On Oct 18, 2008, at 1:12 PM, Noel O'Boyle wrote:
Also see BioPython. It has some wrappers around NCBI's functionality
already, but I haven't looked at using it with PubChem...
It's a different SOAP interface.
More specifically, I don't think the Biopython code is even
calling SOAP - I think it calls the equivalent URI-based version.
It definitely doesn't use the WSDL.
Greg Landrum:
I did a bit of exploring of the Pubchem Power User Gateway this
morning and discovered that they have a SOAP interface:
http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap_help.html
I've fought with WSDL and DTD->code generation solutions too
much. Last time I did a SOAP interface for a client I ended
up generating XML templates for submission (using debug mode
in soaplib; not SOAPpy or ZSI) and using those to create
the new inputs.
To parse I used ElementTree, so I didn't have to worry about ...
You will need to
have ZSI installed and to run wsdl2py as indicated on the above page.
The problem I had with the old Biopython DTD->code generation
code was that additions to the DTD ended up breaking the parser.
That's an aspect of the lack of support for semantics like "must
ignore unknown tags" in the code generator I used.
The problem I had with using SOAP in general has been that
the hugeness of the spec and its vagaries mean that ZSI often
didn't quite match up to the Java or .Net servers. In one
case the Java server I was talking to returned an MTOM-encoded
SOAP document and not SOAP document format that any of the
Python libs supported.
NCBI doesn't have this problem, but my interactions with
SOAP left a bad taste in my mouth, as it were.
Andrew
[email protected]
