PS. It gets worse: if I read the file into a string and call
pybel.readstring( "sdf", string, opt = { "canonical" : None } )
it works. So here's the scenario:
I'm running under mod_wsgi.
The app uses urllib.urlretrieve() to fetch an sdf file from pubchem and
saves it on disk. Immediately after that it calls
pybel.readfile( "sdf", sdf, opt = { "canonical" : None } ).next()
and that works and returns a pybel molecule. When I get to the same
pybel.readfile( "sdf", sdf, opt = { "canonical" : None } ).next()
later, from a different web form, that fails with
File "/opt/lib/pybel.py", line 145, in filereader
notatend = obconversion.ReadFile(obmol,filename)
TypeError: in method 'OBConversion_ReadFile', argument 3 of type
'std::string'
On the off-chance that pybel/obabel/.so keeps the state between wsgi
invocations I tried changing the readfile call to
list( pybel.readfile( "sdf", sdf, opt = { "canonical" : None } ) )
and returning list[0] -- no dice, still the same error.
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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