def exportAsCombine(self, outputpath): # parameter outputpath must be a full path of a zip file you wish to create
# Temporary failsafe - Should be revised once libphrasedml adopts returning of model name
reModel = r"""(\w*) = model ('|")(.*)('|")"""
# rePlot = r"""plot ('|")(.*)('|") (.*)"""
lines = self.phrasedmlStr.splitlines()
for i, s in enumerate(lines):
reSearchModel = re.split(reModel, s)
# reSearchPlot = re.split(rePlot, s)
if len(reSearchModel) > 1:
modelsource = str(reSearchModel[3])
modelname = os.path.basename(modelsource)
if ".xml" or ".sbml" not in modelsource:
modelname = modelname + ".xml"
s = s.replace(modelsource, modelname)
lines[i] = s
# if len(reSearchPlot) > 1:
# plottitle = str(reSearchPlot[2])
revphrasedml = "\n".join(lines)
phrasedml.setReferencedSBML(modelname, te.antimonyTosbml(self.antimonyStr))
combine.export(outputpath, self.antimonyStr, modelname, revphrasedml)
phrasedml.clearReferencedSBML()
def addPhrasedml(self, phrasedmlStr, antimonyStr, arcname=None):
""" Adds SEDML file as phraSEDML string into COMBINE archive.
:param phrasedmlStr: phraSEDML string
:param antimonyStr: antimony string to be referenced
:param arcname: (optional) desired name of SEDML file
"""
warnings.warn('Use inline_omex instead.', DeprecationWarning)
# FIXME: This does not work for multiple referenced models !.
reModel = r"""(\w*) = model ('|")(.*)('|")"""
phrasedmllines = phrasedmlStr.splitlines()
for k, line in enumerate(phrasedmllines):
reSearchModel = re.split(reModel, line)
if len(reSearchModel) > 1:
modelsource = str(reSearchModel[3])
modelname = os.path.basename(modelsource)
modelname = str(modelname).replace(".xml", '')
phrasedml.setReferencedSBML(modelsource,
te.antimonyToSBML(antimonyStr))
sedmlstr = phrasedml.convertString(phrasedmlStr)
if sedmlstr is None:
raise Exception(phrasedml.getLastError())
phrasedml.clearReferencedSBML()
self.addSEDML(sedmlstr, arcname)
def exportAsCombine(self, outputPath, execute=False):
""" Creates COMBINE archive for given antimony and phrasedml files.
If execute=True all phrasedml are executed and the results written
:param exportPath: full path of the combine zip file to create
:type exportPath: str
"""
# Create empty archive
m = tecombine.CombineArchive()
# Add antimony models to archive
for aStr in self.antimonyList:
r = te.loada(aStr)
name = r.getModel().getModelName()
m.addAntimonyStr(aStr, "{}.xml".format(name))
# Add phrasedml models to archive
for k, phrasedmlStr in enumerate(self.phrasedmlList):
phrasedml.clearReferencedSBML()
self._setReferencedSBML(phrasedmlStr)
m.addPhraSEDMLStr(phrasedmlStr, self._phrasedmlFileName(k), master=True)
phrasedml.clearReferencedSBML()
# Add README.md to archive
readmeStr = self.createReadmeString(outputPath)
m.addStr(readmeStr, location='README.md', filetype='md')
# add output files to archive
if execute:
for phrasedmlStr in self.phrasedmlList:
# execute in temporary directory
workingDir = tempfile.mkdtemp(suffix="_sedml")
execStr = self._toPython(phrasedmlStr, workingDir=workingDir)
exec execStr
# Add output files to archive
files = [f for f in os.listdir(workingDir)]
for f in files:
filepath = os.path.join(workingDir, f)
if f.endswith('.xml'):
# SBML or SEDML resulting from antimony/phrasedml (already in archive)
pass
elif f.endswith('.md'):
# README.md (already in archive)
pass
elif f.endswith('.png'):
# outputPlot2D | outputPlot3D
m.addFile(filepath, filetype="png")
elif f.endswith('.csv'):
# outputReport
m.addFile(filepath, filetype="csv")
else:
warnings.warn('Unsupported file type not written in COMBINE archive: {}'.format(filepath))
# remove temporary workingDir
shutil.rmtree(workingDir)
# Write archive
m.write(outputPath)
def exportToCombine(self, outfile):
'''Exports this Omex instance to a Combine archive.
:param outfile: A path to the output file'''
import phrasedml
phrasedml.clearReferencedSBML()
archive = CombineArchive()
description = OmexDescription()
description.setAbout(self.about)
description.setDescription(self.description)
description.setCreated(OmexDescription.getCurrentDateAndTime())
# TODO: pass in creator
if self.creator is not None:
creator = VCard()
creator.setFamilyName(self.creator['last_name'])
creator.setGivenName(self.creator['first_name'])
creator.setEmail(self.creator['email'])
creator.setOrganization(self.creator['organization'])
description.addCreator(creator)
archive.addMetadata('.', description)
# Write out to temporary files
# TODO: can add content via strings now
workingDir = tempfile.mkdtemp(suffix="_sedml")
files = [] # Keep a list of files to remove
for t in self.getSedmlAssets():
fname = os.path.join(workingDir, os.path.normpath(t.getLocation()))
dname = os.path.dirname(fname)
if not os.path.exists(dname):
os.makedirs(dname)
with open(fname, 'w') as f:
files.append(fname)
f.write(t.getContent())
archive.addFile(fname, t.getLocation(),
KnownFormats.lookupFormat("sedml"),
t.getMaster())
for t in self.getSbmlAssets():
fname = os.path.join(workingDir, os.path.normpath(t.getLocation()))
dname = os.path.dirname(fname)
if not os.path.exists(dname):
os.makedirs(dname)
with open(fname, 'w') as f:
files.append(fname)
f.write(t.getContent())
archive.addFile(
fname, t.getLocation(), KnownFormats.lookupFormat("sbml"),
t.getMaster() if t.getMaster() is not None else False)
archive.writeToFile(outfile)
for f in files:
os.remove(f)
def exportToCombine(self, outfile):
""" Export Omex instance as combine archive.
:param outfile: A path to the output file"""
import phrasedml
phrasedml.clearReferencedSBML()
archive = libcombine.CombineArchive()
description = libcombine.OmexDescription()
description.setAbout(self.about)
description.setDescription(self.description)
time_now = libcombine.OmexDescription.getCurrentDateAndTime()
description.setCreated(time_now)
# TODO: pass in creator
if self.creator is not None:
creator = libcombine.VCard()
creator.setFamilyName(self.creator['last_name'])
creator.setGivenName(self.creator['first_name'])
creator.setEmail(self.creator['email'])
creator.setOrganization(self.creator['organization'])
description.addCreator(creator)
archive.addMetadata('.', description)
# Write out to temporary files
# TODO: can add content via strings now
workingDir = tempfile.mkdtemp(suffix="_sedml")
files = [] # Keep a list of files to remove
def addAssetToArchive(asset, format):
""" Helper to add asset of given format. """
fname = os.path.join(workingDir,
os.path.normpath(asset.getLocation()))
dname = os.path.dirname(fname)
if not os.path.exists(dname):
os.makedirs(dname)
with open(fname, 'w') as f:
files.append(fname)
f.write(t.getContent())
archive.addFile(fname, asset.getLocation(),
libcombine.KnownFormats.lookupFormat(format),
asset.getMaster())
try:
for t in self.getSedmlAssets():
addAssetToArchive(t, 'sedml')
for t in self.getSbmlAssets():
addAssetToArchive(t, 'sbml')
archive.writeToFile(outfile)
finally:
# put this in finally to make sure files are removed even under Exception
for f in files:
os.remove(f)
def exportToCombine(self, outfile):
""" Export Omex instance as combine archive.
:param outfile: A path to the output file"""
import phrasedml
phrasedml.clearReferencedSBML()
archive = libcombine.CombineArchive()
description = libcombine.OmexDescription()
description.setAbout(self.about)
description.setDescription(self.description)
time_now = libcombine.OmexDescription.getCurrentDateAndTime()
description.setCreated(time_now)
# TODO: pass in creator
if self.creator is not None:
creator = libcombine.VCard()
creator.setFamilyName(self.creator['last_name'])
creator.setGivenName(self.creator['first_name'])
creator.setEmail(self.creator['email'])
creator.setOrganization(self.creator['organization'])
description.addCreator(creator)
archive.addMetadata('.', description)
# Write out to temporary files
# TODO: can add content via strings now
workingDir = tempfile.mkdtemp(suffix="_sedml")
files = [] # Keep a list of files to remove
def addAssetToArchive(asset, format):
""" Helper to add asset of given format. """
fname = os.path.join(workingDir, os.path.normpath(asset.getLocation()))
dname = os.path.dirname(fname)
if not os.path.exists(dname):
os.makedirs(dname)
with open(fname, 'w') as f:
files.append(fname)
f.write(t.getContent())
archive.addFile(fname,
asset.getLocation(),
libcombine.KnownFormats.lookupFormat(format),
asset.getMaster())
try:
for t in self.getSedmlAssets():
addAssetToArchive(t, 'sedml')
for t in self.getSbmlAssets():
addAssetToArchive(t, 'sbml')
archive.writeToFile(outfile)
finally:
# put this in finally to make sure files are removed even under Exception
for f in files:
os.remove(f)
def createpython(self): # Create and return Python script given antimony and phrasedml strings
rePath = r"(\w*).load\('(.*)'\)"
reLoad = r"(\w*) = roadrunner.RoadRunner\(\)"
reModel = r"""(\w*) = model ('|")(.*)('|")"""
phrasedmllines = self.phrasedmlStr.splitlines()
for i, s in enumerate(phrasedmllines):
reSearchModel = re.split(reModel, s)
if len(reSearchModel) > 1:
modelsource = str(reSearchModel[3])
modelname = os.path.basename(modelsource)
modelname = str(modelname).replace(".xml", "")
phrasedml.setReferencedSBML(modelsource, te.antimonyTosbml(self.antimonyStr))
sedmlstr = phrasedml.convertString(self.phrasedmlStr)
if sedmlstr == None:
raise Exception(phrasedml.getLastError())
phrasedml.clearReferencedSBML()
fd1, sedmlfilepath = tempfile.mkstemp()
os.write(fd1, sedmlstr)
pysedml = te.SedmlToRr.sedml_to_python(sedmlfilepath)
if self.modelispath == False:
lines = pysedml.splitlines()
for i, s in enumerate(lines):
reSearchPath = re.split(rePath, s)
if len(reSearchPath) > 1:
del lines[i]
for i, s in enumerate(lines):
reSearchLoad = re.split(reLoad, s)
if len(reSearchLoad) > 1:
s = s.replace("roadrunner.RoadRunner()", "te.loada(" + str(modelname) + ")")
lines[i] = s
if not "import tellurium" in pysedml:
if "import roadrunner" in pysedml:
for i, s in enumerate(lines):
if "import roadrunner" in s:
del lines[i]
lines.insert(i, "import tellurium as te")
else:
pass
pysedml = "\n".join(lines)
# List of replacements
pysedml = pysedml.replace('"compartment"', '"compartment_"')
pysedml = pysedml.replace("'compartment'", "'compartment_'")
outputstr = str(modelname) + " = '''" + self.antimonyStr + "'''\n\n" + pysedml
os.close(fd1)
os.remove(sedmlfilepath)
return outputstr
def executeOmex(self):
'''Executes this Omex instance.'''
import phrasedml
phrasedml.clearReferencedSBML()
workingDir = tempfile.mkdtemp(suffix="_sedml")
self.writeFiles(workingDir)
from tellurium import executeSEDML
for sedml_asset in self.getSedmlAssets():
if sedml_asset.getMaster():
sedml_path = os.path.join(workingDir, sedml_asset.getLocation())
executeSEDML(sedml_path,
workingDir=os.path.dirname(sedml_path))
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))
def executeOmex(self):
""" Executes this Omex instance.
:return:
"""
import phrasedml
phrasedml.clearReferencedSBML()
workingDir = tempfile.mkdtemp(suffix="_sedml")
self.writeFiles(workingDir)
from tellurium import executeSEDML
for sedml_asset in self.getSedmlAssets():
if sedml_asset.getMaster():
sedml_path = os.path.join(workingDir, sedml_asset.getLocation())
executeSEDML(sedml_path,
workingDir=os.path.dirname(sedml_path))
def getSedmlString(self):
reModel = r"""(\w*) = model ('|")(.*)('|")"""
phrasedmllines = self.phrasedmlStr.splitlines()
for i, s in enumerate(phrasedmllines):
reSearchModel = re.split(reModel, s)
if len(reSearchModel) > 1:
modelsource = str(reSearchModel[3])
phrasedml.setReferencedSBML(modelsource, te.antimonyToSbml(self.antimonyStr))
sedmlstr = phrasedml.convertString(self.phrasedmlStr)
if sedmlstr == None:
raise Exception(phrasedml.getLastError())
phrasedml.clearReferencedSBML()
return sedmlstr
def checkKisaoAlgorithmParameter(self, exp, kisao, name, value):
""" Helper function for checking kisao parameter. """
p = exp.phrasedmlList[0]
# check that set AlgorithmParameter set correctly in SED-ML
phrasedml.clearReferencedSBML()
exp._setReferencedSBML(p)
sedml = exp._phrasedmlToSEDML(p)
doc = libsedml.readSedMLFromString(sedml)
simulation = doc.getSimulation('sim0')
algorithm = simulation.getAlgorithm()
pdict = {
p.getKisaoID(): p
for p in algorithm.getListOfAlgorithmParameters()
}
self.assertTrue(kisao in pdict)
pkey = SEDMLCodeFactory.algorithmParameterToParameterKey(pdict[kisao])
if pkey.dtype == str:
self.assertEqual(pkey.value, value)
else:
# numerical parameter
self.assertAlmostEqual(float(pkey.value), value)
# check that integrator is set in python code
pystr = exp._toPython(p)
print(simulation.getElementName())
print(pystr)
if simulation.getTypeCode() is libsedml.SEDML_SIMULATION_STEADYSTATE:
if pkey.dtype == str:
self.assertTrue(
".steadyStateSolver.setValue('{}', '{}')".format(
name, value) in pystr)
else:
# numerical parameter
self.assertTrue(".steadyStateSolver.setValue('{}', {})".format(
name, value) in pystr)
else:
if pkey.dtype == str:
self.assertTrue(".integrator.setValue('{}', '{}')".format(
name, value) in pystr)
else:
# numerical parameter
self.assertTrue(".integrator.setValue('{}', {})".format(
name, value) in pystr)
def toPhrasedml(self):
# assign sbml resources
# print('toPhrasedml sbml resources:')
phrasedml.clearReferencedSBML()
for sbml_resource in self.sbml_map:
# print(' {} -> {}'.format(sbml_resource, self.sbml_map[sbml_resource][:30]))
phrasedml.setReferencedSBML(sbml_resource, self.sbml_map[sbml_resource])
# convert to phrasedml
if self.sedml_str:
result = phrasedml.convertString(self.sedml_str)
if result is None:
raise RuntimeError(phrasedml.getLastError())
return self.fixModelRefs(phrasedml.getLastPhraSEDML())
elif self.sedml_path:
result = phrasedml.convertFile(self.sedml_str)
if result is None:
raise RuntimeError(phrasedml.getLastError())
return self.fixModelRefs(phrasedml.getLastPhraSEDML())
def toPhrasedml(self):
# assign sbml resources
# print('toPhrasedml sbml resources:')
phrasedml.clearReferencedSBML()
for sbml_resource in self.sbml_map:
# print(' {} -> {}'.format(sbml_resource, self.sbml_map[sbml_resource][:30]))
phrasedml.setReferencedSBML(sbml_resource, self.sbml_map[sbml_resource])
# convert to phrasedml
if self.sedml_str:
result = phrasedml.convertString(self.sedml_str)
if result is None:
raise RuntimeError(phrasedml.getLastError())
return self.fixModelRefs(phrasedml.getLastPhraSEDML())
elif self.sedml_path:
result = phrasedml.convertFile(self.sedml_str)
if result is None:
raise RuntimeError(phrasedml.getLastError())
return self.fixModelRefs(phrasedml.getLastPhraSEDML())
def addPhrasedml(self, phrasedmlStr, antimonyStr, arcname=None):
""" Adds phrasedml via conversion to SEDML. """
# FIXME: This does not work for multiple referenced models !.
reModel = r"""(\w*) = model ('|")(.*)('|")"""
phrasedmllines = phrasedmlStr.splitlines()
for k, line in enumerate(phrasedmllines):
reSearchModel = re.split(reModel, line)
if len(reSearchModel) > 1:
modelsource = str(reSearchModel[3])
modelname = os.path.basename(modelsource)
modelname = str(modelname).replace(".xml", '')
phrasedml.setReferencedSBML(modelsource, te.antimonyToSBML(antimonyStr))
sedmlstr = phrasedml.convertString(phrasedmlStr)
if sedmlstr is None:
raise Exception(phrasedml.getLastError())
phrasedml.clearReferencedSBML()
self.addSEDML(sedmlstr, arcname)
def checkKisaoIntegrator(self, exp, kisao, name):
""" Helper function for checking kisao integrator. """
p = exp.phrasedmlList[0]
# is kisao correct in SedDocument
phrasedml.clearReferencedSBML()
exp._setReferencedSBML(p)
sedml = exp._phrasedmlToSEDML(p)
doc = libsedml.readSedMLFromString(sedml)
simulation = doc.getSimulation('sim0')
algorithm = simulation.getAlgorithm()
self.assertEqual(algorithm.getKisaoID(), kisao)
# is integrator/solver set in python code
pystr = exp._toPython(p)
if simulation.getTypeCode() is libsedml.SEDML_SIMULATION_STEADYSTATE:
self.assertTrue(".setSteadyStateSolver('{}')".format(name) in pystr)
else:
self.assertTrue(".setIntegrator('{}')".format(name) in pystr)
def _toPython(self, phrasedmlStr, workingDir=None):
""" Create and return python script given phrasedml string.
:param phrasedmlStr: Name of PhraSEDML string defined in the code
:type phrasedmlStr: str
:returns: python string to execute
:rtype: str
"""
warnings.warn('Use inline_omex instead.', DeprecationWarning)
if phrasedmlStr is None:
phrasedmlStr = self._getDefaultPhrasedml()
# Models have to be resolved from phrasedml string and set as referenced
phrasedml.clearReferencedSBML()
self._setReferencedSBML(phrasedmlStr)
# check if conversion is possible
self._phrasedmlToSEDML(phrasedmlStr)
# create temporary working directory
import tempfile
isTmpDir = False
if workingDir is None:
workingDir = tempfile.mkdtemp(suffix="_sedml")
isTmpDir = True
# Export archive
expId = self.getId()
expArchive = os.path.join(workingDir, "{}.omex".format(expId))
self.exportAsCombine(expArchive)
# Create python code from archive
# This is the clean way to generate the code !
pycode = tesedml.sedmlToPython(expArchive)
# remove the temporary directory
if isTmpDir:
shutil.rmtree(workingDir)
return pycode
def checkKisaoAlgorithmParameter(self, exp, kisao, name, value):
""" Helper function for checking kisao parameter. """
p = exp.phrasedmlList[0]
# check that set AlgorithmParameter set correctly in SED-ML
phrasedml.clearReferencedSBML()
exp._setReferencedSBML(p)
sedml = exp._phrasedmlToSEDML(p)
doc = libsedml.readSedMLFromString(sedml)
simulation = doc.getSimulation('sim0')
algorithm = simulation.getAlgorithm()
pdict = {p.getKisaoID(): p for p in algorithm.getListOfAlgorithmParameters()}
self.assertTrue(kisao in pdict)
pkey = SEDMLCodeFactory.algorithmParameterToParameterKey(pdict[kisao])
if pkey.dtype == str:
self.assertEqual(pkey.value, value)
else:
# numerical parameter
self.assertAlmostEqual(float(pkey.value), value)
# check that integrator is set in python code
pystr = exp._toPython(p)
print(simulation.getElementName())
print(pystr)
if simulation.getTypeCode() is libsedml.SEDML_SIMULATION_STEADYSTATE:
if pkey.dtype == str:
self.assertTrue(".steadyStateSolver.setValue('{}', '{}')".format(name, value) in pystr)
else:
# numerical parameter
self.assertTrue(".steadyStateSolver.setValue('{}', {})".format(name, value) in pystr)
else:
if pkey.dtype == str:
self.assertTrue(".integrator.setValue('{}', '{}')".format(name, value) in pystr)
else:
# numerical parameter
self.assertTrue(".integrator.setValue('{}', {})".format(name, value) in pystr)
def addPhrasedml(self, phrasedmlStr, antimonyStr, arcname=None):
""" Adds SEDML file as phraSEDML string into COMBINE archive.
:param phrasedmlStr: phraSEDML string
:param antimonyStr: antimony string to be referenced
:param arcname: (optional) desired name of SEDML file
"""
warnings.warn('Use inline_omex instead.', DeprecationWarning)
# FIXME: This does not work for multiple referenced models !.
reModel = r"""(\w*) = model ('|")(.*)('|")"""
phrasedmllines = phrasedmlStr.splitlines()
for k, line in enumerate(phrasedmllines):
reSearchModel = re.split(reModel, line)
if len(reSearchModel) > 1:
modelsource = str(reSearchModel[3])
modelname = os.path.basename(modelsource)
modelname = str(modelname).replace(".xml", '')
phrasedml.setReferencedSBML(modelsource, te.antimonyToSBML(antimonyStr))
sedmlstr = phrasedml.convertString(phrasedmlStr)
if sedmlstr is None:
raise Exception(phrasedml.getLastError())
phrasedml.clearReferencedSBML()
self.addSEDML(sedmlstr, arcname)
def exportAsCombine(self, outputPath, execute=False):
""" Creates COMBINE archive for given antimony and phrasedml files.
If execute=True all phrasedml are executed and the results written
:param exportPath: full path of the combine zip file to create
:type exportPath: str
"""
# Create empty archive
m = tecombine.CombineArchive()
# Add antimony models to archive
for aStr in self.antimonyList:
r = te.loada(aStr)
name = r.getModel().getModelName()
m.addAntimonyStr(aStr, "{}.xml".format(name))
# Add phrasedml models to archive
for k, phrasedmlStr in enumerate(self.phrasedmlList):
phrasedml.clearReferencedSBML()
self._setReferencedSBML(phrasedmlStr)
m.addPhraSEDMLStr(phrasedmlStr,
self._phrasedmlFileName(k),
master=True)
phrasedml.clearReferencedSBML()
# Add README.md to archive
readmeStr = self.createReadmeString(outputPath)
m.addStr(readmeStr, location='README.md', filetype='md')
# add output files to archive
if execute:
for phrasedmlStr in self.phrasedmlList:
# execute in temporary directory
workingDir = tempfile.mkdtemp(suffix="_sedml")
execStr = self._toPython(phrasedmlStr, workingDir=workingDir)
exec execStr
# Add output files to archive
files = [f for f in os.listdir(workingDir)]
for f in files:
filepath = os.path.join(workingDir, f)
if f.endswith('.xml'):
# SBML or SEDML resulting from antimony/phrasedml (already in archive)
pass
elif f.endswith('.md'):
# README.md (already in archive)
pass
elif f.endswith('.png'):
# outputPlot2D | outputPlot3D
m.addFile(filepath, filetype="png")
elif f.endswith('.csv'):
# outputReport
m.addFile(filepath, filetype="csv")
else:
warnings.warn(
'Unsupported file type not written in COMBINE archive: {}'
.format(filepath))
# remove temporary workingDir
shutil.rmtree(workingDir)
# Write archive
m.write(outputPath)
