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#!/usr/bin/python3
##
## @file print_groups.py
## @brief Example printing the groups contained in an sbml file
## @author Frank T. Bergmann
##
## <!--------------------------------------------------------------------------
## This sample program is distributed under a different license than the rest
## of libSBML. This program uses the open-source MIT license, as follows:
##
## Copyright (c) 2013-2018 by the California Institute of Technology
## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
## and the University of Heidelberg (Germany), with support from the National
## Institutes of Health (USA) under grant R01GM070923. All rights reserved.
##
## Permission is hereby granted, free of charge, to any person obtaining a
## copy of this software and associated documentation files (the "Software"),
## to deal in the Software without restriction, including without limitation
## the rights to use, copy, modify, merge, publish, distribute, sublicense,
## and/or sell copies of the Software, and to permit persons to whom the
## Software is furnished to do so, subject to the following conditions:
##
## The above copyright notice and this permission notice shall be included in
## all copies or substantial portions of the Software.
##
## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
## THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
## FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
## DEALINGS IN THE SOFTWARE.
##
## Neither the name of the California Institute of Technology (Caltech), nor
## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
## of Heidelberg, nor the names of any contributors, may be used to endorse
## or promote products derived from this software without specific prior
## written permission.
## ------------------------------------------------------------------------ -->
import sys
import os.path
from libsbml import *
def print_member(member):
print (" > Member")
if member.isSetIdRef():
print (" idRef : {0}".format(member.getIdRef()))
if member.isSetMetaIdRef():
print (" metaIdRef : {0}".format(member.getMetaIdRef()))
def print_group(group):
if group is None:
return
print ("# Group")
if group.isSetId():
print (" id : {0}".format(group.getId()))
if group.isSetName():
print (" name : {0}".format(group.getName()))
if group.isSetSBOTerm():
print (" SBO term : {0}".format(group.getSBOTermID()))
if group.isSetKind():
print (" kind : {0}".format(group.getKindAsString()))
members = group.getListOfMembers()
for member in members:
print_member(member)
def main (args):
"""Usage: print_groups filename
"""
if len(args) != 2:
print(main.__doc__)
sys.exit(2)
filename = args[1]
document = readSBML(filename)
errors = document.getNumErrors(LIBSBML_SEV_ERROR)
print("filename: {0}\n".format(filename))
if errors > 0:
document.printErrors()
return errors
# Model
m = document.getModel()
plug = m.getPlugin('groups')
if plug is None:
print("This file does not have groups enabled");
return
list = plug.getListOfGroups()
print("number of groups: {0}\n".format(list.size()))
for group in list:
print_group(group)
if __name__ == '__main__':
main(sys.argv)
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