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 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 __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 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 _setReferencedSBML(self, phrasedmlStr):
""" Set phrasedml referenced SBML for given phrasedml String. """
modelNames = []
for aStr in self.antimonyList:
r = te.loada(aStr)
name = r.getModel().getModelName()
modelNames.append(name)
sources = self._modelsFromPhrasedml(phrasedmlStr)
for source, name in sources.iteritems():
# not a antimony model
if name not in modelNames:
continue
# set as referenced model
aStr = self.antimonyList[modelNames.index(name)]
phrasedml.setReferencedSBML(source, te.antimonyToSBML(aStr))
def _setReferencedSBML(self, phrasedmlStr):
""" Set phrasedml referenced SBML for given phrasedml String. """
modelNames = []
for aStr in self.antimonyList:
r = te.loada(aStr)
name = r.getModel().getModelName()
modelNames.append(name)
sources = self._modelsFromPhrasedml(phrasedmlStr)
for source, name in sources.iteritems():
# not a antimony model
if name not in modelNames:
continue
# set as referenced model
aStr = self.antimonyList[modelNames.index(name)]
phrasedml.setReferencedSBML(source, te.antimonyToSBML(aStr))
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 phrasedmltosedml(self, phrasedml_str, sbml_file, **kwargs):
"""Generate SEDML file from phrasedml.
Example of phrasedml_str:
phrasedml_str = '''
model1 = model "{}"
...
...
'''
:param phrasedml_str: text-based way to represent SEDML
:type phrasedml_str: str
:param sbml_file: the SBML xml file/path to the file
:type sbml_file: str
:return: the sedml string
:rtype: str
"""
try:
with open(sbml_file, "r+") as f:
sbml_str = f.read()
except IOError:
print("Error in opening sbml file")
phrasedml_str = phrasedml_str.format(sbml_file)
phrasedml.setReferencedSBML(sbml_file, sbml_str)
sedml_str = phrasedml.convertString(phrasedml_str)
if sedml_str is None:
raise RuntimeError(phrasedml.getLastError())
sedml_file = os.path.join(self.workingdir0, "sedml.xml")
for key, value in kwargs.items():
if "outputfile" in key:
sedml_file = value
with open(sedml_file, "wb") as f:
f.write(sedml_str.encode("utf-8"))
return sedml_str
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)
S1 -> S2; k1*S1
S1 = 10; S2 = 0
k1 = 1
end
'''
phrasedml_str = '''
model1 = model "myModel"
sim1 = simulate uniform(0, 5, 100)
task1 = run sim1 on model1
plot "Figure 1" time vs S1, S2
'''
# create the sedml xml string from the phrasedml
sbml_str = te.antimonyToSBML(antimony_str)
phrasedml.setReferencedSBML("myModel", sbml_str)
sedml_str = phrasedml.convertString(phrasedml_str)
if sedml_str == None:
print(phrasedml.getLastPhrasedError())
print(sedml_str)
# In[2]:
# Create the temporary files and execute the code
import tempfile
f_sbml = tempfile.NamedTemporaryFile(prefix="myModel", suffix=".xml")
f_sbml.write(sbml_str)
f_sbml.flush()
print(f_sbml.name)
# ### SED-ML L1V2 specification example
# Repressilator example which demonstrates the use of phrasedml with URN examples.
#
# The examples are the reference examples from the SED-ML specification document available from http://sed-ml.sourceforge.net/documents/sed-ml-L1V2.pdf (Introduction Section).
# In[1]:
#!!! DO NOT CHANGE !!! THIS FILE WAS CREATED AUTOMATICALLY FROM NOTEBOOKS !!! CHANGES WILL BE OVERWRITTEN !!! CHANGE CORRESPONDING NOTEBOOK FILE !!!
from __future__ import print_function
import tellurium as te
import phrasedml
# Get SBML from URN and set for phrasedml
urn = "urn:miriam:biomodels.db:BIOMD0000000012"
sbmlStr = te.temiriam.getSBMLFromBiomodelsURN(urn=urn)
phrasedml.setReferencedSBML(urn, sbmlStr)
# <SBML species>
# PX - LacI protein
# PY - TetR protein
# PZ - cI protein
# X - LacI mRNA
# Y - TetR mRNA
# Z - cI mRNA
# <SBML parameters>
# ps_a - tps_active: Transcrition from free promotor in transcripts per second and promotor
# ps_0 - tps_repr: Transcrition from fully repressed promotor in transcripts per second and promotor
phrasedmlStr = """
model1 = model "{}"
S1 -> S2; k1*S1
S1 = 10; S2 = 0
k1 = 1
end
'''
phrasedml_str = '''
model1 = model "myModel"
sim1 = simulate uniform(0, 5, 100)
task1 = run sim1 on model1
plot "Figure 1" time vs S1, S2
'''
# create the sedml xml string from the phrasedml
sbml_str = te.antimonyToSBML(antimony_str)
phrasedml.setReferencedSBML("myModel", sbml_str)
sedml_str = phrasedml.convertString(phrasedml_str)
if sedml_str == None:
print(phrasedml.getLastPhrasedError())
print(sedml_str)
# In[2]:
# Create the temporary files and execute the code
import tempfile
f_sbml = tempfile.NamedTemporaryFile(prefix="myModel", suffix=".xml")
f_sbml.write(sbml_str)
f_sbml.flush()
print(f_sbml.name)
# ### SED-ML L1V2 specification example
# Repressilator example which demonstrates the use of phrasedml with URN examples.
#
# The examples are the reference examples from the SED-ML specification document available from http://sed-ml.sourceforge.net/documents/sed-ml-L1V2.pdf (Introduction Section).
# In[1]:
#!!! DO NOT CHANGE !!! THIS FILE WAS CREATED AUTOMATICALLY FROM NOTEBOOKS !!! CHANGES WILL BE OVERWRITTEN !!! CHANGE CORRESPONDING NOTEBOOK FILE !!!
from __future__ import print_function
import tellurium as te
import phrasedml
# Get SBML from URN and set for phrasedml
urn = "urn:miriam:biomodels.db:BIOMD0000000012"
sbmlStr = te.temiriam.getSBMLFromBiomodelsURN(urn=urn)
phrasedml.setReferencedSBML(urn, sbmlStr)
# <SBML species>
# PX - LacI protein
# PY - TetR protein
# PZ - cI protein
# X - LacI mRNA
# Y - TetR mRNA
# Z - cI mRNA
# <SBML parameters>
# ps_a - tps_active: Transcrition from free promotor in transcripts per second and promotor
# ps_0 - tps_repr: Transcrition from fully repressed promotor in transcripts per second and promotor
phrasedmlStr = """
model1 = model "{}"
def test_repressilator(self):
# Get SBML from URN and set for phrasedml
urn = "urn:miriam:biomodels.db:BIOMD0000000012"
sbml_str = temiriam.getSBMLFromBiomodelsURN(urn=urn)
return_code = phrasedml.setReferencedSBML(urn, sbml_str)
assert return_code # valid SBML
# <SBML species>
# PX - LacI protein
# PY - TetR protein
# PZ - cI protein
# X - LacI mRNA
# Y - TetR mRNA
# Z - cI mRNA
# <SBML parameters>
# ps_a - tps_active: Transcription from free promotor in transcripts per second and promotor
# ps_0 - tps_repr: Transcription from fully repressed promotor in transcripts per second and promotor
phrasedml_str = """
model1 = model "{}"
model2 = model model1 with ps_0=1.3E-5, ps_a=0.013
sim1 = simulate uniform(0, 1000, 1000)
task1 = run sim1 on model1
task2 = run sim1 on model2
# A simple timecourse simulation
plot "Timecourse of repressilator" task1.time vs task1.PX, task1.PZ, task1.PY
# Applying preprocessing
plot "Timecourse after pre-processing" task2.time vs task2.PX, task2.PZ, task2.PY
# Applying postprocessing
plot "Timecourse after post-processing" task1.PX/max(task1.PX) vs task1.PZ/max(task1.PZ), \
task1.PY/max(task1.PY) vs task1.PX/max(task1.PX), \
task1.PZ/max(task1.PZ) vs task1.PY/max(task1.PY)
""".format(urn)
# convert to sedml
print(phrasedml_str)
sedml_str = phrasedml.convertString(phrasedml_str)
if sedml_str is None:
print(phrasedml.getLastError())
raise IOError("sedml could not be generated")
# run SEDML directly
try:
tmp_dir = tempfile.mkdtemp()
executeSEDML(sedml_str, workingDir=tmp_dir)
finally:
shutil.rmtree(tmp_dir)
# create combine archive and execute
try:
tmp_dir = tempfile.mkdtemp()
sedml_location = "repressilator_sedml.xml"
sedml_path = os.path.join(tmp_dir, sedml_location)
omex_path = os.path.join(tmp_dir, "repressilator.omex")
with open(sedml_path, "w") as f:
f.write(sedml_str)
entries = [
omex.Entry(location=sedml_location, formatKey="sedml", master=True)
]
omex.combineArchiveFromEntries(omexPath=omex_path, entries=entries, workingDir=tmp_dir)
executeCombineArchive(omex_path, workingDir=tmp_dir)
finally:
shutil.rmtree(tmp_dir)
model1 = model "test1"
model2 = model "test2"
model3 = model model1 with S1=S2+20
sim1 = simulate uniform(0, 6, 100)
task1 = run sim1 on model1
task2 = run sim1 on model2
plot "Timecourse test1" task1.time vs task1.S1, task1.S2
plot "Timecourse test2" task2.time vs task2.X1, task2.X2
"""
# phrasedml.setReferencedSBML("test1")
exp = te.experiment(phrasedmlList=[phrasedmlStr], antimonyList=[antTest1Str])
print(exp)
# set first model
phrasedml.setReferencedSBML("test1", te.antimonyToSBML(antTest1Str))
phrasedml.setReferencedSBML("test2", te.antimonyToSBML(antTest2Str))
sedmlstr = phrasedml.convertString(phrasedmlStr)
if sedmlstr is None:
raise Exception(phrasedml.getLastError())
print(sedmlstr)
# In[3]:
# In[3]:
"""
from __future__ import absolute_import, print_function
import os
import tempfile
import shutil
from tellurium import temiriam
from tellurium.sedml.tesedml import executeCombineArchive, executeSEDML
from tellurium.utils import omex
import phrasedml
# Get SBML from URN and set for phrasedml
urn = "urn:miriam:biomodels.db:BIOMD0000000012"
sbml_str = temiriam.getSBMLFromBiomodelsURN(urn=urn)
return_code = phrasedml.setReferencedSBML(urn, sbml_str)
print('valid SBML', return_code)
# <SBML species>
# PX - LacI protein
# PY - TetR protein
# PZ - cI protein
# X - LacI mRNA
# Y - TetR mRNA
# Z - cI mRNA
# <SBML parameters>
# ps_a - tps_active: Transcription from free promotor in transcripts per second and promotor
# ps_0 - tps_repr: Transcription from fully repressed promotor in transcripts per second and promotor
phrasedml_str = """
def test_repressilator(self):
# Get SBML from URN and set for phrasedml
urn = "urn:miriam:biomodels.db:BIOMD0000000012"
sbml_str = temiriam.getSBMLFromBiomodelsURN(urn=urn)
return_code = phrasedml.setReferencedSBML(urn, sbml_str)
assert return_code # valid SBML
# <SBML species>
# PX - LacI protein
# PY - TetR protein
# PZ - cI protein
# X - LacI mRNA
# Y - TetR mRNA
# Z - cI mRNA
# <SBML parameters>
# ps_a - tps_active: Transcription from free promotor in transcripts per second and promotor
# ps_0 - tps_repr: Transcription from fully repressed promotor in transcripts per second and promotor
phrasedml_str = """
model1 = model "{}"
model2 = model model1 with ps_0=1.3E-5, ps_a=0.013
sim1 = simulate uniform(0, 1000, 1000)
task1 = run sim1 on model1
task2 = run sim1 on model2
# A simple timecourse simulation
plot "Timecourse of repressilator" task1.time vs task1.PX, task1.PZ, task1.PY
# Applying preprocessing
plot "Timecourse after pre-processing" task2.time vs task2.PX, task2.PZ, task2.PY
# Applying postprocessing
plot "Timecourse after post-processing" task1.PX/max(task1.PX) vs task1.PZ/max(task1.PZ), \
task1.PY/max(task1.PY) vs task1.PX/max(task1.PX), \
task1.PZ/max(task1.PZ) vs task1.PY/max(task1.PY)
""".format(urn)
# convert to sedml
print(phrasedml_str)
sedml_str = phrasedml.convertString(phrasedml_str)
if sedml_str is None:
print(phrasedml.getLastError())
raise IOError("sedml could not be generated")
# run SEDML directly
try:
tmp_dir = tempfile.mkdtemp()
executeSEDML(sedml_str, workingDir=tmp_dir)
finally:
shutil.rmtree(tmp_dir)
# create combine archive and execute
try:
tmp_dir = tempfile.mkdtemp()
sedml_location = "repressilator_sedml.xml"
sedml_path = os.path.join(tmp_dir, sedml_location)
omex_path = os.path.join(tmp_dir, "repressilator.omex")
with open(sedml_path, "w") as f:
f.write(sedml_str)
entries = [
omex.Entry(location=sedml_location,
formatKey="sedml",
master=True)
]
omex.combineArchiveFromEntries(omexPath=omex_path,
entries=entries,
workingDir=tmp_dir)
executeCombineArchive(omex_path, workingDir=tmp_dir)
finally:
shutil.rmtree(tmp_dir)
"""
from __future__ import absolute_import, print_function
import os
import tempfile
import shutil
from tellurium import temiriam
from tellurium.sedml.tesedml import executeCombineArchive, executeSEDML
from tellurium.utils import omex
import phrasedml
# Get SBML from URN and set for phrasedml
urn = "urn:miriam:biomodels.db:BIOMD0000000012"
sbml_str = temiriam.getSBMLFromBiomodelsURN(urn=urn)
return_code = phrasedml.setReferencedSBML(urn, sbml_str)
print('valid SBML', return_code)
# <SBML species>
# PX - LacI protein
# PY - TetR protein
# PZ - cI protein
# X - LacI mRNA
# Y - TetR mRNA
# Z - cI mRNA
# <SBML parameters>
# ps_a - tps_active: Transcription from free promotor in transcripts per second and promotor
# ps_0 - tps_repr: Transcription from fully repressed promotor in transcripts per second and promotor
phrasedml_str = """
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)
