def example(model_id):
# convert xpp to sbml
xpp_dir = './xpp_example'
out_dir = './xpp_example/results'
xpp_file = os.path.join(xpp_dir, "{}.ode".format(model_id))
sbml_file = os.path.join(out_dir, "{}.xml".format(model_id))
xpp.xpp2sbml(xpp_file=xpp_file, sbml_file=sbml_file)
sbmlreport.create_sbml_report(sbml_file, out_dir=out_dir, validate=False)
# test simulation
r = roadrunner.RoadRunner(sbml_file)
s = r.simulate(start=0, end=1000, steps=100)
fig, (ax1, ax2) = plt.subplots(nrows=1, ncols=2, figsize=(14, 7))
axes = (ax1, ax2)
for ax in axes:
for sid in r.timeCourseSelections[1:]:
ax.plot(s['time'], s[sid], label=sid)
ax2.set_yscale('log')
for ax in axes:
ax.set_ylabel('Value [?]')
ax.set_xlabel('Time [?]')
ax.legend()
fig.savefig(os.path.join(out_dir, "{}.png".format(model_id)),
bbox_inches='tight')
def create_model(modules, target_dir, annotations=None, suffix=None, create_report=True, mid=None):
""" Create SBML model from module information.
This is the entry point for creating models.
The model information is provided as a list of importable python modules.
Additional model annotations can be provided.
:param modules: iteratable of strings of python modules
:param target_dir: directory in which to create SBML files
:param annotations: list of annotations for SBML
:param suffix: Suffix for SBML filename
:param create_report: boolean switch to create SBML report
:param mid: model id to use for saving file
:return:
"""
# preprocess
logging.info(bcolors.OKBLUE + '\n\n' + '-'*120 + '\n' + str(modules) + '\n' + '-'*120 + bcolors.ENDC)
model_dict = Preprocess.dict_from_modules(modules)
# create SBML model
core_model = CoreModel.from_dict(model_dict=model_dict)
logging.debug(core_model.get_info())
core_model.create_sbml()
# write file
if not os.path.exists(target_dir):
logging.warning("Target directory does not exist and is created: {}".format(target_dir))
os.makedirs(target_dir)
if mid is None:
mid = core_model.model.getId()
if suffix is not None:
filename = '{}{}.xml'.format(mid, suffix)
else:
filename = '{}.xml'.format(mid)
sbml_path = os.path.join(target_dir, filename)
core_model.write_sbml(sbml_path, validate=True)
# annotate
if annotations is not None:
# overwrite the normal file
annotation.annotate_sbml_file(sbml_path, annotations, sbml_path)
# create report
if create_report:
logging.info("Create SBML report:'{}'".format(sbml_path))
sbmlreport.create_sbml_report(sbml_path=sbml_path, out_dir=target_dir, validate=False)
return [model_dict, core_model, sbml_path]
debug, show_errors = False, False
# test single model
# ode_all = ["./87762/Neuron_KATP/NeuronKATP_Stoch.ode"]
# debug, show_errors = True, True
for k, xpp_file in enumerate(sorted(ode_all)):
# convert xpp to sbml
basename = os.path.basename(xpp_file)
sbml_file = os.path.join(out_dir, "{}.xml".format(basename))
try:
print('[{}]'.format(k))
xpp.xpp2sbml(xpp_file=xpp_file, sbml_file=sbml_file, force_lower=force_lower, validate=False, debug=debug)
success = True
sbmlreport.create_sbml_report(sbml_file, out_dir=out_dir, validate=False)
Nall, Nerr, Nwarn = validation.check_sbml(sbml_file, name=None, ucheck=False, show_errors=show_errors)
valid = (Nerr == 0)
simulates = False
if valid:
try:
simulate(sbml_file)
simulates = True
except:
# simulation exception
simulates = False
print()
traceback.print_exc(file=sys.stdout)
print()
except:
"""
Writing report with distrib information.
"""
from sbmlutils.report import sbmlreport
if __name__ == "__main__":
for path in [
"./distrib_normal.xml", "./distrib_all.xml",
"./uncertainty_distribution.xml", "./uncertainty_uncertspan.xml",
"./uncertainty_uncertvalue.xml"
]:
print(path)
sbmlreport.create_sbml_report(path, out_dir="./results/")
"""
Writing report with distrib information.
"""
from sbmlutils.report import sbmlreport
if __name__ == "__main__":
for path in ["./distrib_normal.xml",
"./distrib_all.xml",
"./uncertainty_distribution.xml",
"./uncertainty_uncertspan.xml",
"./uncertainty_uncertvalue.xml"]:
print(path)
sbmlreport.create_sbml_report(path, out_dir="./results/")
def test_vdp_report(self):
tmpdir = tempfile.mkdtemp(suffix="_sbml_report")
sbmlreport.create_sbml_report(data.VDP_SBML, tmpdir)
def test_glucose_report(self):
tmpdir = tempfile.mkdtemp(suffix="_sbml_report")
sbmlreport.create_sbml_report(data.GLUCOSE_SBML, tmpdir)
def test_galactose_report(self):
tmpdir = tempfile.mkdtemp(suffix="_sbml_report")
sbmlreport.create_sbml_report(data.GALACTOSE_SINGLECELL_SBML, tmpdir)
def test_demo_report(self):
tmpdir = tempfile.mkdtemp(suffix="_sbml_report")
sbmlreport.create_sbml_report(data.DEMO_SBML, tmpdir)
"""
Script to check the model files.
"""
import os
from os import walk
from sbmlutils.validation import check_sbml
from sbmlutils.report import sbmlreport
# directory to write files to
directory = os.path.dirname(os.path.abspath(__file__))
xml_files = []
for (dirpath, dirnames, filenames) in walk(directory):
xml_files.extend([name for name in filenames if name.endswith('.xml')])
break
print(xml_files)
# perform a model validation
for sbml_file in xml_files:
check_sbml(sbml_file)
# create the model reports
for sbml_file in xml_files:
sbmlreport.create_sbml_report(sbml_file, directory)
p.setName(port_sid)
p.setMetaId(port_sid)
p.setSBOTerm(599) # port
p.setIdRef(sid)
return p
# add ports
cmodel = model.getPlugin("comp") # type: libsbml.CompModelPlugin
for sid in ['Vplasma', 'glcEXT', 'lacEXT', 'phosEXT', 'pyrEXT']:
create_port(sid)
output_path = os.path.join(target_dir, "{}.xml".format(name))
libsbml.writeSBMLToFile(doc, output_path)
return output_path
if __name__ == "__main__":
from sbmlutils.report import sbmlreport
if False:
sbmlreport.create_sbml_report(MODEL_PATH,
out_dir=os.path.join(
path_dir, "./input/"))
target_dir = os.path.join(path_dir, './model/')
name = 'rbc_parasite_model'
output_path = prepare_rbc_model(model_path=MODEL_PATH,
name=name,
target_dir=target_dir)
sbmlreport.create_sbml_report(output_path,
out_dir=os.path.join(path_dir, "./model/"))
"""
Script to check the model files.
"""
import os
from os import walk
from sbmlutils.validation import check_sbml
from sbmlutils.report import sbmlreport
# directory to write files to
directory = os.path.dirname(os.path.abspath(__file__))
xml_files = []
for (dirpath, dirnames, filenames) in walk(directory):
xml_files.extend([name for name in filenames if name.endswith('.xml')])
break
print(xml_files)
# perform a model validation
for sbml_file in xml_files:
check_sbml(sbml_file)
# create the model reports
for sbml_file in xml_files:
sbmlreport.create_sbml_report(sbml_file, directory)
def create_model(modules,
target_dir,
annotations=None,
suffix=None,
create_report=True,
mid=None):
""" Create SBML model from module information.
This is the entry point for creating models.
The model information is provided as a list of importable python modules.
Additional model annotations can be provided.
:param modules: iteratable of strings of python modules
:param target_dir: directory in which to create SBML files
:param annotations: list of annotations for SBML
:param suffix: Suffix for SBML filename
:param create_report: boolean switch to create SBML report
:param mid: model id to use for saving file
:return:
"""
# preprocess
logging.info(bcolors.OKBLUE + '\n\n' + '-' * 120 + '\n' + str(modules) +
'\n' + '-' * 120 + bcolors.ENDC)
model_dict = Preprocess.dict_from_modules(modules)
# create SBML model
core_model = CoreModel.from_dict(model_dict=model_dict)
logging.debug(core_model.get_info())
core_model.create_sbml()
# write file
if not os.path.exists(target_dir):
logging.warning(
"Target directory does not exist and is created: {}".format(
target_dir))
os.makedirs(target_dir)
if mid is None:
mid = core_model.model.getId()
if suffix is not None:
filename = '{}{}.xml'.format(mid, suffix)
else:
filename = '{}.xml'.format(mid)
sbml_path = os.path.join(target_dir, filename)
core_model.write_sbml(sbml_path, validate=True)
# annotate
if annotations is not None:
# overwrite the normal file
annotator.annotate_sbml_file(sbml_path, annotations, sbml_path)
# create report
if create_report:
logging.info("Create SBML report:'{}'".format(sbml_path))
sbmlreport.create_sbml_report(sbml_path=sbml_path,
out_dir=target_dir,
validate=False)
return [model_dict, core_model, sbml_path]
# rbc
creator.create_model(
modules=['pylimax.models.glucose_pkpd.glucose_rbc_model'],
target_dir=target_dir,
annotations=None,
create_report=create_report)
# liver
creator.create_model(
modules=['pylimax.models.glucose_pkpd.glucose_liver_model'],
target_dir=target_dir,
annotations=None,
create_report=create_report)
# exit()
# create comp model
[_, _, body_path] = creator.create_model(
modules=['pylimax.models.glucose_pkpd.glucose_pkpd_model'],
target_dir=target_dir,
annotations=None,
create_report=create_report)
from pylimax.models.glucose_pkpd.glucose_pkpd_model import mid, version
flat_body_path = os.path.join(target_dir,
"{}_{}_flat.xml".format(mid, version))
flattenSBMLFile(body_path, output_path=flat_body_path)
# create model report
sbmlreport.create_sbml_report(flat_body_path, out_dir=target_dir)
import os.path
from sbmlutils.report import sbmlreport
if __name__ == "__main__":
# create the sbml report
f_path = os.path.join(os.path.curdir, 'yeast_glycolysis.xml')
print(f_path)
sbmlreport.create_sbml_report(sbml_path=f_path, out_dir=os.path.curdir)