Rebase

src/jmh/java/net/sf/jabref/benchmarks/Benchmarks.java

@@ -45,7 +45,7 @@ public class Benchmarks {
     private String htmlConversionString;
 
     @Setup
-    public void init() throws IOException {
+    public void init() throws Exception {
         Globals.prefs = JabRefPreferences.getInstance();
 
         Random randomizer = new Random();
@@ -79,7 +79,7 @@ public ParserResult parse() throws IOException {
     }
 
     @Benchmark
-    public String write() throws SaveException {
+    public String write() throws Exception {
         BibtexDatabaseWriter<StringSaveSession> databaseWriter = new BibtexDatabaseWriter<>(StringSaveSession::new);
         StringSaveSession saveSession = databaseWriter.savePartOfDatabase(
                 new BibDatabaseContext(database, new MetaData(), new Defaults()), database.getEntries(),

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

@@ -69,12 +69,12 @@ private static List<FieldChange> applySaveActions(List<BibEntry> toChange, MetaD
         List<FieldChange> changes = new ArrayList<>();
 
         Optional<FieldFormatterCleanups> saveActions = metaData.getSaveActions();
-        if (saveActions.isPresent()) {
+        saveActions.ifPresent(actions -> {
             // save actions defined -> apply for every entry
             for (BibEntry entry : toChange) {
-                changes.addAll(saveActions.get().applySaveActions(entry));
+                changes.addAll(actions.applySaveActions(entry));
             }
-        }
+        });
 
         return changes;
     }
@@ -104,11 +104,11 @@ private static List<Comparator<BibEntry>> getSaveComparators(SavePreferences pre
     }
 
     /*
-         * We have begun to use getSortedEntries() for both database save operations
-         * and non-database save operations.  In a non-database save operation
-         * (such as the exportDatabase call), we do not wish to use the
-         * global preference of saving in standard order.
-         */
+     * We have begun to use getSortedEntries() for both database save operations
+     * and non-database save operations.  In a non-database save operation
+     * (such as the exportDatabase call), we do not wish to use the
+     * global preference of saving in standard order.
+    */
     public static List<BibEntry> getSortedEntries(BibDatabaseContext bibDatabaseContext, List<BibEntry> entriesToSort,
             SavePreferences preferences) {
         Objects.requireNonNull(bibDatabaseContext);
@@ -242,14 +242,6 @@ protected void writeMetaData(MetaData metaData) throws SaveException {
 
     protected abstract void writePreamble(String preamble) throws SaveException;
 
-    private void writeUserCommentsForString(BibtexString string, Writer out) throws IOException {
-        String userComments = string.getUserComments();
-
-        if(!userComments.isEmpty()) {
-            out.write(userComments + Globals.NEWLINE);
-        }
-    }
-
     /**
      * Write all strings in alphabetical order, modified to produce a safe (for
      * BibTeX) order of the strings if they reference each other.

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

@@ -87,12 +87,18 @@ protected void writePreamble(String preamble) throws SaveException {
     @Override
     protected void writeString(BibtexString bibtexString, boolean isFirstString, int maxKeyLength, Boolean reformatFile) throws SaveException {
         try {
-            //if the string has not been modified, write it back as it was
+            // If the string has not been modified, write it back as it was
             if (!reformatFile && !bibtexString.hasChanged()) {
                 getWriter().write(bibtexString.getParsedSerialization());
                 return;
             }
 
+            // Write user comments
+            String userComments = bibtexString.getUserComments();
+            if(!userComments.isEmpty()) {
+                getWriter().write(userComments + Globals.NEWLINE);
+            }
+
             if (isFirstString) {
                 getWriter().write(Globals.NEWLINE);
             }

src/test/java/net/sf/jabref/exporter/BibtexDatabaseWriterTest.java

@@ -277,7 +277,7 @@ public void roundtrip() throws Exception {
     }
 
     @Test
-    public void roundtripWithUserComment() throws IOException {
+    public void roundtripWithUserComment() throws Exception {
         Path testBibtexFile = Paths.get("src/test/resources/testbib/bibWithUserComments.bib");
         Charset encoding = StandardCharsets.UTF_8;
         ParserResult result = BibtexParser.parse(ImportFormat.getReader(testBibtexFile, encoding));
@@ -286,14 +286,14 @@ public void roundtripWithUserComment() throws IOException {
         BibDatabaseContext context = new BibDatabaseContext(result.getDatabase(), result.getMetaData(),
                 new Defaults(BibDatabaseMode.BIBTEX));
 
-        databaseWriter.writePartOfDatabase(stringWriter, context, result.getDatabase().getEntries(), preferences);
+        StringSaveSession session = databaseWriter.savePartOfDatabase(context, result.getDatabase().getEntries(), preferences);
         try (Scanner scanner = new Scanner(testBibtexFile,encoding.name())) {
-            assertEquals(scanner.useDelimiter("\\A").next(), stringWriter.toString());
+            assertEquals(scanner.useDelimiter("\\A").next(), session.getStringValue());
         }
     }
 
     @Test
-    public void roundtripWithUserCommentAndEntryChange() throws IOException {
+    public void roundtripWithUserCommentAndEntryChange() throws Exception {
         Path testBibtexFile = Paths.get("src/test/resources/testbib/bibWithUserComments.bib");
         Charset encoding = StandardCharsets.UTF_8;
         ParserResult result = BibtexParser.parse(ImportFormat.getReader(testBibtexFile, encoding));
@@ -305,39 +305,37 @@ public void roundtripWithUserCommentAndEntryChange() throws IOException {
         BibDatabaseContext context = new BibDatabaseContext(result.getDatabase(), result.getMetaData(),
                 new Defaults(BibDatabaseMode.BIBTEX));
 
-        databaseWriter.writePartOfDatabase(stringWriter, context, result.getDatabase().getEntries(), preferences);
+        StringSaveSession session = databaseWriter.savePartOfDatabase(context, result.getDatabase().getEntries(), preferences);
 
         try (Scanner scanner = new Scanner(Paths.get("src/test/resources/testbib/bibWithUserCommentAndEntryChange.bib"),encoding.name())) {
-            assertEquals(scanner.useDelimiter("\\A").next(), stringWriter.toString());
+            assertEquals(scanner.useDelimiter("\\A").next(), session.getStringValue());
         }
     }
 
     @Test
-    public void roundtripWithUserCommentBeforeStringAndChange() throws IOException {
+    public void roundtripWithUserCommentBeforeStringAndChange() throws Exception {
         Path testBibtexFile = Paths.get("src/test/resources/testbib/complex.bib");
         Charset encoding = StandardCharsets.UTF_8;
         ParserResult result = BibtexParser.parse(ImportFormat.getReader(testBibtexFile, encoding));
 
-        BibtexString string = result.getDatabase().getStringValues().iterator().next();
-        if(string.getContent().isEmpty()) {
-            // do nothing
-        } else {
-            string.setContent("my first string");
+        for (BibtexString string : result.getDatabase().getStringValues()) {
+            // Mark them as changed
+            string.setContent(string.getContent());
         }
 
         SavePreferences preferences = new SavePreferences().withEncoding(encoding).withSaveInOriginalOrder(true);
         BibDatabaseContext context = new BibDatabaseContext(result.getDatabase(), result.getMetaData(),
                 new Defaults(BibDatabaseMode.BIBTEX));
 
-        databaseWriter.writePartOfDatabase(stringWriter, context, result.getDatabase().getEntries(), preferences);
+        StringSaveSession session = databaseWriter.savePartOfDatabase(context, result.getDatabase().getEntries(), preferences);
 
         try (Scanner scanner = new Scanner(testBibtexFile,encoding.name())) {
-            assertEquals(scanner.useDelimiter("\\A").next(), stringWriter.toString());
+            assertEquals(scanner.useDelimiter("\\A").next(), session.getStringValue());
         }
     }
 
     @Test
-    public void writeSavedSerializationOfEntryIfUnchanged() throws IOException {
+    public void writeSavedSerializationOfEntryIfUnchanged() throws Exception {
         BibEntry entry = new BibEntry();
         entry.setType(BibtexEntryTypes.ARTICLE);
         entry.setField("author", "Mr. author");

src/test/resources/testbib/complex.bib

@@ -5,6 +5,7 @@ @Preamble{preamble
 This is some arbitrary user comment that should be preserved
 
 @String{firstString  = {my first string}}
+This is some user comment in front of a string, should also be preserved.
 @String{secondString = {}}
 
 @ARTICLE{1102917,