Merge branch 'master' into implement-1356

# Conflicts:
#	CHANGELOG.md

Author: lenhard

CHANGELOG.md

@@ -19,6 +19,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Updated German translation
 - When resolving duplicate BibTeX-keys there is now an "Ignore" button. "Cancel" and close key now quits the resolving.
 - The [online forum](http://discourse.jabref.org/) is now directly accessible via the "Help" menu
+- Implemented [#1338](https://github.com/JabRef/jabref/issues/1338): clicking on a crossref in the main table selects the parent entry and added a button in the entry editor to select the parent entry.
 
 ### Fixed
 - Fixed [#1530](https://github.com/JabRef/jabref/issues/1530): Unescaped hashes in the url field are ignored by the integrity checker
@@ -34,6 +35,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Fixed [#1507](https://github.com/JabRef/jabref/issues/1507): Keywords are now separated by the delimiter specified in the preferences
 - Fixed [#1484](https://github.com/JabRef/jabref/issues/1484): HTML export handles some UTF characters wrong
 - Fixed [#1534](https://github.com/JabRef/jabref/issues/1534): "Mark entries imported into database" does not work correctly
+- Fixed [#1500](https://github.com/JabRef/jabref/issues/1500): Renaming of explicit groups now changes entries accordingly
+- Fixed issue where field changes were not undoable if the time stamp was updated on editing
 
 ### Removed
 

CONTRIBUTING.md

@@ -41,7 +41,7 @@ More information on this can be found via `man git-shortlog`.
 
 
 ### Modify the header
-The headers of each `.java` file states "JabREf contributors".
+The headers of each `.java` file states "JabRef contributors".
 Author credits are given using the `AUTHORS` file and by using the `git blame` functionality.
 
 For instance,

src/main/java/net/sf/jabref/Globals.java

@@ -15,6 +15,8 @@
 */
 package net.sf.jabref;
 
+import java.util.Optional;
+
 import net.sf.jabref.collab.FileUpdateMonitor;
 import net.sf.jabref.exporter.AutoSaveManager;
 import net.sf.jabref.gui.GlobalFocusListener;
@@ -64,8 +66,18 @@ public class Globals {
      */
     public static JournalAbbreviationLoader journalAbbreviationLoader;
 
+    // Key binding preferences
     private static KeyBindingPreferences keyPrefs;
 
+    // Background tasks
+    private static GlobalFocusListener focusListener;
+    private static FileUpdateMonitor fileUpdateMonitor;
+    private static StreamEavesdropper streamEavesdropper;
+
+    // Autosave manager
+    private static AutoSaveManager autoSaveManager;
+
+    // Key binding preferences
     public static KeyBindingPreferences getKeyPrefs() {
         if (keyPrefs == null) {
             keyPrefs = new KeyBindingPreferences(prefs);
@@ -75,23 +87,29 @@ public static KeyBindingPreferences getKeyPrefs() {
 
 
     // Background tasks
-    public static GlobalFocusListener focusListener;
-    public static FileUpdateMonitor fileUpdateMonitor;
-    public static StreamEavesdropper streamEavesdropper;
-
     public static void startBackgroundTasks() {
         Globals.focusListener = new GlobalFocusListener();
 
         Globals.streamEavesdropper = StreamEavesdropper.eavesdropOnSystem();
 
         Globals.fileUpdateMonitor = new FileUpdateMonitor();
-        JabRefExecutorService.INSTANCE.executeWithLowPriorityInOwnThread(Globals.fileUpdateMonitor, "FileUpdateMonitor");
+        JabRefExecutorService.INSTANCE.executeWithLowPriorityInOwnThread(Globals.fileUpdateMonitor,
+                "FileUpdateMonitor");
+    }
+
+    public static GlobalFocusListener getFocusListener() {
+        return focusListener;
     }
 
+    public static FileUpdateMonitor getFileUpdateMonitor() {
+        return fileUpdateMonitor;
+    }
 
-    // Autosave manager
-    public static AutoSaveManager autoSaveManager;
+    public static StreamEavesdropper getStreamEavesdropper() {
+        return streamEavesdropper;
+    }
 
+    // Autosave manager
     public static void startAutoSaveManager(JabRefFrame frame) {
         Globals.autoSaveManager = new AutoSaveManager(frame);
         Globals.autoSaveManager.startAutoSaveTimer();
@@ -105,4 +123,8 @@ public static void stopAutoSaveManager() {
             Globals.autoSaveManager = null;
         }
     }
+
+    public static Optional<AutoSaveManager> getAutoSaveManager() {
+        return Optional.ofNullable(Globals.autoSaveManager);
+    }
 }

src/main/java/net/sf/jabref/JabRefPreferences.java

@@ -36,6 +36,7 @@
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
+import java.util.Optional;
 import java.util.Set;
 import java.util.prefs.BackingStoreException;
 import java.util.prefs.InvalidPreferencesFormatException;
@@ -1013,10 +1014,10 @@ public List<String> getStringList(String key) {
 
         StringReader rd = new StringReader(names);
         List<String> res = new ArrayList<>();
-        String rs;
+        Optional<String> rs;
         try {
-            while ((rs = getNextUnit(rd)) != null) {
-                res.add(rs);
+            while ((rs = getNextUnit(rd)).isPresent()) {
+                res.add(rs.get());
             }
         } catch (IOException ignored) {
             // Ignored
@@ -1205,7 +1206,7 @@ private Object getObject(String key) {
     }
 
 
-    private static String getNextUnit(Reader data) throws IOException {
+    private static Optional<String> getNextUnit(Reader data) throws IOException {
         // character last read
         // -1 if end of stream
         // initialization necessary, because of Java compiler
@@ -1240,12 +1241,12 @@ private static String getNextUnit(Reader data) throws IOException {
             }
         }
         if (res.length() > 0) {
-            return res.toString();
+            return Optional.of(res.toString());
         } else if (c == -1) {
             // end of stream
-            return null;
+            return Optional.empty();
         } else {
-            return "";
+            return Optional.of("");
         }
     }
 
@@ -1265,22 +1266,22 @@ public void storeCustomEntryType(CustomEntryType tp, int number) {
     /**
      * Retrieves all information about the entry type in preferences, with the tag given by number.
      */
-    public CustomEntryType getCustomEntryType(int number) {
+    public Optional<CustomEntryType> getCustomEntryType(int number) {
         String nr = String.valueOf(number);
         String name = get(JabRefPreferences.CUSTOM_TYPE_NAME + nr);
         if (name == null) {
-            return null;
+            return Optional.empty();
         }
         List<String> req = getStringList(JabRefPreferences.CUSTOM_TYPE_REQ + nr);
         List<String> opt = getStringList(JabRefPreferences.CUSTOM_TYPE_OPT + nr);
         List<String> priOpt = getStringList(JabRefPreferences.CUSTOM_TYPE_PRIOPT + nr);
         if (priOpt.isEmpty()) {
-            return new CustomEntryType(EntryUtil.capitalizeFirst(name), req, opt);
+            return Optional.of(new CustomEntryType(EntryUtil.capitalizeFirst(name), req, opt));
         }
         List<String> secondary = new ArrayList<>(opt);
         secondary.removeAll(priOpt);
 
-        return new CustomEntryType(EntryUtil.capitalizeFirst(name), req, priOpt, secondary);
+        return Optional.of(new CustomEntryType(EntryUtil.capitalizeFirst(name), req, priOpt, secondary));
 
     }
 
@@ -1297,17 +1298,6 @@ public void purgeCustomEntryTypes(int number) {
         purgeSeries(JabRefPreferences.CUSTOM_TYPE_PRIOPT, number);
     }
 
-    public void purgeCustomEntryTypes() {
-        int number = 0;
-        if(getCustomEntryType(number) != null) {
-            number++;
-        }
-
-        for(int i = 0; i < number; i++) {
-            purgeCustomEntryTypes(i);
-        }
-    }
-
     /**
      * Removes all entries keyed by prefix+number, where number is equal to or higher than the given number.
      *

src/main/java/net/sf/jabref/MetaData.java

@@ -85,9 +85,9 @@ private MetaData(Map<String, String> inData) throws ParseException {
             List<String> orderedData = new ArrayList<>();
             // We must allow for ; and \ in escape sequences.
             try {
-                String unit;
-                while ((unit = getNextUnit(data)) != null) {
-                    orderedData.add(unit);
+                Optional<String> unit;
+                while ((unit = getNextUnit(data)).isPresent()) {
+                    orderedData.add(unit.get());
                 }
             } catch (IOException ex) {
                 LOGGER.error("Weird error while parsing meta data.", ex);
@@ -200,7 +200,7 @@ public void setGroups(GroupTreeNode root) {
     /**
      * Reads the next unit. Units are delimited by ';'.
      */
-    private static String getNextUnit(Reader reader) throws IOException {
+    private static Optional<String> getNextUnit(Reader reader) throws IOException {
         int c;
         boolean escape = false;
         StringBuilder res = new StringBuilder();
@@ -217,9 +217,9 @@ private static String getNextUnit(Reader reader) throws IOException {
             }
         }
         if (res.length() > 0) {
-            return res.toString();
+            return Optional.of(res.toString());
         }
-        return null;
+        return Optional.empty();
     }
 
     public DBStrings getDBStrings() {

src/main/java/net/sf/jabref/bst/BibtexCaseChanger.java

@@ -280,7 +280,7 @@ private int convertCharIfBraceLevelIsZero(char[] c, int start, StringBuilder sb,
 
     /**
      * Determine whether there starts a special char at pos (e.g., oe, AE). Return it as string.
-     * If nothing found, return null
+     * If nothing found, return Optional.empty()
      *
      * Also used by BibtexPurify
      *

src/main/java/net/sf/jabref/collab/ChangeScanner.java

@@ -95,7 +95,7 @@ public void run() {
         try {
 
             // Parse the temporary file.
-            File tempFile = Globals.fileUpdateMonitor.getTempFile(panel.fileMonitorHandle());
+            File tempFile = Globals.getFileUpdateMonitor().getTempFile(panel.fileMonitorHandle());
             ParserResult pr = OpenDatabaseAction.loadDatabase(tempFile, Globals.prefs.getDefaultEncoding());
             inTemp = pr.getDatabase();
             mdInTemp = pr.getMetaData();
@@ -166,7 +166,7 @@ private void storeTempDatabase() {
                         .fromPreference(Globals.prefs.getBoolean(JabRefPreferences.BIBLATEX_DEFAULT_MODE)));
                 BibDatabaseWriter databaseWriter = new BibDatabaseWriter();
                 SaveSession ss = databaseWriter.saveDatabase(new BibDatabaseContext(inTemp, mdInTemp, defaults), prefs);
-                ss.commit(Globals.fileUpdateMonitor.getTempFile(panel.fileMonitorHandle()));
+                ss.commit(Globals.getFileUpdateMonitor().getTempFile(panel.fileMonitorHandle()));
             } catch (SaveException ex) {
                 LOGGER.warn("Problem updating tmp file after accepting external changes", ex);
             }

src/main/java/net/sf/jabref/exporter/SaveDatabaseAction.java

@@ -132,7 +132,7 @@ public void run() {
                 success = saveDatabase(panel.getBibDatabaseContext().getDatabaseFile(), false,
                         panel.getBibDatabaseContext().getMetaData().getEncoding());
 
-                Globals.fileUpdateMonitor.updateTimeStamp(panel.getFileMonitorHandle());
+                Globals.getFileUpdateMonitor().updateTimeStamp(panel.getFileMonitorHandle());
             } else {
                 // No file lock
                 success = false;
@@ -331,7 +331,7 @@ public void saveAs() throws Throwable {
         }
         // Register so we get notifications about outside changes to the file.
         try {
-            panel.setFileMonitorHandle(Globals.fileUpdateMonitor.addUpdateListener(panel,
+            panel.setFileMonitorHandle(Globals.getFileUpdateMonitor().addUpdateListener(panel,
                     panel.getBibDatabaseContext().getDatabaseFile()));
         } catch (IOException ex) {
             LOGGER.error("Problem registering file change notifications", ex);
@@ -368,7 +368,7 @@ public boolean isCanceled() {
      */
     private boolean checkExternalModification() {
         // Check for external modifications:
-        if (panel.isUpdatedExternally() || Globals.fileUpdateMonitor.hasBeenModified(panel.getFileMonitorHandle())) {
+        if (panel.isUpdatedExternally() || Globals.getFileUpdateMonitor().hasBeenModified(panel.getFileMonitorHandle())) {
             String[] opts = new String[] {Localization.lang("Review changes"), Localization.lang("Save"),
                     Localization.lang("Cancel")};
             int answer = JOptionPane.showOptionDialog(panel.frame(),

src/main/java/net/sf/jabref/external/AutoSetLinks.java

@@ -78,26 +78,26 @@ public static Runnable autoSetLinks(final Collection<BibEntry> entries, final Na
             diag.setTitle(Localization.lang("Automatically setting file links"));
             diag.getContentPane().add(prog, BorderLayout.CENTER);
             diag.getContentPane().add(label, BorderLayout.SOUTH);
-    
+
             diag.pack();
             diag.setLocationRelativeTo(diag.getParent());
         }
-    
+
         Runnable r = new Runnable() {
-    
+
             @Override
             public void run() {
                 // determine directories to search in
                 List<File> dirs = new ArrayList<>();
                 List<String> dirsS = databaseContext.getFileDirectory();
                 dirs.addAll(dirsS.stream().map(File::new).collect(Collectors.toList()));
-    
+
                 // determine extensions
                 Collection<String> extensions = new ArrayList<>();
                 for (final ExternalFileType type : types) {
                     extensions.add(type.getExtension());
                 }
-    
+
                 // Run the search operation:
                 Map<BibEntry, List<File>> result;
                 if (Globals.prefs.getBoolean(JabRefPreferences.AUTOLINK_USE_REG_EXP_SEARCH_KEY)) {
@@ -106,17 +106,15 @@ public void run() {
                 } else {
                     result = FileUtil.findAssociatedFiles(entries, extensions, dirs);
                 }
-    
+
                 boolean foundAny = false;
                 // Iterate over the entries:
                 for (Entry<BibEntry, List<File>> entryFilePair : result.entrySet()) {
                     FileListTableModel tableModel;
-                    String oldVal = entryFilePair.getKey().getField(Globals.FILE_FIELD);
+                    Optional<String> oldVal = entryFilePair.getKey().getFieldOptional(Globals.FILE_FIELD);
                     if (singleTableModel == null) {
                         tableModel = new FileListTableModel();
-                        if (oldVal != null) {
-                            tableModel.setContent(oldVal);
-                        }
+                        oldVal.ifPresent(tableModel::setContent);
                     } else {
                         assert entries.size() == 1;
                         tableModel = singleTableModel;
@@ -146,15 +144,15 @@ public void run() {
                             }
                             FileListEntry flEntry = new FileListEntry(f.getName(), f.getPath(), type);
                             tableModel.addEntry(tableModel.getRowCount(), flEntry);
-    
+
                             String newVal = tableModel.getStringRepresentation();
                             if (newVal.isEmpty()) {
                                 newVal = null;
                             }
                             if (ce != null) {
                                 // store undo information
                                 UndoableFieldChange change = new UndoableFieldChange(entryFilePair.getKey(),
-                                        Globals.FILE_FIELD, oldVal, newVal);
+                                        Globals.FILE_FIELD, oldVal.orElse(null), newVal);
                                 ce.addEdit(change);
                             }
                             // hack: if table model is given, do NOT modify entry
@@ -167,12 +165,12 @@ public void run() {
                         }
                     }
                 }
-    
+
                 // handle callbacks and dialog
                 // FIXME: The ID signals if action was successful :/
                 final int id = foundAny ? 1 : 0;
                 SwingUtilities.invokeLater(new Runnable() {
-    
+
                     @Override
                     public void run() {
                         if (diag != null) {