Hello group! This is probably a silly newbie mistake but consider the
following program:
import libsbml
def getSBMLModel(biomodel_path):
reader = libsbml.SBMLReader()
sbml_doc = reader.readSBML(biomodel_path)
sbml_model = None
if sbml_doc.getNumErrors() > 0:
print 'I couldn\'t read the file %s!' % biomodel_path
return None
else:
sbml_model = sbml_doc.getModel()
return sbml_doc.getModel() # None if file couldn't be opened
def way_1(biomodel_path):
reader = libsbml.SBMLReader()
sbml_doc = reader.readSBML(biomodel_path)
sbml_model = sbml_doc.getModel()
if sbml_model == None:
return
l = sbml_model.getListOfSpecies()
print 'In way_1(): Got list %s with the length %i' % (l, len(l))
def way_2(biomodel_path):
sbml_model = getSBMLModel(biomodel_path)
if sbml_model == None:
return
l = sbml_model.getListOfSpecies()
print 'In way_2(): Got list %s with the length %i' % (l, len(l))
file = '../BIOMD0000000003.xml'
# Changing the order of these two calls doesn't help, only way_1() works.
way_1(file)
way_2(file)
When run, the output is:
In way_1(): Got list <libsbml.ListOfSpecies; proxy of <Swig Object of
type 'ListOfSpecies *' at 0x291c8bc> > with the length 3
In way_2(): Got list <libsbml.ListOfSpecies; proxy of <Swig Object of
type 'ListOfSpecies *' at 0x27fb57c> > with the length 0
I don't get it way the species list obtained in way_2() is empty? For
the input file I'm using I should be getting 3 species for the test file
I'm using.
I'm sorry that this program uses a third-party library which is probably
unknown to many, but since I make a lot of newbie mistakes I thought
that it's very likely that this is a issue in how I use python, not a
library issue. To compensate somewhat I tried to show my entire test
program and its output and make that test program as clear as possible.
So if anyone knows why I get this behavior I would like to hear it and I
will have learned something today too! :)
- WP
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