The following "CML" file from our Xindice database
<entry src:col="/db/wwmm/nci/entry" src:key="nci_006229.xml"> <identifier tautomeric="0" version="0.932Beta"> <basic>C10H8,1H-2H-6H-10-8H-4H-3H-7H-9(10)5H-1</basic> <charge/> </identifier> <molecule formalCharge="0" id="NSC6229"> <formula>C 10 H 8</formula> ... snipped ... </entry>
has namespaced prefixes added by Xindice but without the namespace URI (xmlns:src). This is an invalid file if validation is enforced but I think is otherwise OK. Under java1.4 there is no problem but under 1.5 the applet stops at a black background with the Java console error:
SmarterJmolAdapter:The Resolver thinks:Cml SmarterJmolAdapter:The Resolver thinks:Cml SmarterJmolAdapter:The Resolver thinks:Cml SmarterJmolAdapter:The Resolver thinks:Cml Using JAXP/SAX XML parser. Using JAXP/SAX XML parser. Using JAXP/SAX XML parser. SAX FATAL:The prefix "src" for attribute "src:col" associated with an element type "molecule" is not bound. org.xml.sax.SAXParseException: The prefix "src" for attribute "src:col" associated with an element type "molecule" is not bound.
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source)
at org.jmol.adapter.smarter.CmlReader.readAtomSetCollection(CmlReader.java:71)
...... and more
I think this should be trapped and reported as it fooled us for at least a day! In the future it is almost certain that people will submit "invalid" files on a regular basis and so validation should be switched off by default.
I think this problem is intermediate between validation and non-validation. Without a schema there can be no validation so it's not a validation error, but it is certainly well-formed. I am not quite sure whether it is reasonable for a parser to throw a fatal error with the above file (It is also not very helpful for Xindice to emit it like this, although it is possible it is our fault). I suppose we shall retrofit the namespaceURI.
Even advance brings its own crop of problems!
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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