Keep @Comment text in a bib file

CHANGELOG.md

@@ -24,6 +24,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - [#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 [#636](https://github.com/JabRef/jabref/issues/636): DOI in export filters

src/main/java/net/sf/jabref/importer/fileformat/BibtexParser.java

@@ -243,22 +243,18 @@ private void parseAndAddEntry(String type) {
     }
 
     private void parseJabRefComment(Map<String, String> meta) throws IOException {
-        StringBuilder buffer = parseBracketedTextExactly();
-        /**
-         *
-         * Metadata are used to store Bibkeeper-specific
-         * information in .bib files.
-         *
-         * Metadata are stored in bibtex files in the format
-         *
-         * @comment{jabref-meta: type:data0;data1;data2;...}
-         *
-         * Each comment that starts with the META_FLAG is stored
-         * in the meta HashMap, with type as key. Unluckily, the
-         * old META_FLAG bibkeeper-meta: was used in JabRef 1.0
-         * and 1.1, so we need to support it as well. At least
-         * for a while. We'll always save with the new one.
-         */
+        StringBuilder buffer = null;
+        try {
+            buffer = parseBracketedTextExactly();
+        } catch (IOException e) {
+            /* if we get an IO Exception here, than we have an unbracketed comment,
+            * which means that we should just return and the comment will be picked up as arbitrary text
+            *  by the parser
+             */
+            LOGGER.info("Found unbracketed comment");
+            return;
+        }
+
         String comment = buffer.toString().replaceAll("[\\x0d\\x0a]", "");
         if (comment.substring(0,
                 Math.min(comment.length(), MetaData.META_FLAG.length())).equals(
@@ -297,11 +293,8 @@ private void parseJabRefComment(Map<String, String> meta) throws IOException {
 
             // custom entry types are always re-written by JabRef and not stored in the file
             dumpTextReadSoFarToString();
-        } else {
-            // FIXME: user comments are simply dropped
-            // at least, we log that we ignored the comment
-            LOGGER.info("Dropped comment from database: " + comment);
         }
+
     }
 
 
@@ -329,14 +322,14 @@ private String dumpTextReadSoFarToString() {
         // if there is no entry found, simply return the content (necessary to parse text remaining after the last entry)
         if (indexOfAt == -1) {
             return purgeEOFCharacters(result);
-        } else if(result.contains(SavePreferences.ENCODING_PREFIX)) {
+        } else if (result.contains(SavePreferences.ENCODING_PREFIX)) {
             // purge the encoding line if it exists
             int runningIndex = result.indexOf(SavePreferences.ENCODING_PREFIX);
-            while(runningIndex < indexOfAt) {
-                if(result.charAt(runningIndex) == '\n') {
+            while (runningIndex < indexOfAt) {
+                if (result.charAt(runningIndex) == '\n') {
                     break;
-                } else if(result.charAt(runningIndex) == '\r') {
-                    if(result.charAt(runningIndex + 1) == '\n') {
+                } else if (result.charAt(runningIndex) == '\r') {
+                    if (result.charAt(runningIndex + 1) == '\n') {
                         runningIndex++;
                     }
                     break;
@@ -413,10 +406,10 @@ private void skipSpace() throws IOException {
 
     private void skipOneNewline() throws IOException {
         skipSpace();
-        if(peek() == '\r') {
+        if (peek() == '\r') {
             read();
         }
-        if(peek() == '\n') {
+        if (peek() == '\n') {
             read();
         }
     }
@@ -460,7 +453,7 @@ private int peek() throws IOException {
     private int read() throws IOException {
         int character = pushbackReader.read();
 
-        if(! isEOFCharacter(character)) {
+        if (!isEOFCharacter(character)) {
             pureTextFromFile.offerLast((char) character);
         }
         if (character == '\n') {
@@ -474,7 +467,7 @@ private void unread(int character) throws IOException {
             line--;
         }
         pushbackReader.unread(character);
-        if(pureTextFromFile.getLast() == character) {
+        if (pureTextFromFile.getLast() == character) {
             pureTextFromFile.pollLast();
         }
     }
@@ -799,7 +792,7 @@ private String parseKey() throws IOException {
     private StringBuffer parseBracketedText() throws IOException {
         StringBuffer value = new StringBuffer();
 
-        consume('{','(');
+        consume('{', '(');
 
         int brackets = 0;
 
@@ -834,18 +827,18 @@ private StringBuffer parseBracketedText() throws IOException {
             }
         }
 
-        consume('}',')');
+        consume('}', ')');
 
         return value;
     }
 
-    private boolean isClosingBracketNext () {
+    private boolean isClosingBracketNext() {
         try {
             int peek = peek();
             boolean isCurlyBracket = peek == '}';
             boolean isRoundBracket = peek == ')';
             return isCurlyBracket || isRoundBracket;
-        } catch(IOException e) {
+        } catch (IOException e) {
             return false;
         }
     }

src/main/java/net/sf/jabref/model/entry/BibEntry.java

@@ -634,7 +634,7 @@ public String getUserComments() {
 
             try {
                 // get the text before the entry
-                String prolog = parsedSerialization.substring(0, parsedSerialization.indexOf('@'));
+                String prolog = parsedSerialization.substring(0, parsedSerialization.lastIndexOf('@'));
 
                 // delete trailing whitespaces (between entry and text)
                 prolog = prolog.replaceFirst("\\s+$", "");

src/test/java/net/sf/jabref/importer/fileformat/BibtexParserTest.java

@@ -1556,4 +1556,79 @@ public void preserveEncodingPrefixInsideEntry() {
         assertEquals(Collections.singletonList(expected), parsed);
     }
 
+    @Test
+    public void parseBracketedComment() throws IOException {
+        String commentText = "@Comment{someComment}";
+        ParserResult result = BibtexParser.parse(new StringReader(commentText));
+
+        assertEquals(commentText, result.getDatabase().getEpilog());
+    }
+
+    @Test
+    public void parseRegularCommentBeforeEntry() throws IOException {
+        // @formatter:off
+        String bibtexEntry = "@Comment{someComment} " + OS.NEWLINE +
+                "@Article{test," + OS.NEWLINE +
+                "  Author                   = {Foo Bar}," + OS.NEWLINE +
+                "  Journal                  = {International Journal of Something}," + OS.NEWLINE +
+                "  Note                     = {some note}," + OS.NEWLINE +
+                "  Number                   = {1}" + OS.NEWLINE +
+                "}";
+        // @formatter:on
+
+        ParserResult result = BibtexParser.parse(new StringReader(bibtexEntry));
+        Collection<BibEntry> entries = result.getDatabase().getEntries();
+        BibEntry entry = entries.iterator().next();
+
+        assertEquals(bibtexEntry, entry.getParsedSerialization());
+    }
+
+    @Test
+    public void parseCommentWithoutBrackets () throws IOException {
+        String commentText = "@Comment someComment";
+        ParserResult result = BibtexParser.parse(new StringReader(commentText));
+
+        assertEquals(commentText, result.getDatabase().getEpilog());
+    }
+
+    @Test
+    public void parseCommentWithoutBracketsBeforeEntry() throws IOException {
+        // @formatter:off
+        String bibtexEntry = "@Comment someComment  " + OS.NEWLINE +
+                "@Article{test," + OS.NEWLINE +
+                "  Author                   = {Foo Bar}," + OS.NEWLINE +
+                "  Journal                  = {International Journal of Something}," + OS.NEWLINE +
+                "  Note                     = {some note}," + OS.NEWLINE +
+                "  Number                   = {1}" + OS.NEWLINE +
+                "}";
+        // @formatter:on
+
+        ParserResult result = BibtexParser.parse(new StringReader(bibtexEntry));
+        Collection<BibEntry> entries = result.getDatabase().getEntries();
+        BibEntry entry = entries.iterator().next();
+
+        assertEquals(bibtexEntry, entry.getParsedSerialization());
+    }
+
+    @Test
+    public void parseCommentContainingEntries() throws IOException {
+        // @formatter:off
+        String bibtexEntry = "@Comment{@article{myarticle,}" + OS.NEWLINE +
+                "@inproceedings{blabla, title={the proceedings of blabla}; }" + OS.NEWLINE +
+                "} " + OS.NEWLINE +
+                "@Article{test," + OS.NEWLINE +
+                "  Author                   = {Foo Bar}," + OS.NEWLINE +
+                "  Journal                  = {International Journal of Something}," + OS.NEWLINE +
+                "  Note                     = {some note}," + OS.NEWLINE +
+                "  Number                   = {1}" + OS.NEWLINE +
+                "}";
+        // @formatter:on
+
+        ParserResult result = BibtexParser.parse(new StringReader(bibtexEntry));
+        Collection<BibEntry> entries = result.getDatabase().getEntries();
+        BibEntry entry = entries.iterator().next();
+
+        assertEquals(bibtexEntry, entry.getParsedSerialization());
+    }
+
 }

src/test/resources/testbib/bibWithUserCommentAndEntryChange.bib

@@ -5,6 +5,11 @@ @Preamble{preamble
 @String{firstString  = {my first string}}
 @String{secondString = {}}
 
+@Comment { this is a bracketed comment that should be preserved
+
+Regardless auf how much space there is inbetween
+}
+
 @ARTICLE{1102917,
   author = {E. Bardram},
   title = {The trouble with login: on usability and computer security in ubiquitous
@@ -21,6 +26,8 @@ @ARTICLE{1102917
   publisher = {Springer-Verlag}
 }
 
+@Comment this in an unbracketed comment that should be preserved as well
+
 This is some arbitrary user comment that should be preserved
 
 @InProceedings{1137631,

src/test/resources/testbib/bibWithUserComments.bib

@@ -5,6 +5,11 @@ @Preamble{preamble
 @String{firstString  = {my first string}}
 @String{secondString = {}}
 
+@Comment { this is a bracketed comment that should be preserved
+
+Regardless auf how much space there is inbetween
+}
+
 @ARTICLE{1102917,
   author = {E. Bardram},
   title = {The trouble with login: on usability and computer security in ubiquitous
@@ -21,6 +26,8 @@ @ARTICLE{1102917
   publisher = {Springer-Verlag}
 }
 
+@Comment this in an unbracketed comment that should be preserved as well
+
 This is some arbitrary user comment that should be preserved
 
 @INPROCEEDINGS{1137631,