Re: [cml/ccml-discuss] Validation problem - was Namespaces [was: CMLRSS plugin]

[peter murray-r. <pm...@ca...>]

At 12:55 09/03/2006, Tobias Helmus wrote:
>CMLBuilder builder = new CMLBuilder();
>CMLElement cmlElement = null;
>try {
>   cmlElement = (CMLElement)builder.parseString(localResourceString);
>} catch (IOException e) {
>   e.printStackTrace();
>   setParsed(false);
>   return false;
>}

I am baffled at present. I took your code - it is now in 
org.xmlcml.cml.element.test.Standalone.main
and reads:
         String localResourceString =
                 "" +
                 "<cml:molecule" +
                 " xmlns:cml='http://www.xml-cml.org/schema'" +
//              " xsi:schemaLocation='http://www.xml-cml.org/schema 
../../schema.xsd'" +
//              " xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance'"+
                 "       >" +
                 "       <cml:atomArray atomID='a1 a2 a3 a4' " +
                 "      elementType='C C O O' formalCharge='0 0 0 0' />" +
                 "   <cml:bondArray atomRef1='a1 a2 a2' atomRef2='a2 a3 a4'" +
                 "      order='1 2 1' />" +
                 "</cml:molecule>"+
                 "";

             CMLBuilder builder = new CMLBuilder();
//            builder.setParsed(false);
             CMLElement cmlElement = null;
             try {
               cmlElement = 
(CMLElement)builder.parseString(localResourceString);
             } catch (Exception e) {
               e.printStackTrace();
//            return false;
             }
             cmlElement.debug();


I now ran this from a DOS window (completely outside Eclipse, etc.) , 
with a new classpath:

C:\Documents and Settings\pmr>echo %classpath%
C:\pmr\jumbo51\bin;C:\pmr\jumbo51\lib\xom-1.1b2.jar

and the command:

C:\Documents and Settings\pmr>java org.xmlcml.cml.element.test.Standalone 1

and got the output:

<?xml version="1.0" encoding="UTF-8"?>
<molecule xmlns="http://www.xml-cml.org/schema" 
xmlns:cml="http://www.xml-cml.or
g/schema">
  <atomArray atomID="a1 a2 a3 a4" elementType="C C O O" 
formalCharge="0 0 0 0"/>
  <bondArray atomRef1="a1 a2 a2" atomRef2="a2 a3 a4" order="1 2 1"/>
</molecule>

which is what is expected. Can you make sure you do not have anything 
strange in the classpath?

P.




Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road,  Cambridge CB2 1EW, UK
+44-1223-763069