Merge remote-tracking branch 'upstream/master' into fileDirPattern

* upstream/master: (24 commits) hotfix NPE in the main table (#2158) Enhance side pane toggle (#1605) Added gray background text to authors field to assist newcomers (#2147) Rewrite google scholar fetcher to new infrastructure (#2101) Found entries will be shown when dropping a pdf with xmp meta data (#2150) Japanese translation (#2155) Add shortcuts to context menu (#2131) [WIP] Doi resolution ignore (#2154) Fix DuplicationChecker and key generator (#2151) just close popup on first ESC keep entry in sight Fix isSharedDatabaseAlreadyPresent check. don't change entry after search if editing an entry (#2129) Change download URL to downloads.jabref.org (#2145) fix switching edited textfield in the entry editor with TAB (#2138) Update me.champeau.gradle.jmh' version from 0.3.0 to 0.3.1 Update install4j plugin from 6.1.2 to 6.1.3 Remove gradle plugin com.github.youribonnaffe.gradle.format as it is deprecated and the config uses a non-existing file Update gradle from 3.0 to 3.1 Fix changing the font size not working when importing preferences (#2069) ... # Conflicts: # src/main/java/net/sf/jabref/gui/externalfiles/DroppedFileHandler.java # src/main/java/net/sf/jabref/gui/importer/fetcher/GoogleScholarFetcher.java
JabRef · Oct 13, 2016 · d4c9b88 · d4c9b88
2 parents 6472b4e + 57027c0
commit d4c9b88
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 ### Changed
 - Source tab in the entry editor displays "BibLaTeX Source" when using biblatex mode
+- [koppor#171](https://github.com/koppor/jabref/issues/171): Add Shortcuts to context menu
 - Add session restoring functionality for shared database. Related to [#1703](https://github.com/JabRef/jabref/issues/1703)
 - Implementation of LiveUpdate for PostgreSQL & Oracle systems. Related to [#970](https://github.com/JabRef/jabref/issues/970).
 - [koppor#31](https://github.com/koppor/jabref/issues/31): Number column in the main table is always Left aligned
@@ -59,8 +60,11 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Improve language quality of the German translation of shared database
 - Change "Recent files" to "Recent databases" to keep the file menu consistent
 - Customized importer files need to be slightly changed since the class `ImportFormat` was renamed to `Importer`
+- [koppor#5](https://github.com/koppor/jabref/issues/5) When entries are found while dropping a pdf with xmp meta data the found entries will be displayed in the import dialog
+- [koppor#61](https://github.com/koppor/jabref/issues/61) Display gray background text in "Author" and "Editor" field to assist newcomers
 
 ### Fixed
+- Fixed [#2089](https://github.com/JabRef/jabref/issues/2089): Fixed faulty cite key generation
 - Fixed [#2092](https://github.com/JabRef/jabref/issues/2092): "None"-button in date picker clears the date field
 - Fixed [#1993](https://github.com/JabRef/jabref/issues/1993): Various optimizations regarding search performance
 - Fixed [koppor#160](https://github.com/koppor/jabref/issues/160): Tooltips now working in the main table
@@ -88,6 +92,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Fixed InvalidBackgroundColor flickering with Ctrl-s and File > Save database
 - Fixed loop when pulling changes (shared database) when current selected field has changed
 - Fixed [#1958](https://github.com/JabRef/jabref/issues/1958): Verbatim fields are no longer checked for HTML encoded characters by integrity checks
+- Fixed [#1808](https://github.com/JabRef/jabref/issues/1808): Font preference dialog now keeps changes
 - Fixed [#1937](https://github.com/JabRef/jabref/issues/1937): If no help page for the current chosen language exists, the english help page will be shown
 - Fixed [#2060](https://github.com/JabRef/jabref/issues/2060): Medline fetcher now imports data in UTF-8 encoding
 - Fixed file menu displays wrong hotkey in the German translation

diff --git a/build.gradle b/build.gradle
@@ -14,13 +14,11 @@ buildscript {
 }
 
 plugins {
-    id "com.install4j.gradle" version "6.1.2"
+    id "com.install4j.gradle" version "6.1.3"
     id 'com.github.johnrengelman.shadow' version '1.2.3'
-    // TODO replaced by spotless plugin, needs to be updated
-    id "com.github.youribonnaffe.gradle.format" version "1.5"
     // If this is updated to 0.0.9, check configurations.errorprone
     id "net.ltgt.errorprone" version "0.0.8"
-    id 'me.champeau.gradle.jmh' version '0.3.0'
+    id 'me.champeau.gradle.jmh' version '0.3.1'
 }
 
 apply plugin: "java"
@@ -247,6 +245,11 @@ test {
     }
 }
 
+task copyTestResources(type: Copy) {
+    from "${projectDir}/src/test/resources"
+    into "${buildDir}/classes/test"
+}
+processTestResources.dependsOn copyTestResources
 
 task databaseTest(type: Test) {
     testClassesDir = sourceSets.databaseTest.output.classesDir
@@ -272,13 +275,6 @@ jacocoTestReport {
     }
 }
 
-// enables `gradlew format`. Currently `LabelPatternUtil.java` is destroyed. Use with care!
-format {
-    configurationFile = file('ide-settings/formatter_settings.xml')
-    // default: reformat main and test
-    //files = sourceSets.main.java
-}
-
 shadowJar {
     classifier 'fat'
 

diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,6 +1,6 @@
-#Tue Sep 06 12:44:33 CEST 2016
+#Tue Oct 11 00:24:20 CEST 2016
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-3.0-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-3.1-bin.zip
diff --git a/gradlew b/gradlew
@@ -161,4 +161,9 @@ function splitJvmOpts() {
 eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS
 JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"
 
+# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
+if [[ "$(uname)" == "Darwin" ]] && [[ "$HOME" == "$PWD" ]]; then
+  cd "$(dirname "$0")"
+fi
+
 exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"
diff --git a/gradlew.bat b/gradlew.bat
@@ -49,7 +49,6 @@ goto fail
 @rem Get command-line arguments, handling Windows variants
 
 if not "%OS%" == "Windows_NT" goto win9xME_args
-if "%@eval[2+2]" == "4" goto 4NT_args
 
 :win9xME_args
 @rem Slurp the command line arguments.
@@ -60,11 +59,6 @@ set _SKIP=2
 if "x%~1" == "x" goto execute
 
 set CMD_LINE_ARGS=%*
-goto execute
-
-:4NT_args
-@rem Get arguments from the 4NT Shell from JP Software
-set CMD_LINE_ARGS=%$
 
 :execute
 @rem Setup the command line

diff --git a/src/main/java/net/sf/jabref/collab/FileUpdatePanel.java b/src/main/java/net/sf/jabref/collab/FileUpdatePanel.java
@@ -17,10 +17,7 @@
 import net.sf.jabref.gui.SidePaneManager;
 import net.sf.jabref.logic.l10n.Localization;
 
-public class FileUpdatePanel extends SidePaneComponent implements ActionListener,
-        ChangeScanner.DisplayResultCallback {
-
-    public static final String NAME = "fileUpdate";
+public class FileUpdatePanel extends SidePaneComponent implements ActionListener, ChangeScanner.DisplayResultCallback {
 
     private final SidePaneManager manager;
 
@@ -65,14 +62,19 @@ public BasePanel getPanel() {
      */
     @Override
     public void componentClosing() {
-        manager.unregisterComponent(FileUpdatePanel.NAME);
+        manager.unregisterComponent(FileUpdatePanel.class);
     }
 
     @Override
     public int getRescalingWeight() {
         return 0;
     }
 
+    @Override
+    public ToggleAction getToggleAction() {
+        throw new UnsupportedOperationException();
+    }
+
     /**
      * actionPerformed
      *

diff --git a/src/main/java/net/sf/jabref/gui/BasePanel.java b/src/main/java/net/sf/jabref/gui/BasePanel.java
@@ -20,7 +20,6 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
@@ -70,6 +69,7 @@
 import net.sf.jabref.gui.importer.actions.AppendDatabaseAction;
 import net.sf.jabref.gui.journals.AbbreviateAction;
 import net.sf.jabref.gui.journals.UnabbreviateAction;
+import net.sf.jabref.gui.keyboard.KeyBinding;
 import net.sf.jabref.gui.maintable.MainTable;
 import net.sf.jabref.gui.maintable.MainTableDataModel;
 import net.sf.jabref.gui.maintable.MainTableFormat;
@@ -112,6 +112,7 @@
 import net.sf.jabref.logic.util.io.FileUtil;
 import net.sf.jabref.logic.util.io.RegExpFileSearch;
 import net.sf.jabref.model.FieldChange;
+import net.sf.jabref.model.bibtexkeypattern.AbstractBibtexKeyPattern;
 import net.sf.jabref.model.database.BibDatabase;
 import net.sf.jabref.model.database.BibDatabaseContext;
 import net.sf.jabref.model.database.DatabaseLocation;
@@ -395,12 +396,6 @@ private void setupActions() {
 
         });
 
-        // The action for toggling the groups interface
-        actions.put(Actions.TOGGLE_GROUPS, (BaseAction) () -> {
-            sidePaneManager.toggle("groups");
-            frame.groupToggle.setSelected(sidePaneManager.isComponentVisible("groups"));
-        });
-
         actions.put(FindUnlinkedFilesDialog.ACTION_COMMAND, (BaseAction) () -> {
             final FindUnlinkedFilesDialog dialog = new FindUnlinkedFilesDialog(frame, frame, BasePanel.this);
             dialog.setLocationRelativeTo(frame);
@@ -434,65 +429,47 @@ public void init() {
             // Run second, on a different thread:
             @Override
             public void run() {
-                BibEntry bes;
-
-                // First check if any entries have keys set already. If so, possibly remove
-                // them from consideration, or warn about overwriting keys.
-                // This is a partial clone of net.sf.jabref.gui.entryeditor.EntryEditor.GenerateKeyAction.actionPerformed(ActionEvent)
-                for (final Iterator<BibEntry> i = entries.iterator(); i.hasNext();) {
-                    bes = i.next();
-                    if (bes.hasCiteKey()) {
-                        if (Globals.prefs.getBoolean(JabRefPreferences.AVOID_OVERWRITING_KEY)) {
-                            // Remove the entry, because its key is already set:
-                            i.remove();
-                        } else if (Globals.prefs.getBoolean(JabRefPreferences.WARN_BEFORE_OVERWRITING_KEY)) {
-                            // Ask if the user wants to cancel the operation:
-                            CheckBoxMessage cbm = new CheckBoxMessage(
-                                    Localization.lang("One or more keys will be overwritten. Continue?"),
-                                    Localization.lang("Disable this confirmation dialog"), false);
-                            final int answer = JOptionPane.showConfirmDialog(frame, cbm,
-                                    Localization.lang("Overwrite keys"), JOptionPane.YES_NO_OPTION);
-                            if (cbm.isSelected()) {
-                                Globals.prefs.putBoolean(JabRefPreferences.WARN_BEFORE_OVERWRITING_KEY, false);
-                            }
-                            if (answer == JOptionPane.NO_OPTION) {
-                                // Ok, break off the operation.
-                                canceled = true;
-                                return;
-                            }
-                            // No need to check more entries, because the user has already confirmed
-                            // that it's ok to overwrite keys:
-                            break;
+                // We don't want to generate keys for entries which already have one thus remove the entries
+                if (Globals.prefs.getBoolean(JabRefPreferences.AVOID_OVERWRITING_KEY)) {
+                    entries.removeIf(BibEntry::hasCiteKey);
+
+                // if we're going to override some cite keys warn the user about it
+                } else if (Globals.prefs.getBoolean(JabRefPreferences.WARN_BEFORE_OVERWRITING_KEY)) {
+                    if (entries.parallelStream().anyMatch(BibEntry::hasCiteKey)) {
+                        CheckBoxMessage cbm = new CheckBoxMessage(
+                                Localization.lang("One or more keys will be overwritten. Continue?"),
+                                Localization.lang("Disable this confirmation dialog"), false);
+                        final int answer = JOptionPane.showConfirmDialog(frame, cbm,
+                                Localization.lang("Overwrite keys"), JOptionPane.YES_NO_OPTION);
+                        Globals.prefs.putBoolean(JabRefPreferences.WARN_BEFORE_OVERWRITING_KEY, !cbm.isSelected());
+
+                        // The user doesn't want to overide cite keys
+                        if (answer == JOptionPane.NO_OPTION) {
+                            canceled = true;
+                            return;
                         }
                     }
                 }
 
-                Map<BibEntry, String> oldvals = new HashMap<>();
-                // Iterate again, removing already set keys. This is skipped if overwriting
-                // is disabled, since all entries with keys set will have been removed.
-                if (!Globals.prefs.getBoolean(JabRefPreferences.AVOID_OVERWRITING_KEY)) {
-                    for (BibEntry entry : entries) {
-                        bes = entry;
-                        // Store the old value:
-                        oldvals.put(bes, bes.getCiteKeyOptional().orElse(null));
-                        bes.clearCiteKey();
-                    }
-                }
-
+                // generate the new cite keys for each entry
                 final NamedCompound ce = new NamedCompound(Localization.lang("Autogenerate BibTeX keys"));
-
-                // Finally, set the new keys:
+                AbstractBibtexKeyPattern citeKeyPattern = bibDatabaseContext.getMetaData()
+                        .getCiteKeyPattern(Globals.prefs.getBibtexKeyPatternPreferences().getKeyPattern());
                 for (BibEntry entry : entries) {
-                    bes = entry;
-                    BibtexKeyPatternUtil.makeLabel(bibDatabaseContext.getMetaData()
-                            .getCiteKeyPattern(Globals.prefs.getBibtexKeyPatternPreferences().getKeyPattern()),
-                            bibDatabaseContext.getDatabase(),
-                            bes, Globals.prefs.getBibtexKeyPatternPreferences());
-                    ce.addEdit(new UndoableKeyChange(bibDatabaseContext.getDatabase(), bes, oldvals.get(bes),
-                            bes.getCiteKeyOptional().orElse(null)));
+                    String oldCiteKey = entry.getCiteKeyOptional().orElse("");
+                    BibtexKeyPatternUtil.makeLabel(citeKeyPattern, bibDatabaseContext.getDatabase(),
+                            entry, Globals.prefs.getBibtexKeyPatternPreferences());
+                    String newCiteKey = entry.getCiteKeyOptional().orElse("");
+                    if (!oldCiteKey.equals(newCiteKey)) {
+                        ce.addEdit(new UndoableKeyChange(entry, oldCiteKey, newCiteKey));
+                    }
                 }
                 ce.end();
-                getUndoManager().addEdit(ce);
+
+                // register the undo event only if new cite keys were generated
+                if (ce.hasEdits()) {
+                    getUndoManager().addEdit(ce);
+                }
             }
 
             // Run third, on EDT:
@@ -1217,7 +1194,7 @@ public void listen(EntryAddedEvent addedEntryEvent) {
             }
 
             // Automatically add new entry to the selected group (or set of groups)
-            if (Globals.prefs.getBoolean(JabRefPreferences.AUTO_ASSIGN_GROUP) && frame.groupToggle.isSelected()) {
+            if (Globals.prefs.getBoolean(JabRefPreferences.AUTO_ASSIGN_GROUP) && frame.getGroupSelector().getToggleAction().isSelected()) {
                 final List<BibEntry> entries = Collections.singletonList(addedEntryEvent.getBibEntry());
                 final TreePath[] selection = frame.getGroupSelector().getGroupsTree().getSelectionPaths();
                 if (selection != null) {
@@ -1301,6 +1278,7 @@ public void listen(EntryChangedEvent entryChangedEvent) {
 
         @Subscribe
         public void listen(EntryRemovedEvent removedEntryEvent) {
+            // IMO only used to update the status (found X entries)
             frame.getGlobalSearchBar().performSearch();
         }
     }
@@ -1381,6 +1359,30 @@ private void createMainTable() {
         };
         mainTable.addSelectionListener(groupsHighlightListener);
 
+        String clearSearch = "clearSearch";
+        mainTable.getInputMap().put(Globals.getKeyPrefs().getKey(KeyBinding.CLEAR_SEARCH), clearSearch);
+        mainTable.getActionMap().put(clearSearch, new AbstractAction() {
+            @Override
+            public void actionPerformed(ActionEvent e) {
+                // need to close these here, b/c this action overshadows the responsible actions when the main table is selected
+                switch (mode) {
+                    case SHOWING_NOTHING:
+                        frame.getGlobalSearchBar().endSearch();
+                        break;
+                    case SHOWING_PREVIEW:
+                        getPreviewPanel().close();
+                        break;
+                    case SHOWING_EDITOR:
+                    case WILL_SHOW_EDITOR:
+                        getCurrentEditor().close();
+                        break;
+                    default:
+                        LOGGER.warn("unknown BasePanelMode: '" + mode + "', doing nothing");
+                        break;
+                }
+            }
+        });
+
         mainTable.getActionMap().put(Actions.CUT, new AbstractAction() {
 
             @Override
@@ -1903,7 +1905,6 @@ public boolean showDeleteConfirmationDialog(int numberOfEntries) {
     public void autoGenerateKeysBeforeSaving() {
         if (Globals.prefs.getBoolean(JabRefPreferences.GENERATE_KEYS_BEFORE_SAVING)) {
             NamedCompound ce = new NamedCompound(Localization.lang("Autogenerate BibTeX keys"));
-            boolean any = false;
 
             for (BibEntry bes : bibDatabaseContext.getDatabase().getEntries()) {
                 Optional<String> oldKey = bes.getCiteKeyOptional();
@@ -1912,13 +1913,12 @@ public void autoGenerateKeysBeforeSaving() {
                             .getCiteKeyPattern(Globals.prefs.getBibtexKeyPatternPreferences().getKeyPattern()),
                             bibDatabaseContext.getDatabase(),
                             bes, Globals.prefs.getBibtexKeyPatternPreferences());
-                    ce.addEdit(new UndoableKeyChange(bibDatabaseContext.getDatabase(), bes, null,
-                            bes.getCiteKeyOptional().get())); // Cite key is set here
-                    any = true;
+                    ce.addEdit(new UndoableKeyChange(bes, oldKey.orElse(""), bes.getCiteKeyOptional().get()));
                 }
             }
+
             // Store undo information, if any:
-            if (any) {
+            if (ce.hasEdits()) {
                 ce.end();
                 getUndoManager().addEdit(ce);
             }
@@ -2117,15 +2117,15 @@ public void fileUpdated() {
 
             // Check if there is already a notification about external
             // changes:
-            boolean hasAlready = sidePaneManager.hasComponent(FileUpdatePanel.NAME);
+            boolean hasAlready = sidePaneManager.hasComponent(FileUpdatePanel.class);
             if (hasAlready) {
-                sidePaneManager.hideComponent(FileUpdatePanel.NAME);
-                sidePaneManager.unregisterComponent(FileUpdatePanel.NAME);
+                sidePaneManager.hideComponent(FileUpdatePanel.class);
+                sidePaneManager.unregisterComponent(FileUpdatePanel.class);
             }
             FileUpdatePanel pan = new FileUpdatePanel(BasePanel.this, sidePaneManager,
                     getBibDatabaseContext().getDatabaseFile().orElse(null), scanner);
-            sidePaneManager.register(FileUpdatePanel.NAME, pan);
-            sidePaneManager.show(FileUpdatePanel.NAME);
+            sidePaneManager.register(pan);
+            sidePaneManager.show(FileUpdatePanel.class);
         };
 
         if (scanner.changesFound()) {
@@ -2149,10 +2149,10 @@ public void cleanUp() {
         }
         // Check if there is a FileUpdatePanel for this BasePanel being shown. If so,
         // remove it:
-        if (sidePaneManager.hasComponent("fileUpdate")) {
-            FileUpdatePanel fup = (FileUpdatePanel) sidePaneManager.getComponent("fileUpdate");
+        if (sidePaneManager.hasComponent(FileUpdatePanel.class)) {
+            FileUpdatePanel fup = (FileUpdatePanel) sidePaneManager.getComponent(FileUpdatePanel.class);
             if (fup.getPanel() == this) {
-                sidePaneManager.hideComponent("fileUpdate");
+                sidePaneManager.hideComponent(FileUpdatePanel.class);
             }
         }
     }