def fromPhrasedML(cls, phrasedmlStr, location, master=None):
sedmlStr = phrasedml.convertString(phrasedmlStr)
# necessary to add xml extensions to antimony models
phrasedml.addDotXMLToModelSources()
sedmlStr = phrasedml.getLastSEDML()
if sedmlStr is None:
raise Exception(phrasedml.getLastError())
return cls.fromRaw(raw=sedmlStr, location=location, filetype='sed-ml', master=master)
def fromPhrasedML(cls, phrasedmlStr, location, master=None):
sedmlStr = phrasedml.convertString(phrasedmlStr)
# necessary to add xml extensions to antimony models
phrasedml.addDotXMLToModelSources()
sedmlStr = phrasedml.getLastSEDML()
if sedmlStr is None:
raise Exception(phrasedml.getLastError())
return cls.fromRaw(raw=sedmlStr,
location=location,
filetype='sed-ml',
master=master)
def __init__(self, sources):
""" Converts a dictionary of PhraSEDML files and list of Antimony files into sedml/sbml.
:param sources: Sources returned from partitionInlineOMEXString
"""
from .convert_omex import Omex, SbmlAsset, SedmlAsset, readCreator
from .convert_antimony import antimonyConverter
phrasedml.clearReferencedSBML()
from .. import DumpJSONInfo
self.omex = Omex(description=DumpJSONInfo(), creator=readCreator())
# Convert antimony to sbml
for t, loc, master in ((x['source'],
x['location'] if 'location' in x else None,
x['master'] if 'master' in x else None)
for x in sources if x['type'] == 'antimony'):
modulename, sbmlstr = antimonyConverter().antimonyToSBML(t)
outpath = loc if loc is not None else modulename + '.xml'
self.omex.addSbmlAsset(SbmlAsset(outpath, sbmlstr, master=master))
# Convert phrasedml to sedml
for t, loc, master in ((x['source'],
x['location'] if 'location' in x else None,
x['master'] if 'master' in x else None)
for x in sources if x['type'] == 'phrasedml'):
for sbml_asset in self.omex.getSbmlAssets():
if sbml_asset.location:
if loc:
path = os.path.relpath(sbml_asset.location,
os.path.dirname(loc))
else:
path = sbml_asset.location
else:
path = sbml_asset.getModuleName()
# make windows paths like unix paths
if os.path.sep == '\\':
path = path.replace(os.path.sep, '/')
phrasedml.setReferencedSBML(path, sbml_asset.getContent())
phrasedml.convertString(t)
phrasedml.addDotXMLToModelSources(False)
sedml = phrasedml.getLastSEDML()
if sedml is None:
raise RuntimeError(
'Unable to convert PhraSEDML to SED-ML: {}'.format(
phrasedml.getLastError()))
outpath = loc if loc is not None else 'main.xml'
self.omex.addSedmlAsset(SedmlAsset(outpath, sedml, master=master))
def __init__(self, sources):
""" Converts a dictionary of PhraSEDML files and list of Antimony files into sedml/sbml.
:param sources: Sources returned from partitionInlineOMEXString
"""
from .convert_omex import Omex, SbmlAsset, SedmlAsset, readCreator
from .convert_antimony import antimonyConverter
phrasedml.clearReferencedSBML()
from .. import DumpJSONInfo
self.omex = Omex(
description=DumpJSONInfo(),
creator=readCreator()
)
# Convert antimony to sbml
for t, loc, master in (
(x['source'], x['location'] if 'location' in x else None, x['master'] if 'master' in x else None)
for x in sources if x['type'] == 'antimony'):
modulename, sbmlstr = antimonyConverter().antimonyToSBML(t)
outpath = loc if loc is not None else modulename + '.xml'
self.omex.addSbmlAsset(SbmlAsset(outpath, sbmlstr, master=master))
# Convert phrasedml to sedml
for t, loc, master in (
(x['source'], x['location'] if 'location' in x else None, x['master'] if 'master' in x else None)
for x in sources if x['type'] == 'phrasedml'):
for sbml_asset in self.omex.getSbmlAssets():
if sbml_asset.location:
if loc:
path = os.path.relpath(sbml_asset.location, os.path.dirname(loc))
else:
path = sbml_asset.location
else:
path = sbml_asset.getModuleName()
# make windows paths like unix paths
if os.path.sep == '\\':
path = path.replace(os.path.sep, '/')
phrasedml.setReferencedSBML(path, sbml_asset.getContent())
phrasedml.convertString(t)
phrasedml.addDotXMLToModelSources(False)
sedml = phrasedml.getLastSEDML()
if sedml is None:
raise RuntimeError('Unable to convert PhraSEDML to SED-ML: {}'.format(phrasedml.getLastError()))
outpath = loc if loc is not None else 'main.xml'
self.omex.addSedmlAsset(SedmlAsset(outpath, sedml, master=master))
import phrasedml, os
with open('./model/BIOMD0000000144.xml') as f:
sbml_str = f.read()
with open('./experiment/Calzone2007-simulation-figure-1B.xml') as f:
sedml_in = f.read()
phrasedml.setReferencedSBML('../model/BIOMD0000000144.xml', sbml_str)
phrasedml.convertString(sedml_in)
phrased_str = phrasedml.getLastPhraSEDML()
phrasedml.convertString(phrased_str)
phrasedml.addDotXMLToModelSources()
sedml_out = phrasedml.getLastSEDML()
if not os.path.exists('phrased'):
os.makedirs('phrased')
with open('./phrased/Calzone2007-simulation-figure-1B.xml', 'w') as f:
f.write(sedml_out)