Improve database writer

CHANGELOG.md

@@ -13,6 +13,8 @@ to [sourceforge feature requests](https://sourceforge.net/p/jabref/features/) by
 ## [Unreleased]
 
 ### Changed
+- Implemented [#756](https://github.com/JabRef/jabref/issues/756): Add possibility to reformat all entries on save (under Preferences, File)
+- Comments and preamble are serialized with capitalized first letter, i.e. `@Comment` instead of `@comment` and `@Preamble` instead of `@PREAMBLE`.
 - Global sorting options and preferences are removed. Databases can still be sorted on save, but this is configured locally and stored in the file
 - OvidImporter now also imports fields: doi, issn, language and keywords
 - Implemented [#647](https://github.com/JabRef/jabref/issues/647): The preview can now be copied
@@ -26,6 +28,7 @@ to [sourceforge feature requests](https://sourceforge.net/p/jabref/features/) by
 
 
 ### Fixed
+- Fixed [#621](https://github.com/JabRef/jabref/issues/621) and [#669](https://github.com/JabRef/jabref/issues/669): Encoding and preamble now end with newline.
 - Make BibTex parser more robust against missing newlines
 - Fix bug that prevented the import of BibTex entries having only a key as content
 - Fixed [#666](https://github.com/JabRef/jabref/issues/666): MS Office 2007 export is working again

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

@@ -32,8 +32,6 @@ public BibDatabaseContext(BibDatabase database, MetaData metaData, Defaults defa
         this.defaults = Objects.requireNonNull(defaults);
         this.database = Objects.requireNonNull(database);
         this.metaData = Objects.requireNonNull(metaData);
-
-        this.setMode(getMode());
     }
 
     public BibDatabaseContext(BibDatabase database, MetaData metaData, File file, Defaults defaults) {

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

@@ -309,11 +309,13 @@ public Optional<Vector<ParserResult>> processArguments(String[] args, boolean in
                         if (!pr.isInvalid()) {
                             try {
                                 System.out.println(Localization.lang("Saving") + ": " + data[0]);
-                                Defaults defaults = new Defaults(BibDatabaseMode.fromPreference(Globals.prefs.getBoolean(JabRefPreferences.BIBLATEX_MODE)));
-                                SaveSession session = FileActions.saveDatabase(
-                                        new BibDatabaseContext(pr.getDatabase(), pr.getMetaData(), defaults),
-                                        new File(data[0]), Globals.prefs, false, false,
-                                        Globals.prefs.getDefaultEncoding(), false);
+                                SavePreferences prefs = SavePreferences.loadForSaveFromPreferences(Globals.prefs);
+                                Defaults defaults = new Defaults(BibDatabaseMode
+                                        .fromPreference(Globals.prefs.getBoolean(JabRefPreferences.BIBLATEX_MODE)));
+                                BibDatabaseWriter databaseWriter = new BibDatabaseWriter();
+                                SaveSession session = databaseWriter.saveDatabase(
+                                        new BibDatabaseContext(pr.getDatabase(), pr.getMetaData(), defaults), prefs);
+
                                 // Show just a warning message if encoding didn't work for all characters:
                                 if (!session.getWriter().couldEncodeAll()) {
                                     System.err.println(Localization.lang("Warning") + ": "
@@ -323,7 +325,7 @@ public Optional<Vector<ParserResult>> processArguments(String[] args, boolean in
                                             + " "
                                             + session.getWriter().getProblemCharacters());
                                 }
-                                session.commit();
+                                session.commit(new File(data[0]));
                             } catch (SaveException ex) {
                                 System.err.println(Localization.lang("Could not save file.") + "\n"
                                         + ex.getLocalizedMessage());
@@ -399,10 +401,14 @@ public Optional<Vector<ParserResult>> processArguments(String[] args, boolean in
 
                             try {
                                 System.out.println(Localization.lang("Saving") + ": " + subName);
-                                Defaults defaults = new Defaults(BibDatabaseMode.fromPreference(Globals.prefs.getBoolean(JabRefPreferences.BIBLATEX_MODE)));
-                                SaveSession session = FileActions.saveDatabase(new BibDatabaseContext(newBase, defaults),
-                                        new File(subName), Globals.prefs, false, false,
-                                        Globals.prefs.getDefaultEncoding(), false);
+                                SavePreferences prefs = SavePreferences.loadForSaveFromPreferences(Globals.prefs);
+                                BibDatabaseWriter databaseWriter = new BibDatabaseWriter();
+                                Defaults defaults = new Defaults(BibDatabaseMode
+                                        .fromPreference(Globals.prefs.getBoolean(JabRefPreferences.BIBLATEX_MODE)));
+                                SaveSession session = databaseWriter.saveDatabase(
+                                        new BibDatabaseContext(newBase, defaults), prefs);
+
+
                                 // Show just a warning message if encoding didn't work for all characters:
                                 if (!session.getWriter().couldEncodeAll()) {
                                     System.err.println(Localization.lang("Warning") + ": "
@@ -412,7 +418,7 @@ public Optional<Vector<ParserResult>> processArguments(String[] args, boolean in
                                             + " "
                                             + session.getWriter().getProblemCharacters());
                                 }
-                                session.commit();
+                                session.commit(new File(subName));
                             } catch (SaveException ex) {
                                 System.err.println(Localization.lang("Could not save file.") + "\n"
                                         + ex.getLocalizedMessage());

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

@@ -60,7 +60,6 @@
 public class JabRefPreferences {
     private static final Log LOGGER = LogFactory.getLog(JabRefPreferences.class);
     public static final String EXTERNAL_FILE_TYPES = "externalFileTypes";
-
     /**
      * HashMap that contains all preferences which are set by default
      */
@@ -110,6 +109,7 @@ public class JabRefPreferences {
     public static final String TABLE_SECONDARY_SORT_DESCENDING = "secDescending";
     public static final String TABLE_TERTIARY_SORT_FIELD = "terSort";
     public static final String TABLE_TERTIARY_SORT_DESCENDING = "terDescending";
+    public static final String REFORMAT_FILE_ON_SAVE_AND_EXPORT = "reformatFileOnSaveAndExport";
     public static final String EXPORT_IN_ORIGINAL_ORDER = "exportInOriginalOrder";
     public static final String EXPORT_IN_SPECIFIED_ORDER = "exportInSpecifiedOrder";
     public static final String EXPORT_PRIMARY_SORT_FIELD = "exportPriSort";
@@ -505,6 +505,8 @@ private JabRefPreferences() {
         defaults.put(TABLE_TERTIARY_SORT_FIELD, "title");
         defaults.put(TABLE_TERTIARY_SORT_DESCENDING, Boolean.FALSE);
 
+        defaults.put(REFORMAT_FILE_ON_SAVE_AND_EXPORT, Boolean.FALSE);
+
         // export order
         defaults.put(EXPORT_IN_ORIGINAL_ORDER, Boolean.FALSE);
         defaults.put(EXPORT_IN_SPECIFIED_ORDER, Boolean.FALSE);

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

@@ -24,14 +24,17 @@
 import net.sf.jabref.logic.labelPattern.DatabaseLabelPattern;
 import net.sf.jabref.model.database.BibDatabase;
 import net.sf.jabref.sql.DBStrings;
-import net.sf.jabref.logic.util.strings.StringUtil;
 
 public class MetaData implements Iterable<String> {
 
     public static final String META_FLAG = "jabref-meta: ";
+    public static final String SAVE_ORDER_CONFIG = "saveOrderConfig";
     private static final String PREFIX_KEYPATTERN = "keypattern_";
     private static final String KEYPATTERNDEFAULT = "keypatterndefault";
     static final String DATABASE_TYPE = "DATABASE_TYPE";
+    public static final String GROUPSVERSION = "groupsversion";
+    public static final String GROUPSTREE = "groupstree";
+    public static final String GROUPS = "groups";
 
     private final Map<String, List<String>> metaData = new HashMap<>();
     private GroupTreeNode groupsRoot;
@@ -70,16 +73,16 @@ public MetaData(Map<String, String> inData, BibDatabase db) {
                 } catch (IOException ex) {
                     System.err.println("Weird error while parsing meta data.");
                 }
-                if ("groupsversion".equals(entry.getKey())) {
+                if (GROUPSVERSION.equals(entry.getKey())) {
                     if (!orderedData.isEmpty()) {
                         groupsVersionOnDisk = Integer.parseInt(orderedData.get(0));
                     }
-                } else if ("groupstree".equals(entry.getKey())) {
+                } else if (GROUPSTREE.equals(entry.getKey())) {
                     groupsTreePresent = true;
                     treeGroupsData = orderedData; // save for later user
                     // actual import operation is handled later because "groupsversion"
                     // tag might not yet have been read
-                } else if ("groups".equals(entry.getKey())) {
+                } else if (GROUPS.equals(entry.getKey())) {
                     flatGroupsData = orderedData;
                 } else {
                     putData(entry.getKey(), orderedData);
@@ -260,55 +263,6 @@ public void setGroups(GroupTreeNode root) {
         groupTreeValid = true;
     }
 
-    /**
-     * Writes all data to the specified writer, using each object's toString()
-     * method.
-     */
-    public void writeMetaData(Writer out) throws IOException {
-        // write all meta data except groups
-        SortedSet<String> sortedKeys = new TreeSet<>(metaData.keySet());
-
-        for (String key : sortedKeys) {
-
-            StringBuffer sb = new StringBuffer();
-            sb.append(Globals.NEWLINE).append(Globals.NEWLINE);
-            List<String> orderedData = metaData.get(key);
-            sb.append("@comment{").append(META_FLAG).append(key).append(':');
-            for (String data : orderedData) {
-                sb.append(StringUtil.quote(data, ";", '\\')).append(';');
-            }
-            sb.append('}');
-
-            out.write(sb.toString());
-        }
-        // write groups if present. skip this if only the root node exists
-        // (which is always the AllEntriesGroup).
-        if ((groupsRoot != null) && (groupsRoot.getChildCount() > 0)) {
-            StringBuffer sb = new StringBuffer();
-            // write version first
-            sb.append(Globals.NEWLINE).append(Globals.NEWLINE);
-            sb.append("@comment{").append(META_FLAG).append("groupsversion:");
-            sb.append(VersionHandling.CURRENT_VERSION).append(";}");
-
-            out.write(sb.toString());
-
-            // now write actual groups
-            sb = new StringBuffer();
-            sb.append(Globals.NEWLINE).append(Globals.NEWLINE);
-            sb.append("@comment{").append(META_FLAG).append("groupstree:");
-            sb.append(Globals.NEWLINE);
-            // GroupsTreeNode.toString() uses "\n" for separation
-            StringTokenizer tok = new StringTokenizer(groupsRoot.getTreeAsString(), Globals.NEWLINE);
-            while (tok.hasMoreTokens()) {
-                StringBuffer s = new StringBuffer(StringUtil.quote(tok.nextToken(), ";", '\\')).append(';');
-                sb.append(s);
-                sb.append(Globals.NEWLINE);
-            }
-            sb.append('}');
-            out.write(sb.toString());
-        }
-    }
-
     /**
      * Reads the next unit. Units are delimited by ';'.
      */

src/main/java/net/sf/jabref/bibtex/BibEntryWriter.java

@@ -27,14 +27,17 @@ public BibEntryWriter(LatexFieldFormatter fieldFormatter, boolean write) {
     }
 
     public void write(BibEntry entry, Writer out, BibDatabaseMode bibDatabaseMode) throws IOException {
+        write(entry, out, bibDatabaseMode, false);
+    }
+    public void write(BibEntry entry, Writer out, BibDatabaseMode bibDatabaseMode, Boolean reformat) throws IOException {
         // if the entry has not been modified, write it as it was
-        if (!entry.hasChanged()) {
+        if (!reformat && !entry.hasChanged()) {
             out.write(entry.getParsedSerialization());
             return;
         }
-        out.write(Globals.NEWLINE + Globals.NEWLINE);
-
+        out.write(Globals.NEWLINE);
         writeRequiredFieldsFirstRemainingFieldsSecond(entry, out, bibDatabaseMode);
+        out.write(Globals.NEWLINE);
     }
 
     public void writeWithoutPrependedNewlines(BibEntry entry, Writer out, BibDatabaseMode bibDatabaseMode) throws IOException {

src/main/java/net/sf/jabref/bibtex/comparator/FieldComparator.java

@@ -17,6 +17,7 @@
 
 import net.sf.jabref.gui.InternalBibtexFields;
 import net.sf.jabref.gui.maintable.MainTableFormat;
+import net.sf.jabref.logic.config.SaveOrderConfig;
 import net.sf.jabref.logic.util.strings.StringUtil;
 import net.sf.jabref.model.entry.AuthorList;
 import net.sf.jabref.model.entry.MonthUtil;
@@ -27,6 +28,7 @@
 import java.text.ParseException;
 import java.text.RuleBasedCollator;
 import java.util.Comparator;
+import java.util.Objects;
 
 /**
  *
@@ -71,7 +73,7 @@ public FieldComparator(String field) {
     }
 
     public FieldComparator(String field, boolean reversed) {
-        this.fieldName = field;
+        this.fieldName = Objects.requireNonNull(field);
         this.field = field.split(MainTableFormat.COL_DEFINITION_FIELD_SEPARATOR);
         multiplier = reversed ? -1 : 1;
         isTypeHeader = this.field[0].equals(BibEntry.TYPE_HEADER);
@@ -82,6 +84,10 @@ public FieldComparator(String field, boolean reversed) {
         isNumeric = InternalBibtexFields.isNumeric(this.field[0]);
     }
 
+    public FieldComparator(SaveOrderConfig.SortCriterion sortCriterion) {
+        this(sortCriterion.field, sortCriterion.descending);
+    }
+
     @Override
     public int compare(BibEntry e1, BibEntry e2) {
         Object f1;

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

@@ -28,8 +28,9 @@
 import org.apache.commons.logging.LogFactory;
 
 import net.sf.jabref.*;
-import net.sf.jabref.exporter.FileActions;
+import net.sf.jabref.exporter.BibDatabaseWriter;
 import net.sf.jabref.exporter.SaveException;
+import net.sf.jabref.exporter.SavePreferences;
 import net.sf.jabref.exporter.SaveSession;
 import net.sf.jabref.groups.GroupTreeNode;
 import net.sf.jabref.gui.BasePanel;
@@ -158,11 +159,14 @@ private void storeTempDatabase() {
             @Override
             public void run() {
                 try {
+                    SavePreferences prefs = SavePreferences.loadForSaveFromPreferences(Globals.prefs)
+                        .withMakeBackup(false)
+                        .withEncoding(panel.getEncoding());
+
                     Defaults defaults = new Defaults(BibDatabaseMode.fromPreference(Globals.prefs.getBoolean(JabRefPreferences.BIBLATEX_MODE)));
-                    SaveSession ss = FileActions.saveDatabase(new BibDatabaseContext(inTemp, mdInTemp, defaults),
-                            Globals.fileUpdateMonitor.getTempFile(panel.fileMonitorHandle()), Globals.prefs, false,
-                            false, panel.getEncoding(), true);
-                    ss.commit();
+                    BibDatabaseWriter databaseWriter = new BibDatabaseWriter();
+                    SaveSession ss = databaseWriter.saveDatabase(new BibDatabaseContext(inTemp, mdInTemp, defaults), prefs);
+                    ss.commit(Globals.fileUpdateMonitor.getTempFile(panel.fileMonitorHandle()));
                 } catch (SaveException ex) {
                     LOGGER.warn("Problem updating tmp file after accepting external changes", ex);
                 }

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

@@ -96,9 +96,13 @@ private static boolean autoSave(BasePanel panel) {
         File databaseFile = panel.getBibDatabaseContext().getDatabaseFile();
         File backupFile = AutoSaveManager.getAutoSaveFile(databaseFile);
         try {
-            SaveSession ss = FileActions.saveDatabase(panel.getBibDatabaseContext(),
-                    backupFile, Globals.prefs, false, false, panel.getEncoding(), true);
-            ss.commit();
+            SavePreferences prefs = SavePreferences.loadForSaveFromPreferences(Globals.prefs)
+                    .withMakeBackup(false)
+                    .withEncoding(panel.getEncoding());
+
+            BibDatabaseWriter databaseWriter = new BibDatabaseWriter();
+            SaveSession ss = databaseWriter.saveDatabase(panel.getBibDatabaseContext(), prefs);
+
         } catch (SaveException e) {
             LOGGER.error("Problem with automatic save", e);
             return false;