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#!/usr/bin/python3
##
## @file convertLayout.py
## @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
from libsbml import *
def convertDocToL2(doc, outputFile):
layoutNsUri = "http://projects.eml.org/bcb/sbml/level2"
layoutNs = LayoutPkgNamespaces(2, 4)
renderNsUri = "http://projects.eml.org/bcb/sbml/render/level2"
renderNs = RenderPkgNamespaces(2, 4)
prop = ConversionProperties(SBMLNamespaces(2,4))
prop.addOption('strict', False)
prop.addOption('setLevelAndVersion', True)
prop.addOption('ignorePackages', True)
doc.convert(prop)
docPlugin = doc.getPlugin("layout")
if docPlugin is not None:
docPlugin.setElementNamespace(layoutNsUri)
doc.getSBMLNamespaces().removePackageNamespace(3, 1, "layout", 1)
doc.getSBMLNamespaces().addPackageNamespace("layout", 1)
rdocPlugin = doc.getPlugin("render")
if rdocPlugin is not None:
rdocPlugin.setElementNamespace(renderNsUri)
doc.getSBMLNamespaces().removePackageNamespace(3, 1, "render", 1)
doc.getSBMLNamespaces().addPackageNamespace("render", 1)
writeSBMLToFile(doc, outputFile)
def convertDocToL3(doc, outputFile):
layoutNsUri = "http://www.sbml.org/sbml/level3/version1/layout/version1"
layoutNs = LayoutPkgNamespaces(3, 1)
renderNsUri = "http://www.sbml.org/sbml/level3/version1/render/version1"
renderNs = RenderPkgNamespaces(3, 1)
prop = ConversionProperties(SBMLNamespaces(3,1))
prop.addOption('strict', False)
prop.addOption('setLevelAndVersion', True)
prop.addOption('ignorePackages', True)
doc.convert(prop)
docPlugin = doc.getPlugin("layout")
if docPlugin is not None:
docPlugin.setElementNamespace(layoutNsUri)
doc.getSBMLNamespaces().removePackageNamespace(3, 1, "layout", 1)
doc.getSBMLNamespaces().addPackageNamespace("layout", 1)
rdocPlugin = doc.getPlugin("render")
if rdocPlugin is not None:
rdocPlugin.setElementNamespace(renderNsUri)
doc.getSBMLNamespaces().removePackageNamespace(3, 1, "render", 1)
doc.getSBMLNamespaces().addPackageNamespace("render", 1)
writeSBMLToFile(doc, outputFile)
def convertFileToL2(inputFile, outputFile):
doc = readSBMLFromFile(inputFile)
convertDocToL2(doc, outputFile)
def convertFileToL3(inputFile, outputFile):
doc = readSBMLFromFile(inputFile)
convertDocToL3(doc, outputFile)
def convertFile(inputFile, outputFile):
doc = readSBMLFromFile(inputFile)
if doc.getLevel() == 3:
convertDocToL2(doc, outputFile)
else:
convertDocToL3(doc, outputFile)
if __name__ == '__main__':
if len(sys.argv) != 3:
print("""
usage: convertLayout <input file> <output file>
""")
sys.exit(1)
convertFile(sys.argv[1], sys.argv[2])
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