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 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))
plot "Figure 1.3 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 SED-ML
sedmlStr = phrasedml.convertString(phrasedmlStr)
if sedmlStr == None:
print(phrasedml.getLastError())
# Run the SED-ML file with results written in workingDir
import tempfile
import shutil
workingDir = tempfile.mkdtemp(suffix="_sedml")
te.executeSEDML(sedmlStr, workingDir=workingDir)
shutil.rmtree(workingDir)
# ### Execute Combine Archive
# Executing the SED-ML from a combine archive.
# In[2]:
import tellurium as te
from tellurium.tests.testdata import sedxDir
import os
omexPath = os.path.join(sedxDir, "BIOMD0000000003.sedx")
print(omexPath)
te.executeSEDML(omexPath)
import re
import os
import matplotlib
# switch the backend of matplotlib, so plots can be tested
matplotlib.pyplot.switch_backend("Agg")
# location of test cases
CASES_DIRECTORY = os.path.join(".", 'testdata', 'sbml-test-cases-2014-10-22')
# find all L3V1 SEDML files
pattern = re.compile("""^\d{5}-sbml-l3v1-sedml.xml$""")
matches = []
for root, dirnames, filenames in os.walk(CASES_DIRECTORY):
for filename in filenames:
if pattern.match(filename):
matches.append(os.path.join(root, filename))
matches = sorted(matches)
# execute the SEDML
import tellurium as te
for match in matches:
print(match)
try:
te.executeSEDML(match)
except RuntimeError:
print("RUNTIME ERROR: {}".format(match))
pass
# Applying postprocessing
plot "Figure 1.3 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 SED-ML
sedmlStr = phrasedml.convertString(phrasedmlStr)
if sedmlStr == None:
print(phrasedml.getLastError())
# Run the SED-ML file with results written in workingDir
import tempfile
import shutil
workingDir = tempfile.mkdtemp(suffix="_sedml")
te.executeSEDML(sedmlStr, workingDir=workingDir)
shutil.rmtree(workingDir)
# ### Execute Combine Archive
# Executing the SED-ML from a combine archive.
# In[2]:
import tellurium as te
from tellurium.tests.testdata import sedxDir
import os
omexPath = os.path.join(sedxDir, "BIOMD0000000003.sedx")
print(omexPath)
te.executeSEDML(omexPath)
plot "Figure 1.3 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)
# [1] convert to SED-ML & run
# convert to SED-ML
sedmlStr = phrasedml.convertString(phrasedmlStr)
if sedmlStr == None:
print(phrasedml.getLastError())
# Run the SED-ML file with results written in workingDir
import tempfile
import shutil
workingDir = tempfile.mkdtemp(suffix="_sedml")
te.executeSEDML(sedmlStr, workingDir=workingDir)
shutil.rmtree(workingDir)
# [2] store as combine archive and run
import os
from tellurium.tecombine import CombineArchive
combine = CombineArchive()
combine.addSEDMLStr(sedmlStr, 'specificationL1V2.sedml')
from tellurium.tests.testdata import sedxDir
combinePath = os.path.join(sedxDir, 'specificationL1V2.sedx')
combine.write(combinePath)
# Run Combine archive
te.executeSEDML(combinePath)
# remove sedx (not hashable due to timestamp)
plot "Figure 1.3 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)
# [1] convert to SED-ML & run
# convert to SED-ML
sedmlStr = phrasedml.convertString(phrasedmlStr)
if sedmlStr == None:
print(phrasedml.getLastError())
# Run the SED-ML file with results written in workingDir
import tempfile
import shutil
workingDir = tempfile.mkdtemp(suffix="_sedml")
te.executeSEDML(sedmlStr, workingDir=workingDir)
shutil.rmtree(workingDir)
# [2] store as combine archive and run
import os
from tellurium.tecombine import CombineArchive
combine = CombineArchive()
combine.addSEDMLStr(sedmlStr, 'specificationL1V2.sedml')
from tellurium.tests.testdata import sedxDir
combinePath = os.path.join(sedxDir, 'specificationL1V2.sedx')
combine.write(combinePath)
# Run Combine archive
te.executeSEDML(combinePath)
