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - The `Move linked files to default file directory`-Cleanup operation respects the `File directory pattern` setting 
 - We separated the `Move file` and `Rename Pdfs` logic and context menu entries in the `General`-Tab for the Field `file` to improve the semantics
 - A scrollbar was added to the cleanup panel, as a result of issue [#2501](https://github.com/JabRef/jabref/issues/2501)
-- Using "Look up DOIs" in the quality menu, it is possible to look up DOIs for multiple entries.
+- Using "Look up document identifier" in the quality menu, it is possible to look up DOIs and other identifiers for multiple entries.
 - F4 opens selected file in current JTable context not just from selected entry inside the main table [#2355](https://github.com/JabRef/jabref/issues/2355)
 - We added an option to copy the title of BibTeX entries to the clipboard through `Edit -> Copy title` (implements [#210](https://github.com/koppor/jabref/issues/210))
 - Several scrollbars were added to the preference dialog which show up when content is too large [#2559](https://github.com/JabRef/jabref/issues/2559)

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

@@ -94,7 +94,6 @@
 import org.jabref.gui.worker.AbstractWorker;
 import org.jabref.gui.worker.CallBack;
 import org.jabref.gui.worker.CitationStyleToClipboardWorker;
-import org.jabref.gui.worker.LookupDOIsWorker;
 import org.jabref.gui.worker.MarkEntriesAction;
 import org.jabref.gui.worker.SendAsEMailAction;
 import org.jabref.logic.autocompleter.AutoCompletePreferences;
@@ -676,7 +675,6 @@ public void update() {
  actions.put(Actions.REMOVE_FROM_GROUP, new GroupAddRemoveDialog(this, false, false));
  actions.put(Actions.MOVE_TO_GROUP, new GroupAddRemoveDialog(this, true, true));
 
- actions.put(Actions.LOOKUP_DOIS, new LookupDOIsWorker(frame));
  actions.put(Actions.DOWNLOAD_FULL_TEXT, new FindFullTextAction(this));
  }
 
@@ -990,23 +988,7 @@ public void runCommand(final String _command) {
  if (o instanceof BaseAction) {
  ((BaseAction) o).action();
  } else {
- // This part uses Spin's features:
- Runnable wrk = ((AbstractWorker) o).getWorker();
- // The Worker returned by getWorker() has been wrapped
- // by Spin.off(), which makes its methods be run in
- // a different thread from the EDT.
- CallBack clb = ((AbstractWorker) o).getCallBack();
-
- ((AbstractWorker) o).init(); // This method runs in this same thread, the EDT.
- // Useful for initial GUI actions, like printing a message.
-
- // The CallBack returned by getCallBack() has been wrapped
- // by Spin.over(), which makes its methods be run on
- // the EDT.
- wrk.run(); // Runs the potentially time-consuming action
- // without freezing the GUI. The magic is that THIS line
- // of execution will not continue until run() is finished.
- clb.update(); // Runs the update() method on the EDT.
+ runWorker((AbstractWorker) o);
  }
  } catch (Throwable ex) {
  // If the action has blocked the JabRefFrame before crashing, we need to unblock it.
@@ -1017,6 +999,26 @@ public void runCommand(final String _command) {
  }
  }
 
+ public static void runWorker(AbstractWorker worker) throws Exception {
+ // This part uses Spin's features:
+ Runnable wrk = worker.getWorker();
+ // The Worker returned by getWorker() has been wrapped
+ // by Spin.off(), which makes its methods be run in
+ // a different thread from the EDT.
+ CallBack clb = worker.getCallBack();
+
+ worker.init(); // This method runs in this same thread, the EDT.
+ // Useful for initial GUI actions, like printing a message.
+
+ // The CallBack returned by getCallBack() has been wrapped
+ // by Spin.over(), which makes its methods be run on
+ // the EDT.
+ wrk.run(); // Runs the potentially time-consuming action
+ // without freezing the GUI. The magic is that THIS line
+ // of execution will not continue until run() is finished.
+ clb.update(); // Runs the update() method on the EDT.
+ }
+
  private boolean saveDatabase(File file, boolean selectedOnly, Charset enc,
  SavePreferences.DatabaseSaveType saveType) throws SaveException {
  SaveSession session;

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

@@ -63,6 +63,7 @@
 import org.jabref.gui.actions.ConnectToSharedDatabaseAction;
 import org.jabref.gui.actions.ErrorConsoleAction;
 import org.jabref.gui.actions.IntegrityCheckAction;
+import org.jabref.gui.actions.LookupIdentifierAction;
 import org.jabref.gui.actions.ManageKeywordsAction;
 import org.jabref.gui.actions.MassSetFieldAction;
 import org.jabref.gui.actions.MnemonicAwareAction;
@@ -110,8 +111,10 @@
 import org.jabref.logic.autosaveandbackup.AutosaveManager;
 import org.jabref.logic.autosaveandbackup.BackupManager;
 import org.jabref.logic.help.HelpFile;
+import org.jabref.logic.importer.IdFetcher;
 import org.jabref.logic.importer.OutputPrinter;
 import org.jabref.logic.importer.ParserResult;
+import org.jabref.logic.importer.WebFetchers;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.search.SearchQuery;
 import org.jabref.logic.undo.AddUndoableActionEvent;
@@ -405,9 +408,7 @@ public void actionPerformed(ActionEvent e) {
  Localization.lang("Send as email"), IconTheme.JabRefIcon.EMAIL.getIcon());
  private final MassSetFieldAction massSetField = new MassSetFieldAction(this);
  private final ManageKeywordsAction manageKeywords = new ManageKeywordsAction(this);
- private final AbstractAction lookupDOIs = new GeneralAction(Actions.LOOKUP_DOIS,
- Localization.menuTitle("Look up DOIs"),
- Localization.lang("Look up DOIs"));
+ private final JMenu lookupIdentifiers = JabRefFrame.subMenu(Localization.menuTitle("Look up document identifier..."));
  private final GeneralAction findUnlinkedFiles = new GeneralAction(
  FindUnlinkedFilesDialog.ACTION_COMMAND,
  FindUnlinkedFilesDialog.ACTION_MENU_TITLE, FindUnlinkedFilesDialog.ACTION_SHORT_DESCRIPTION,
@@ -1176,7 +1177,11 @@ private void fillMenu() {
  quality.add(autoSetFile);
  quality.add(findUnlinkedFiles);
  quality.add(autoLinkFile);
- quality.add(lookupDOIs);
+
+ for (IdFetcher fetcher : WebFetchers.getIdFetchers()) {
+ lookupIdentifiers.add(new LookupIdentifierAction(this, fetcher));
+ }
+ quality.add(lookupIdentifiers);
  quality.add(downloadFullText);
  mb.add(quality);
 
@@ -1360,7 +1365,7 @@ private void initActions() {
  saveAs, saveSelectedAs, saveSelectedAsPlain, editModeAction, undo, redo, cut, deleteEntry, copy, paste, mark, markSpecific, unmark,
  unmarkAll, rankSubMenu, editEntry, selectAll, copyKey, copyCiteKey, copyKeyAndTitle, copyKeyAndLink, editPreamble, editStrings,
  groupSelector.getToggleAction(), makeKeyAction, normalSearch, generalFetcher.getToggleAction(), mergeEntries, cleanupEntries, exportToClipboard, replaceAll,
- sendAsEmail, downloadFullText, lookupDOIs, writeXmpAction, openOfficePanel.getToggleAction(), findUnlinkedFiles, addToGroup, removeFromGroup,
+ sendAsEmail, downloadFullText, lookupIdentifiers, writeXmpAction, openOfficePanel.getToggleAction(), findUnlinkedFiles, addToGroup, removeFromGroup,
  moveToGroup, autoLinkFile, resolveDuplicateKeys, openUrl, openFolder, openFile, togglePreview,
  dupliCheck, autoSetFile, newEntryAction, newSpec, customizeAction, plainTextImport, getMassSetField(), getManageKeywords(),
  pushExternalButton.getMenuAction(), closeDatabaseAction, getNextPreviewStyleAction(), getPreviousPreviewStyleAction(), checkIntegrity,
@@ -1393,7 +1398,7 @@ dupliCheck, autoSetFile, newEntryAction, newSpec, customizeAction, plainTextImpo
  twoEntriesOnlyActions.addAll(Arrays.asList(mergeEntries));
 
  atLeastOneEntryActions.clear();
- atLeastOneEntryActions.addAll(Arrays.asList(downloadFullText, lookupDOIs));
+ atLeastOneEntryActions.addAll(Arrays.asList(downloadFullText, lookupIdentifiers));
 
  tabbedPane.addChangeListener(event -> updateEnabledState());
 

src/main/java/org/jabref/gui/actions/Actions.java

@@ -33,7 +33,6 @@ public class Actions {
  public static final String EXPORT_TO_CLIPBOARD = "exportToClipboard";
  public static final String FOCUS_TABLE = "focusTable";
  public static final String FORWARD = "forward";
- public static final String LOOKUP_DOIS = "lookupDOIs";
  public static final String MAKE_KEY = "makeKey";
  public static final String MANAGE_SELECTORS = "manageSelectors";
  public static final String MARK_ENTRIES = "markEntries";

src/main/java/org/jabref/gui/actions/LookupIdentifierAction.java

@@ -0,0 +1,38 @@
+package org.jabref.gui.actions;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.Action;
+
+import org.jabref.gui.BasePanel;
+import org.jabref.gui.JabRefFrame;
+import org.jabref.gui.worker.LookupIdentifiersWorker;
+import org.jabref.logic.importer.IdFetcher;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+public class LookupIdentifierAction extends MnemonicAwareAction {
+
+ private static final Log LOGGER = LogFactory.getLog(LookupIdentifierAction.class);
+
+ private final JabRefFrame frame;
+ private final IdFetcher fetcher;
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ try {
+ BasePanel.runWorker(new LookupIdentifiersWorker(frame, fetcher));
+ } catch (Exception e) {
+ LOGGER.error(e);
+ }
+ }
+
+ public LookupIdentifierAction(JabRefFrame frame, IdFetcher fetcher) {
+ super();
+ this.frame = frame;
+ this.fetcher = fetcher;
+
+ putValue(Action.NAME, fetcher.getIdentifierName());
+ }
+}

src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java

@@ -20,7 +20,6 @@
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.autosaveandbackup.AutosaveUIManager;
 import org.jabref.gui.worker.AbstractWorker;
-import org.jabref.gui.worker.CallBack;
 import org.jabref.logic.autosaveandbackup.AutosaveManager;
 import org.jabref.logic.autosaveandbackup.BackupManager;
 import org.jabref.logic.exporter.BibtexDatabaseWriter;
@@ -280,23 +279,7 @@ private boolean saveDatabase(File file, boolean selectedOnly, Charset encoding)
  * still runs synchronously using Spin (the method returns only after completing the operation).
  */
  public void runCommand() throws Exception {
- // This part uses Spin's features:
- Runnable worker = getWorker();
- // The Worker returned by getWorker() has been wrapped
- // by Spin.off(), which makes its methods be run in
- // a different thread from the EDT.
- CallBack callback = getCallBack();
-
- init(); // This method runs in this same thread, the EDT.
- // Useful for initial GUI actions, like printing a message.
-
- // The CallBack returned by getCallBack() has been wrapped
- // by Spin.over(), which makes its methods be run on
- // the EDT.
- worker.run(); // Runs the potentially time-consuming action
- // without freezing the GUI. The magic is that THIS line
- // of execution will not continue until run() is finished.
- callback.update(); // Runs the update() method on the EDT.
+ BasePanel.runWorker(this);
  }
 
  public void save() throws Exception {

src/main/java/org/jabref/gui/worker/LookupIdentifiersWorker.java

@@ -0,0 +1,76 @@
+package org.jabref.gui.worker;
+
+import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
+
+import org.jabref.gui.BasePanel;
+import org.jabref.gui.JabRefFrame;
+import org.jabref.gui.undo.NamedCompound;
+import org.jabref.gui.undo.UndoableFieldChange;
+import org.jabref.logic.importer.FetcherException;
+import org.jabref.logic.importer.IdFetcher;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.FieldChange;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.identifier.Identifier;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+public class LookupIdentifiersWorker<T extends Identifier> extends AbstractWorker {
+
+ private final JabRefFrame frame;
+ private final IdFetcher<T> fetcher;
+ private String message;
+
+ private static final Log LOGGER = LogFactory.getLog(LookupIdentifiersWorker.class);
+
+ public LookupIdentifiersWorker(JabRefFrame frame, IdFetcher<T> fetcher) {
+ this.frame = Objects.requireNonNull(frame);
+ this.fetcher = Objects.requireNonNull(fetcher);
+ }
+
+ @Override
+ public void run() {
+ BasePanel basePanel = Objects.requireNonNull(frame.getCurrentBasePanel());
+ List<BibEntry> bibEntries = basePanel.getSelectedEntries();
+ if (!bibEntries.isEmpty()) {
+ String totalCount = Integer.toString(bibEntries.size());
+ NamedCompound namedCompound = new NamedCompound(Localization.lang("Look up %0", fetcher.getIdentifierName()));
+ int count = 0;
+ int foundCount = 0;
+ for (BibEntry bibEntry : bibEntries) {
+ count++;
+ frame.output(Localization.lang("Looking up %0... - entry %1 out of %2 - found %3",
+ fetcher.getIdentifierName(), Integer.toString(count), totalCount, Integer.toString(foundCount)));
+ Optional<T> identifier = Optional.empty();
+ try {
+ identifier = fetcher.findIdentifier(bibEntry);
+ } catch (FetcherException e) {
+ LOGGER.error("Could not fetch " + fetcher.getIdentifierName(), e);
+ }
+ if (identifier.isPresent() && !bibEntry.hasField(identifier.get().getDefaultField())) {
+ Optional<FieldChange> fieldChange = bibEntry.setField(identifier.get().getDefaultField(), identifier.get().getNormalized());
+ if (fieldChange.isPresent()) {
+ namedCompound.addEdit(new UndoableFieldChange(fieldChange.get()));
+ foundCount++;
+ frame.output(Localization.lang("Looking up %0... - entry %1 out of %2 - found %3",
+ Integer.toString(count), totalCount, Integer.toString(foundCount)));
+ }
+ }
+ }
+ namedCompound.end();
+ if (foundCount > 0) {
+ basePanel.getUndoManager().addEdit(namedCompound);
+ basePanel.markBaseChanged();
+ }
+ message = Localization.lang("Determined %0 for %1 entries", fetcher.getIdentifierName(), Integer.toString(foundCount));
+ }
+ }
+
+ @Override
+ public void update() {
+ frame.output(message);
+ }
+}

src/main/java/org/jabref/logic/importer/IdFetcher.java

@@ -3,11 +3,12 @@
 import java.util.Optional;
 
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.identifier.Identifier;
 
 /**
  * Looks for article identifier based on already present bibliographic information.
  */
-public interface IdFetcher<T> extends WebFetcher {
+public interface IdFetcher<T extends Identifier> extends WebFetcher {
 
  /**
  * Looks for an identifier based on the information stored in the given {@link BibEntry}.
@@ -16,4 +17,9 @@ public interface IdFetcher<T> extends WebFetcher {
  * @return the identifier (if an ID was found, otherwise an empty {@link Optional})
  */
  Optional<T> findIdentifier(BibEntry entry) throws FetcherException;
+
+ /**
+ * Returns the name of the identifier that is returned by this fetcher.
+ */
+ String getIdentifierName();
 }