Merge pull request #2442 from JabRef/lookupdoi

Add "Look up DOIs" to Quality menu

CHANGELOG.md

@@ -47,6 +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 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

@@ -988,23 +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.
@@ -1015,6 +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;
@@ -405,6 +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 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,
@@ -1173,6 +1177,11 @@ private void fillMenu() {
         quality.add(autoSetFile);
         quality.add(findUnlinkedFiles);
         quality.add(autoLinkFile);
+
+        for (IdFetcher fetcher : WebFetchers.getIdFetchers()) {
+            lookupIdentifiers.add(new LookupIdentifierAction(this, fetcher));
+        }
+        quality.add(lookupIdentifiers);
         quality.add(downloadFullText);
         mb.add(quality);
 
@@ -1356,7 +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, 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,
@@ -1389,7 +1398,7 @@ dupliCheck, autoSetFile, newEntryAction, newSpec, customizeAction, plainTextImpo
         twoEntriesOnlyActions.addAll(Arrays.asList(mergeEntries));
 
         atLeastOneEntryActions.clear();
-        atLeastOneEntryActions.addAll(Arrays.asList(downloadFullText));
+        atLeastOneEntryActions.addAll(Arrays.asList(downloadFullText, lookupIdentifiers));
 
         tabbedPane.addChangeListener(event -> updateEnabledState());
 

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/entryeditor/FieldExtraComponents.java

@@ -177,7 +177,7 @@ public static Optional<JComponent> getDoiExtraComponent(BasePanel panel, EntryEd
             }
         });
         // lookup doi
-        JButton doiButton = new JButton(Localization.lang("Lookup DOI"));
+        JButton doiButton = new JButton(Localization.lang("Look up DOI"));
         doiButton.addActionListener(actionEvent -> {
             try {
                 Optional<DOI> doi = WebFetchers.getIdFetcherForIdentifier(DOI.class).findIdentifier(entryEditor.getEntry());

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/gui/worker/MarkEntriesAction.java

@@ -18,9 +18,6 @@
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
-/**
- *
- */
 public class MarkEntriesAction extends AbstractWorker implements ActionListener {
 
     private final JabRefFrame frame;

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();
 }

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

@@ -13,6 +13,7 @@
 
 import org.jabref.model.cleanup.Formatter;
 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;
@@ -23,7 +24,7 @@
  * 2. Parse the response to get a list of {@link BibEntry}
  * 3. Extract identifier
  */
-public interface IdParserFetcher<T> extends IdFetcher<T> {
+public interface IdParserFetcher<T extends Identifier> extends IdFetcher<T> {
 
     Log LOGGER = LogFactory.getLog(IdParserFetcher.class);
 

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

@@ -20,6 +20,7 @@
 import org.jabref.logic.importer.fetcher.zbMATH;
 import org.jabref.model.entry.FieldName;
 import org.jabref.model.entry.identifier.DOI;
+import org.jabref.model.entry.identifier.Identifier;
 
 public class WebFetchers {
 
@@ -42,7 +43,7 @@ public static Optional<IdBasedFetcher> getIdBasedFetcherForField(String field, I
     }
 
     @SuppressWarnings("unchecked")
-    public static <T> IdFetcher<T> getIdFetcherForIdentifier(Class<T> clazz) {
+    public static <T extends Identifier> IdFetcher<T> getIdFetcherForIdentifier(Class<T> clazz) {
         if (clazz == DOI.class) {
             return (IdFetcher<T>) new CrossRef();
         } else {
@@ -89,4 +90,11 @@ public static List<EntryBasedFetcher> getEntryBasedFetchers(ImportFormatPreferen
         list.sort(Comparator.comparing(WebFetcher::getName));
         return list;
     }
+
+    public static List<IdFetcher> getIdFetchers() {
+        ArrayList<IdFetcher> list = new ArrayList<>();
+        list.add(new CrossRef());
+        list.sort(Comparator.comparing(WebFetcher::getName));
+        return list;
+    }
 }

src/main/java/org/jabref/logic/importer/fetcher/CrossRef.java

@@ -181,4 +181,9 @@ public Optional<DOI> extractIdentifier(BibEntry inputEntry, List<BibEntry> fetch
 
         return Optional.empty();
     }
+
+    @Override
+    public String getIdentifierName() {
+        return "DOI";
+    }
 }

src/main/java/org/jabref/logic/importer/fetcher/DoiResolution.java

@@ -35,7 +35,7 @@ public Optional<URL> findFullText(BibEntry entry) throws IOException {
 
         Optional<DOI> doi = entry.getField(FieldName.DOI).flatMap(DOI::build);
 
-        if(doi.isPresent()) {
+        if (doi.isPresent()) {
             String sciLink = doi.get().getURIAsASCIIString();
 
             // follow all redirects and scan for a single pdf link