Merge branch 'master' into fileChooserRefactor

* master:
  Unified some equals (JabRef#1640)
  Export OO/LO citations to new database (JabRef#1630)
  Fixed JabRef#1639 (JabRef#1641)
  Replaced some getField and fixed some bugs (JabRef#1631)
  Keep @comment text in a bib file (JabRef#1638)

# Conflicts:
#	src/main/java/net/sf/jabref/importer/AppendDatabaseAction.java

CHANGELOG.md

@@ -20,17 +20,23 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Added ISBN integrity checker
 - Added filter to not show selected integrity checks
 - Enhance the entry customization dialog to give better visual feedback
+- It is now possible to generate a new BIB database from the citations in an OpenOffice/LibreOffice document
 - The arXiv fetcher now also supports free-text search queries
 - [#1345](https://github.com/JabRef/jabref/issues/1345) Cleanup ISSN
 
 ### Fixed
+- Fixed [#1632](https://github.com/JabRef/jabref/issues/1632) User comments (@Comment) with or without brackets are now kept
 - Fixed [#1264](https://github.com/JabRef/jabref/issues/1264): S with caron does not render correctly
 - LaTeX to Unicode converter now handles combining accents
+- Fixed NullPointerException when clicking Browse in Journal abbreviations with empty text field
+- Fixed NullPointerException when opening file in Plain text import
+- Fixed NullPointerException when appending database
 - Fixed [#636](https://github.com/JabRef/jabref/issues/636): DOI in export filters
 - Fixed [#1527](https://github.com/JabRef/jabref/issues/1527): 'Get BibTeX data from DOI' Removes Marking
 - Fixed [#1592](https://github.com/JabRef/jabref/issues/1592): LibreOffice: wrong numbers in citation labels
 - The merge entry dialog showed wrong heading after merging from DOI
 - Fixed [#1321](https://github.com/JabRef/jabref/issues/1321): LaTeX commands in fields not displayed in the list of references
+- Fixed [#1639](https://github.com/JabRef/jabref/issues/1639): Google Scholar fetching works again.
 - Date fields in the BibLatex standard are now always formatted in the correct way, independent of the preferences
 
 ### Removed

src/main/java/net/sf/jabref/gui/JabRefFrame.java

@@ -982,7 +982,7 @@ public BasePanel getBasePanelAt(int i) {
      *
      */
     public List<BasePanel> getBasePanelList() {
-        List<BasePanel> returnList = new ArrayList<>(getBasePanelCount());
+        List<BasePanel> returnList = new ArrayList<>();
         for (int i=0; i< getBasePanelCount(); i++) {
             returnList.add((BasePanel) tabbedPane.getComponentAt(i));
         }

src/main/java/net/sf/jabref/gui/entryeditor/EntryEditor.java

@@ -35,6 +35,7 @@
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Map.Entry;
 import java.util.Objects;
 import java.util.Optional;
 import java.util.Set;
@@ -803,25 +804,30 @@ private boolean storeSource() {
             }
 
             // First, remove fields that the user has removed.
-            for (String field : entry.getFieldNames()) {
-                if (InternalBibtexFields.isDisplayableField(field) && !newEntry.hasField(field)) {
-                    compound.addEdit(new UndoableFieldChange(entry, field, entry.getField(field), null));
-                    entry.clearField(field);
+            for (Entry<String, String> field : entry.getFieldMap().entrySet()) {
+                String fieldName = field.getKey();
+                String fieldValue = field.getValue();
+
+                if (InternalBibtexFields.isDisplayableField(fieldName) && !newEntry.hasField(fieldName)) {
+                    compound.addEdit(
+                            new UndoableFieldChange(entry, fieldName, fieldValue, null));
+                    entry.clearField(fieldName);
                     entryChanged = true;
                 }
             }
 
             // Then set all fields that have been set by the user.
-            for (String field : newEntry.getFieldNames()) {
-                String oldValue = entry.getField(field);
-                String newValue = newEntry.getField(field);
+            for (Entry<String, String> field : newEntry.getFieldMap().entrySet()) {
+                String fieldName = field.getKey();
+                String oldValue = entry.getFieldOptional(fieldName).orElse(null);
+                String newValue = field.getValue();
                 if (!Objects.equals(oldValue, newValue)) {
                     // Test if the field is legally set.
                     new LatexFieldFormatter(LatexFieldFormatterPreferences.fromPreferences(Globals.prefs))
-                            .format(newValue, field);
+                            .format(newValue, fieldName);
 
-                    compound.addEdit(new UndoableFieldChange(entry, field, oldValue, newValue));
-                    entry.setField(field, newValue);
+                    compound.addEdit(new UndoableFieldChange(entry, fieldName, oldValue, newValue));
+                    entry.setField(fieldName, newValue);
                     entryChanged = true;
                 }
             }

src/main/java/net/sf/jabref/gui/journals/ManageJournalsPanel.java

@@ -196,23 +196,29 @@ public ManageJournalsPanel(final JabRefFrame frame) {
         });
 
         browseNew.addActionListener(e -> {
-            Path old = null;
+            String name;
             if (!newNameTf.getText().isEmpty()) {
-                old = Paths.get(newNameTf.getText());
+                name = FileDialogs.getNewFile(frame, Paths.get(newNameTf.getText()).toFile(), Collections.emptyList(), JFileChooser.SAVE_DIALOG,
+                        false);
+            } else {
+                name = FileDialogs.getNewFile(frame, null, Collections.emptyList(), JFileChooser.SAVE_DIALOG, false);
             }
-            String name = FileDialogs.getNewFile(frame, old.toFile(), null, JFileChooser.SAVE_DIALOG, false);
+
             if (name != null) {
                 newNameTf.setText(name);
                 newFile.setSelected(true);
             }
         });
 
         browseOld.addActionListener(e -> {
-            Path old = null;
+            String name;
             if (!personalFile.getText().isEmpty()) {
-                old = Paths.get(personalFile.getText());
+                name = FileDialogs.getNewFile(frame, Paths.get(personalFile.getText()).toFile(),
+                        Collections.emptyList(), JFileChooser.OPEN_DIALOG, false);
+            } else {
+                name = FileDialogs.getNewFile(frame, null, Collections.emptyList(), JFileChooser.OPEN_DIALOG, false);
             }
-            String name = FileDialogs.getNewFile(frame, old.toFile(), null, JFileChooser.OPEN_DIALOG, false);
+
             if (name != null) {
                 personalFile.setText(name);
                 oldFile.setSelected(true);

src/main/java/net/sf/jabref/gui/maintable/SpecialMainTableColumns.java

@@ -18,7 +18,6 @@
 import net.sf.jabref.specialfields.Rank;
 import net.sf.jabref.specialfields.ReadStatus;
 import net.sf.jabref.specialfields.Relevance;
-import net.sf.jabref.specialfields.SpecialFieldValue;
 import net.sf.jabref.specialfields.SpecialFieldsUtils;
 
 public class SpecialMainTableColumns {
@@ -42,12 +41,9 @@ public String getDisplayName() {
 
         @Override
         public Object getColumnValue(BibEntry entry) {
-            SpecialFieldValue rank = Rank.getInstance().parse(entry.getField(SpecialFieldsUtils.FIELDNAME_RANKING));
-            if (rank == null) {
-                return null;
-            } else {
-                return rank.createLabel();
-            }
+
+            return entry.getFieldOptional(SpecialFieldsUtils.FIELDNAME_RANKING)
+                    .flatMap(Rank.getInstance()::parse).map(rank -> rank.createLabel()).orElse(null);
         }
     };
 
@@ -58,13 +54,8 @@ public Object getColumnValue(BibEntry entry) {
         @Override
         public Object getColumnValue(BibEntry entry) {
 
-            SpecialFieldValue prio = Priority.getInstance()
-                    .parse(entry.getField(SpecialFieldsUtils.FIELDNAME_PRIORITY));
-            if (prio == null) {
-                return null;
-            } else {
-                return prio.createLabel();
-            }
+            return entry.getFieldOptional(SpecialFieldsUtils.FIELDNAME_PRIORITY)
+                    .flatMap(Priority.getInstance()::parse).map(prio -> prio.createLabel()).orElse(null);
         }
     };
 
@@ -75,13 +66,8 @@ public Object getColumnValue(BibEntry entry) {
         @Override
         public Object getColumnValue(BibEntry entry) {
 
-            SpecialFieldValue status = ReadStatus.getInstance()
-                    .parse(entry.getField(SpecialFieldsUtils.FIELDNAME_READ));
-            if (status == null) {
-                return null;
-            } else {
-                return status.createLabel();
-            }
+            return entry.getFieldOptional(SpecialFieldsUtils.FIELDNAME_READ)
+                    .flatMap(ReadStatus.getInstance()::parse).map(status -> status.createLabel()).orElse(null);
         }
     };
 

src/main/java/net/sf/jabref/gui/openoffice/CreationException.java

@@ -0,0 +1,28 @@
+/*  Copyright (C) 2016 JabRef contributors.
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License along
+    with this program; if not, write to the Free Software Foundation, Inc.,
+    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+*/
+package net.sf.jabref.gui.openoffice;
+
+/**
+ * Exception used to indicate that the plugin attempted to set a character format that is
+ * not defined in the current OpenOffice document.
+ */
+class CreationException extends Exception {
+
+    public CreationException(String message) {
+        super(message);
+    }
+
+}