[Bug xml/26652] New: XML parsing fails on encoding problem

[egon dot willighagen at gmail dot com]

Ok, to start with the start: JChemPaint did no longer work with 0.90 while it
did with 0.21. After bugging Roman Kennke, it turned out to be a XML reading
problem, which got me here.

I stripped down the code, and I think the following reproduces the bug to the
core:

import java.io.*;
import org.xml.sax.*;

public class XMLErrorTest {

  public static void main(String[] args) {

    try {
      javax.xml.parsers.SAXParserFactory spf =
javax.xml.parsers.SAXParserFactory.newInstance();
      spf.setNamespaceAware(true);
      javax.xml.parsers.SAXParser saxParser = spf.newSAXParser();
      XMLReader parser = saxParser.getXMLReader();
      parser.setFeature("http://xml.org/sax/features/validation";, false);
      Reader input = new FileReader("src/data/templates/list_aminoacids.cml");
      parser.parse(new InputSource(input));

      System.out.println("Parsing succeeded");
    } catch (Exception e) {
      System.out.println("Error while reading XML: " + e.getMessage());
      e.printStackTrace();
    }

  }

}

The XML on which it fails can be found in CDK CVS here:

http://cvs.sourceforge.net/viewcvs.py/cdk/cdk/src/data/templates/list_aminoacids.cml

Though the problem is the first line. So the below XML source gives the same
error. Removing the first line will make the file get parsed without trouble.

<?xml version="1.0" encoding="ISO-8859-1"?>
<list title="List of amino acids"
        xmlns="http://www.xml-cml.org/schema/cml2/core";>

    <molecule id="alanine" dictRef="pdb:aminoAcid">
        <name>alanine</name>
        <name dictRef="pdb:residueName">Ala</name>
        <name dictRef="pdb:oneLetterCode">A</name>
        <scalar dictRef="pdb:id">3</scalar>
        <atomArray>
            <atom id="a1" elementType="C" x2="265.0" y2="989.0"/>
            <atom id="a2" elementType="N" x2="234.0" y2="972.0"
dictRef="pdb:nTerminus"/>
            <atom id="a3" elementType="C" x2="265.0" y2="1025.0"/>
            <atom id="a4" elementType="C" x2="296.0" y2="971.0"
dictRef="pdb:cTerminus"/>
            <atom id="a5" elementType="O" x2="296.0" y2="935.0"/>
            <atom id="a6" elementType="O" x2="327.0" y2="988.0"/>
        </atomArray>
        <bondArray>
            <bond id="b1" atomRefs2="a2 a1" order="S"/>
            <bond id="b2" atomRefs2="a1 a3" order="S"/>
            <bond id="b3" atomRefs2="a1 a4" order="S"/>
            <bond id="b4" atomRefs2="a4 a5" order="D"/>
            <bond id="b5" atomRefs2="a4 a6" order="S"/>
        </bondArray>
    </molecule>

</list>

The error I get is:

Error while reading XML: null
org.xml.sax.SAXParseException
   at gnu.xml.stream.SAXParser.parse (SAXParser.java:660)
   at XMLErrorTest.main (XMLErrorTest.java:16)
Caused by: javax.xml.stream.XMLStreamException
   at gnu.xml.stream.XMLParser.next (XMLParser.java:1184)
   at gnu.xml.stream.XMLParser.hasNext (XMLParser.java:984)
   at gnu.xml.stream.SAXParser.parse (SAXParser.java:377)
   ...1 more
Caused by: java.io.UnsupportedEncodingException: document is not in its
declared encoding UTF-8: ISO-8859-1
   at gnu.xml.stream.XMLParser$Input.setInputEncoding (XMLParser.java:5246)
   at gnu.xml.stream.XMLParser.readXMLDecl (XMLParser.java:1718)
   at gnu.xml.stream.XMLParser.next (XMLParser.java:1121)
   ...3 more

Egon


-- 
           Summary: XML parsing fails on encoding problem
           Product: classpath
           Version: 0.90
            Status: UNCONFIRMED
          Severity: normal
          Priority: P3
         Component: xml
        AssignedTo: dog at gnu dot org
        ReportedBy: egon dot willighagen at gmail dot com


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26652