XOM API for Processing XML with Java

[peter murray-rust <pm286 AT cam.ac.uk>]

I am trying to add XSD functionality to my CML-XOM system (JUMBO) and 
have run into several problems. I would appreciate any clues and hope 
that the description below is sufficient to give some clues. I am 
using XOM1.1+Eclipse3.1.1+junit+xerces+xml-api+xercesSamples on an XP system.

(a) I have constructed simple XML and XSD files of the type:
cml0.xsd:
<xsd:schema
    targetNamespace="http://org.xml-cml.cml/schema";
    xmlns="http://org.xml-cml.cml/schema";
    xmlns:xsd="http://www.w3.org/2001/XMLSchema";
    elementFormDefault="qualified"
>
    <xsd:element name="cml">
        <xsd:complexType>
            <xsd:sequence>
                <xsd:element name="molecule" minOccurs="0" 
maxOccurs="unbounded">
                    <xsd:complexType>
                        <xsd:sequence>
                            <xsd:any processContents="lax" 
minOccurs="0" maxOccurs="unbounded"/>
                        </xsd:sequence>
                        <xsd:attribute name="id"/>
                    </xsd:complexType>
                </xsd:element>
            </xsd:sequence>
        </xsd:complexType>
    </xsd:element>
</xsd:schema>

cml0.xml
<c:cml
    xmlns:c="http://org.xml-cml.cml/schema";
    xsi:schemaLocation="http://org.xml-cml.cml/schema cml0.xsd"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
>
    <c:molecule id="a1"/>
</c:cml>
[Note - I do not like the idea of adding schema references within the 
XML instance but it seems to be one of the current ways of using XSD. 
I do not actually like XSD at all, but feel that I am constrained to 
use it - it solves ca 10% of validation problems in chemistry. 
Schematron adds somewhat more but ultimately we need much more 
expressive semantics.]

The example(s) validate under Xerces in the Eclipse environment (I 
use dom.Counter from the samples to exercise the validation:
        private void xercesValidate(String file) {
                System.out.println("  === xerces validation: "+file+" ====");
                String[] args = {"-v", "-s", "file://"+file};
                dom.Counter.main(args);
        }

Under XOM I have at least two problems:

(A) the *.xml files with schema references fail to parse under XOM 
even if no validation is called for. a typical message is:
nu.xom.ParsingException: Illegal path character
which appears to have a significant whitespace character if I write it as:
[nu.xom.ParsingException: Illegal path character  ] in 
[C:\pmr\schema23\examples\xsd\countType1.xml]
None of my files have whitespace characters in their names but 
temporary filenames might have. I can remove this error simply by 
removing the xsi:schemaLocation attribute.

(B) I have tried to switch on validation using the example in the FAQ:
                System.out.println("  === xom+Xerces validation: 
"+file+" ====");
                Document doc = null;
          try {
                    XMLReader xerces = 
XMLReaderFactory.createXMLReader("org.apache.xerces.parsers.SAXParser");
                    xerces.setFeature("http://apache.org/xml/features/validation/schema";, 
true);
                    Builder parser = new Builder(xerces, /*true*/ false );
                    doc = parser.build(new FileReader(file));
                } catch (Exception e) {
                        fail("should not throw "+e);
...
and I get errors of the following sort:

[Warning] :5:2: schema_reference.4: Failed to read schema document 
'cml0.xsd', because 1) could not find the document; 2) the document 
could not be read; 3) the root element of the document is not <xsd:schema>.
[Error] :5:2: cvc-elt.1: Cannot find the declaration of element 'c:cml'.
[Warning] :6:32: schema_reference.4: Failed to read schema document 
'cml0.xsd', because 1) could not find the document; 2) the document 
could not be read; 3) the root element of the document is not <xsd:schema>.

I would be grateful for pointers as to how to mend this and also ways 
of schema validation which do not require embedding absolute or 
relative addresses within the XML instances. I appreciate that these 
problems might not occur with approaches such as RELAX-NG but I have 
to have an XSD offering (although I deliberately only use a small 
part of its functionality - it is a nightmare for non-experts and it 
is a pity that our ideas on XML-DEV were not heeded at the time.)

TIA

P>


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