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

* upstream/master:
  Add warning message if group with same name is already present (#3077)
  Fix #3062: Ctrl + F works again
  Fix del/copy/paste key trigger main table action in search bar (#3070)
  Fix markdown
  Update gradle from 4.0.1 to 4.0.2
  Fix #3045 Update Transformer plugin
  Reimplement MappedList using a backigList (#3069)
  Fix importing preferences after resetting without restarting (#3065)
  Fix some spotbugs issues (#3060)
  Import dialog when fetch (#3025)
  Adapt CircleCI build
  Adapt CI script
  Closes #3027 and updates install4j to v7

CHANGELOG.md

@@ -12,9 +12,17 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 ### Changed
 
+- If fetched article is already in database, then the entry merge dialog is shown.
+- An error message is now displayed if you try to create a group containing the keyword separator or if there is already a group with the same name. [#3075](https://github.com/JabRef/jabref/issues/3075) and [#1495](https://github.com/JabRef/jabref/issues/1495)
+
 ### Fixed
-We fixed an issue where the fetcher for the Astrophysics Data System (ADS) added some non-bibtex data to the entry returned from the search [#3035](https://github.com/JabRef/jabref/issues/3035)
-We fixed an issue where assigning an entry via drag and drop to a group caused JabRef to stop/freeze completely [#3036](https://github.com/JabRef/jabref/issues/3036)
+
+- We fixed an issue where the fetcher for the Astrophysics Data System (ADS) added some non-bibtex data to the entry returned from the search [#3035](https://github.com/JabRef/jabref/issues/3035)
+- We fixed an issue where assigning an entry via drag and drop to a group caused JabRef to stop/freeze completely [#3036](https://github.com/JabRef/jabref/issues/3036)
+- We fixed the shortcut <kbd>Ctrl</kbd>+<kbd>F</kbd> for the search field.
+- We fixed an issue where the preferences could not be imported without a restart of JabRef [#3064](https://github.com/JabRef/jabref/issues/3064)
+- We fixed an issue where <kbd>DEL</kbd>, <kbd>Ctrl</kbd>+<kbd>C</kbd>, <kbd>Ctrl</kbd>+<kbd>V</kbd> and <kbd>Ctrl</kbd>+<kbd>A</kbd> in the search field triggered corresponding actions in the main table [#3067](https://github.com/JabRef/jabref/issues/3067)
+
 ### Removed
 
 

build.gradle

@@ -1,12 +1,12 @@
 import org.gradle.internal.os.OperatingSystem
 
-// to update the gradle wrapper, execute ./gradlew wrapper --gradle-version 3.0
+// to update the gradle wrapper, execute ./gradlew wrapper --gradle-version 4.0
 
 plugins {
     id 'com.gradle.build-scan' version '1.8'
     id 'com.install4j.gradle' version '6.1.5'
     id 'com.github.johnrengelman.shadow' version '2.0.1'
-    id "de.sebastianboegl.shadow.transformer.log4j" version "2.1.0"
+    id "de.sebastianboegl.shadow.transformer.log4j" version "2.1.1"
     id "com.simonharrer.modernizer" version '1.5.0-1'
     id 'me.champeau.gradle.jmh' version '0.4.3'
     id 'net.ltgt.errorprone' version '0.0.11'

circle.yml

@@ -10,17 +10,17 @@ dependencies:
     # openssl aes-256-cbc -e -in ./buildres/jabref-cert-2016.p12 -out jabref-cert-2016.p12.enc -k {PASSWORD}
     - openssl aes-256-cbc -d -in ./buildres/jabref-cert-2016.p12.enc -out ./buildres/jabref-cert-2016.p12 -k $CERTIFICATE
     - scripts/prepare-install4j.sh
-    - install4j6/bin/install4jc --verbose --license=$INSTALL4J_KEY --win-keystore-password $CERTIFICATE_PW --mac-keystore-password $CERTIFICATE_PW
+    - install4j7/bin/install4jc --verbose --license=$INSTALL4J_KEY --win-keystore-password $CERTIFICATE_PW --mac-keystore-password $CERTIFICATE_PW
   override:
     # We do this to decrease build time by using CircleCI's cache. See https://discuss.circleci.com/t/effective-caching-for-gradle/540 for a longer motivation.
     - ./gradlew compileJava
   cache_directories:
-    - "~/.install4j6"
+    - "~/.install4j7"
     - "~/downloads"
 
 test:
   override:
-    - ./gradlew -Pdev=true -Pinstall4jDir="install4j6" release --stacktrace
+    - ./gradlew -Pdev=true -Pinstall4jDir="install4j7" release --stacktrace
   post:
     # save test reports as build artifacts
     - mkdir -p $CIRCLE_TEST_REPORTS/junit/
@@ -32,7 +32,7 @@ deployment:
    tag: /v[0-9]+(\.[0-9]+)*(-.+)?/
    commands:
       # we have to do a clean build as changing gradle's "project.version" does not lead to a rebuild of resources (mirroring project.version)
-      - ./gradlew -Pinstall4jDir="install4j6" clean release --stacktrace
+      - ./gradlew -Pinstall4jDir="install4j7" clean release --stacktrace
       # upload at all circumstances
       - scripts/upload-to-builds.jabref.org.sh
   development:

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
-#Tue Jul 18 01:58:04 BRT 2017
+#Thu Aug 03 11:08:08 CEST 2017
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.0.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.0.2-bin.zip

scripts/prepare-install4j.sh

@@ -7,20 +7,20 @@ fi
 
 # ensure that tar archive of install4j exists
 cd ~/downloads
-wget --quiet -nc http://download-keycdn.ej-technologies.com/install4j/install4j_unix_6_1_6.tar.gz
+wget --quiet -nc http://download-keycdn.ej-technologies.com/install4j/install4j_unix_7_0_1.tar.gz
 
 # extract tar archive of install4j into the source directory of JabRef
 cd ~/jabref
-# version 6.1.6 is NOT zipped any more - old command line: "-xzf"
-tar -xf ~/downloads/install4j_unix_6_1_6.tar.gz
+# version 7.0.1 is NOT zipped any more - old command line: "-xzf"
+tar -xf ~/downloads/install4j_unix_7_0_1.tar.gz
 # fix directory name (until install4j 6.1.5 it was install4j6
-mv install4j6.1.6 install4j6
+mv install4j7.0.1 install4j7
 
 # fetch JREs
-if [ ! -d ~/.install4j6/jres/ ]; then
-  mkdir -p ~/.install4j6/jres/
+if [ ! -d ~/.install4j7/jres/ ]; then
+  mkdir -p ~/.install4j7/jres/
 fi
-cd ~/.install4j6/jres/
-wget --quiet -nc https://files.jabref.org/jres/windows-x86-1.8.0_131.tar.gz
-wget --quiet -nc https://files.jabref.org/jres/windows-amd64-1.8.0_131.tar.gz
-wget --quiet -nc https://files.jabref.org/jres/macosx-amd64-1.8.0_131_unpacked.tar.gz
+cd ~/.install4j7/jres/
+wget --quiet -nc https://files.jabref.org/jres/windows-x86-1.8.0_141.tar.gz
+wget --quiet -nc https://files.jabref.org/jres/windows-amd64-1.8.0_141.tar.gz
+wget --quiet -nc https://files.jabref.org/jres/macosx-amd64-1.8.0_141_unpacked.tar.gz

src/main/java/org/jabref/Globals.java

@@ -58,7 +58,7 @@ private Globals() {
     }
 
     // Key binding preferences
-    public static KeyBindingRepository getKeyPrefs() {
+    public static synchronized KeyBindingRepository getKeyPrefs() {
         if (keyBindingRepository == null) {
             keyBindingRepository = prefs.getKeyBindingRepository();
         }

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

@@ -2144,7 +2144,9 @@ public void action() {
                 if ((focused != null) && (focused instanceof FieldEditor) && focused.hasFocus()) {
                     // User is currently editing a field:
                     // Check if it is the preamble:
-                    if ((preambleEditor != null) && (focused == preambleEditor.getFieldEditor())) {
+
+                    FieldEditor fieldEditor = (FieldEditor) focused;
+                    if ((preambleEditor != null) && (fieldEditor.equals(preambleEditor.getFieldEditor()))) {
                         preambleEditor.storeCurrentEdit();
                     }
                 }

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

@@ -26,7 +26,9 @@
 import javax.swing.SwingWorker;
 
 import org.jabref.Globals;
+import org.jabref.gui.importer.ImportInspectionDialog;
 import org.jabref.gui.keyboard.KeyBinding;
+import org.jabref.logic.bibtex.DuplicateCheck;
 import org.jabref.logic.bibtexkeypattern.BibtexKeyPatternUtil;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.IdBasedFetcher;
@@ -305,10 +307,22 @@ protected void done() {
                 Optional<BibEntry> result = get();
                 if (result.isPresent()) {
                     final BibEntry bibEntry = result.get();
-                    // Regenerate CiteKey of imported BibEntry
-                    BibtexKeyPatternUtil.makeAndSetLabel(Globals.prefs.getBibtexKeyPatternPreferences().getKeyPattern(), frame.getCurrentBasePanel().getDatabase(), bibEntry, Globals.prefs.getBibtexKeyPatternPreferences());
+                    if ((DuplicateCheck.containsDuplicate(frame.getCurrentBasePanel().getDatabase(), bibEntry, frame.getCurrentBasePanel().getBibDatabaseContext().getMode()).isPresent())) {
+                		//If there are duplicates starts ImportInspectionDialog
+                        final BasePanel panel = (BasePanel) frame.getTabbedPane().getSelectedComponent();
+
+                        ImportInspectionDialog diag = new ImportInspectionDialog(frame, panel, Localization.lang("Import"), false);
+                        diag.addEntry(bibEntry);
+                        diag.entryListComplete();
+                        diag.setLocationRelativeTo(frame);
+                        diag.setVisible(true);
+                        diag.toFront();	 
+                    } else {
+                		// Regenerate CiteKey of imported BibEntry
+                        BibtexKeyPatternUtil.makeAndSetLabel(Globals.prefs.getBibtexKeyPatternPreferences().getKeyPattern(), frame.getCurrentBasePanel().getDatabase(), bibEntry, Globals.prefs.getBibtexKeyPatternPreferences());
+                        frame.getCurrentBasePanel().insertEntry(bibEntry);
+                    }
 
-                    frame.getCurrentBasePanel().insertEntry(bibEntry);
                     dispose();
                 } else if (searchID.trim().isEmpty()) {
                     JOptionPane.showMessageDialog(frame, Localization.lang("The given search ID was empty."), Localization.lang("Empty search ID"), JOptionPane.WARNING_MESSAGE);

src/main/java/org/jabref/gui/entryeditor/EntryEditor.java

@@ -8,7 +8,7 @@
 import java.awt.Insets;
 import java.awt.RenderingHints;
 import java.awt.event.ActionEvent;
-import java.awt.event.KeyListener;
+import java.awt.event.KeyAdapter;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.time.LocalDateTime;
@@ -157,18 +157,7 @@ public EntryEditor(JabRefFrame frame, BasePanel panel, BibEntry entry, String la
 
         JFXPanel container = new JFXPanel();
 
-        container.addKeyListener(new KeyListener() {
-
-            @Override
-            public void keyTyped(java.awt.event.KeyEvent e) {
-                //empty
-            }
-
-            @Override
-            public void keyReleased(java.awt.event.KeyEvent e) {
-                // empty
-
-            }
+        container.addKeyListener(new KeyAdapter() {
 
             @Override
             public void keyPressed(java.awt.event.KeyEvent e) {

src/main/java/org/jabref/gui/groups/GroupDialog.java

@@ -45,6 +45,7 @@
 import org.jabref.model.groups.AutomaticPersonsGroup;
 import org.jabref.model.groups.ExplicitGroup;
 import org.jabref.model.groups.GroupHierarchyType;
+import org.jabref.model.groups.GroupTreeNode;
 import org.jabref.model.groups.RegexKeywordGroup;
 import org.jabref.model.groups.SearchGroup;
 import org.jabref.model.groups.WordKeywordGroup;
@@ -326,18 +327,45 @@ public void actionPerformed(ActionEvent e) {
         okButton.addActionListener(e -> {
                 isOkPressed = true;
             try {
+                String groupName = nameField.getText().trim();
                 if (explicitRadioButton.isSelected()) {
-                    resultingGroup = new ExplicitGroup(nameField.getText().trim(), getContext(),
-                            Globals.prefs.getKeywordDelimiter());
+                    Character keywordDelimiter = Globals.prefs.getKeywordDelimiter();
+                    if (groupName.contains(Character.toString(keywordDelimiter))) {
+                        jabrefFrame.showMessage(
+                                Localization.lang("The group name contains the keyword separator \"%0\" and thus probably does not work as expected.", Character.toString(keywordDelimiter)));
+                    }
+
+                    Optional<GroupTreeNode> rootGroup = jabrefFrame.getCurrentBasePanel().getBibDatabaseContext().getMetaData().getGroups();
+                    if (rootGroup.isPresent()) {
+                        int groupsWithSameName = rootGroup.get().findChildrenSatisfying(group -> group.getName().equals(groupName)).size();
+                        boolean warnAboutSameName = false;
+                        if (editedGroup == null && groupsWithSameName > 0) {
+                            // New group but there is already one group with the same name
+                            warnAboutSameName = true;
+                        }
+                        if (editedGroup != null && !editedGroup.getName().equals(groupName) && groupsWithSameName > 0) {
+                            // Edit group, changed name to something that is already present
+                            warnAboutSameName = true;
+                        }
+
+                        if (warnAboutSameName) {
+                            jabrefFrame.showMessage(
+                                    Localization.lang("There exists already a group with the same name.", Character.toString(keywordDelimiter)));
+                            return;
+                        }
+                    }
+
+                    resultingGroup = new ExplicitGroup(groupName, getContext(),
+                            keywordDelimiter);
                 } else if (keywordsRadioButton.isSelected()) {
                     // regex is correct, otherwise OK would have been disabled
                     // therefore I don't catch anything here
                     if (keywordGroupRegExp.isSelected()) {
-                        resultingGroup = new RegexKeywordGroup(nameField.getText().trim(), getContext(),
+                        resultingGroup = new RegexKeywordGroup(groupName, getContext(),
                                 keywordGroupSearchField.getText().trim(), keywordGroupSearchTerm.getText().trim(),
                                 keywordGroupCaseSensitive.isSelected());
                     } else {
-                        resultingGroup = new WordKeywordGroup(nameField.getText().trim(), getContext(),
+                        resultingGroup = new WordKeywordGroup(groupName, getContext(),
                                 keywordGroupSearchField.getText().trim(), keywordGroupSearchTerm.getText().trim(),
                                 keywordGroupCaseSensitive.isSelected(), Globals.prefs.getKeywordDelimiter(), false);
                     }
@@ -346,20 +374,20 @@ public void actionPerformed(ActionEvent e) {
                         // regex is correct, otherwise OK would have been
                         // disabled
                         // therefore I don't catch anything here
-                        resultingGroup = new SearchGroup(nameField.getText().trim(), getContext(), searchGroupSearchExpression.getText().trim(),
+                        resultingGroup = new SearchGroup(groupName, getContext(), searchGroupSearchExpression.getText().trim(),
                                 isCaseSensitive(), isRegex());
                     } catch (Exception e1) {
                         // should never happen
                     }
                 } else if (autoRadioButton.isSelected()) {
                     if (autoGroupKeywordsOption.isSelected()) {
                         resultingGroup = new AutomaticKeywordGroup(
-                                nameField.getText().trim(), getContext(),
+                                groupName, getContext(),
                                 autoGroupKeywordsField.getText().trim(),
                                 autoGroupKeywordsDeliminator.getText().charAt(0),
                                 autoGroupKeywordsHierarchicalDeliminator.getText().charAt(0));
                     } else {
-                        resultingGroup = new AutomaticPersonsGroup(nameField.getText().trim(), getContext(),
+                        resultingGroup = new AutomaticPersonsGroup(groupName, getContext(),
                                 autoGroupPersonsField.getText().trim());
                     }
                 }

src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java

@@ -150,8 +150,8 @@ public void openFiles(List<Path> filesToOpen, boolean raisePanel) {
             Path file = iterator.next();
             for (int i = 0; i < frame.getTabbedPane().getTabCount(); i++) {
                 BasePanel basePanel = frame.getBasePanelAt(i);
-                if ((basePanel.getBibDatabaseContext().getDatabaseFile().isPresent())
-                        && basePanel.getBibDatabaseContext().getDatabaseFile().get().equals(file)) {
+                if ((basePanel.getBibDatabaseContext().getDatabasePath().isPresent())
+                        && basePanel.getBibDatabaseContext().getDatabasePath().get().equals(file)) {
                     iterator.remove();
                     removed++;
                     // See if we removed the final one. If so, we must perhaps