def run_tellurium(input_path, output_path):
""" Run Combine archive with tellurium and store archive with results.
:param input_path:
:param output_path:
:return:
"""
print('-' * 80)
print('Running tellurium:\n\t', input_path)
print('-' * 80)
import tellurium
import matplotlib
matplotlib.use('Agg')
tellurium.setDefaultPlottingEngine("matplotlib")
filename, extension = os.path.splitext(os.path.basename(input_path))
workingDir = os.path.join(TELLURIUM_DIR, '_te_{}'.format(filename))
if not os.path.exists(workingDir):
os.makedirs(workingDir)
executeCombineArchive(input_path,
workingDir=workingDir,
outputDir=workingDir,
saveOutputs=True)
def test_single_omex(tmpdir):
omex_path = os.path.join(OMEX_TEST_DIR, 'specification/L1V3/L1V3_reading-data-csv-minimal.omex')
contents = omex.listContents(omex_path)
# print(contents[1])
# TODO print generated code
tmp_dir = tempfile.mkdtemp()
try:
tesedml.executeCombineArchive(omexPath=omex_path, workingDir=tmp_dir)
finally:
shutil.rmtree(tmp_dir)
def test_omex_plot_numl_with_model(tmpdir):
results = tesedml.executeCombineArchive(OMEX_PLOT_NUML_WITH_MODEL, workingDir=str(tmpdir))
result = list(results.values())[0]
dg_dict = result['dataGenerators']
assert len(dg_dict) == 5
assert "dgDataS1" in dg_dict
assert "dgDataTime" in dg_dict
assert len(dg_dict["dgDataS1"]) == 200
assert len(dg_dict["dgDataTime"]) == 200
def test_omex_plot_csv(tmpdir):
results = tesedml.executeCombineArchive(OMEX_PLOT_CSV, workingDir=str(tmpdir))
result = list(results.values())[0]
dg_dict = result['dataGenerators']
assert len(dg_dict) == 2
assert "dgDataS1" in dg_dict
assert "dgDataTime" in dg_dict
assert len(dg_dict["dgDataS1"]) == 200
assert len(dg_dict["dgDataTime"]) == 200
def test_omex_plot_numl_with_model(tmpdir):
results = tesedml.executeCombineArchive(OMEX_PLOT_NUML_WITH_MODEL,
workingDir=str(tmpdir))
result = list(results.values())[0]
dg_dict = result['dataGenerators']
assert len(dg_dict) == 5
assert "dgDataS1" in dg_dict
assert "dgDataTime" in dg_dict
assert len(dg_dict["dgDataS1"]) == 200
assert len(dg_dict["dgDataTime"]) == 200
def test_omex_plot_csv(tmpdir):
results = tesedml.executeCombineArchive(OMEX_PLOT_CSV,
workingDir=str(tmpdir))
result = list(results.values())[0]
dg_dict = result['dataGenerators']
assert len(dg_dict) == 2
assert "dgDataS1" in dg_dict
assert "dgDataTime" in dg_dict
assert len(dg_dict["dgDataS1"]) == 200
assert len(dg_dict["dgDataTime"]) == 200
def test_omex_csv_parameters(tmpdir):
results = tesedml.executeCombineArchive(OMEX_CSV_PARAMETERS, workingDir=str(tmpdir))
result = list(results.values())[0]
dgs = result['dataGenerators']
dg_dict = list(dgs.values())[0]
assert len(dg_dict) == 2
assert "dgDataIndex" in dg_dict
assert "dgDataMu" in dg_dict
assert len(dg_dict["dgDataIndex"]) == 10
assert len(dg_dict["dgDataMu"]) == 10
def test_omex_csv_parameters(tmpdir):
results = tesedml.executeCombineArchive(OMEX_CSV_PARAMETERS,
workingDir=str(tmpdir))
result = list(results.values())[0]
dgs = result['dataGenerators']
dg_dict = list(dgs.values())[0]
assert len(dg_dict) == 2
assert "dgDataIndex" in dg_dict
assert "dgDataMu" in dg_dict
assert len(dg_dict["dgDataIndex"]) == 10
assert len(dg_dict["dgDataMu"]) == 10
def execute_omex(archive_id, debug=False):
"""
Execute omex.
"""
matplotlib.pyplot.switch_backend("Agg")
print("*** START RUNNING OMEX ***")
results = {}
# get archive, raises ObjectDoesNotExist
archive = Archive.objects.get(pk=archive_id)
omex_path = str(archive.file.path)
# execute archive
try:
tmp_dir = tempfile.mkdtemp()
# dictionary of files to data generators
te_result = tesedml.executeCombineArchive(omex_path,
workingDir=tmp_dir,
createOutputs=False)
# JSON serializable results (np.array to list)
dgs_json = {}
for f_tmp, result in te_result.items():
sedml_location = f_tmp.replace(tmp_dir + "/", "")
dgs = result['dataGenerators']
# print(sedml_location)
for key in dgs:
dgs[key] = dgs[key].tolist()
# print(key, ':', dgs[key])
dgs_json[sedml_location] = dgs
# print("-" * 80)
# store results of execution for rendering
results['dgs'] = dgs_json
# results['code'] = te_result['code']
finally:
# cleanup
shutil.rmtree(tmp_dir)
print("*** FINISHED RUNNING OMEX ***")
return results
def test(self=None):
""" Test failes if Exception in execution of f. """
if self is not None:
print(filePath)
tesedml.executeCombineArchive(omexPath=filePath, workingDir=self.test_dir)
def test_omex_jws_adlung2017_fig2gl(tmpdir):
results = tesedml.executeCombineArchive(OMEX_CSV_JWS_ADLUNG2017_FIG2G, workingDir=str(tmpdir))
result = list(results.values())[0]
dg_dict = result['dataGenerators']
assert len(dg_dict) == 40
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)
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)
shutil.copy(omex_path, "repressilator.omex")
executeCombineArchive(omex_path, workingDir=tmp_dir)
finally:
shutil.rmtree(tmp_dir)
def test_omex_executeCombineArchive(self):
tesedml.executeCombineArchive(omexPath=OMEX_SHOWCASE, workingDir=self.test_dir)
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)
shutil.copy(omex_path, "repressilator.omex")
executeCombineArchive(omex_path, workingDir=tmp_dir)
finally:
shutil.rmtree(tmp_dir)
def test_omex_executeCombineArchive(self):
tesedml.executeCombineArchive(omexPath=OMEX_SHOWCASE,
workingDir=self.test_dir)
def test_omex_jws_adlung2017_fig2gl(tmpdir):
results = tesedml.executeCombineArchive(OMEX_CSV_JWS_ADLUNG2017_FIG2G,
workingDir=str(tmpdir))
result = list(results.values())[0]
dg_dict = result['dataGenerators']
assert len(dg_dict) == 40
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)