def example(model_id: str) -> None:
"""XPP example conversion."""
# convert xpp to sbml
xpp_dir = Path(__file__).parent / "xpp_example"
out_dir = xpp_dir / "results"
xpp_file = xpp_dir / f"{model_id}.ode"
sbml_file = out_dir / f"{model_id}.xml"
xpp.xpp2sbml(xpp_file=xpp_file, sbml_file=sbml_file)
sbmlreport.create_report(sbml_file, output_dir=out_dir, validate=False)
# test simulation
r = roadrunner.RoadRunner(str(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(out_dir / f"{model_id}.png", bbox_inches="tight")
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_report(sbml_file, target_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 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 xpp_check(tmp_path, ode_id, Nall=0, Nerr=0, Nwarn=0):
sbml_file = tmp_path / f"{ode_id}.xml"
xpp_file = DATA_DIR / "xpp" / f"{ode_id}.ode"
xpp.xpp2sbml(xpp_file=xpp_file, sbml_file=sbml_file)
vresults = validate_sbml(sbml_file, units_consistency=False)
assert vresults.all_count == Nall
assert vresults.error_count == Nerr
assert vresults.warning_count == Nwarn
def xpp_check(self, ode_id, Nall=0, Nerr=0, Nwarn=0):
tmp_dir = tempfile.mkdtemp(suffix="_xpp")
sbml_file = os.path.join(tmp_dir, "{}.xml".format(ode_id))
xpp_file = os.path.join(xpp_dir, "{}.ode".format(ode_id))
xpp.xpp2sbml(xpp_file=xpp_file, sbml_file=sbml_file)
Nall_res, Nerr_res, Nwarn_res = validation.check_sbml(sbml_file, ucheck=False)
assert Nall_res == Nall
assert Nerr_res == Nerr
assert Nwarn_res == Nwarn
def xpp_check(self, ode_id, Nall=0, Nerr=0, Nwarn=0):
tmp_dir = tempfile.mkdtemp(suffix="_xpp")
sbml_file = os.path.join(tmp_dir, "{}.xml".format(ode_id))
xpp_file = os.path.join(xpp_dir, "{}.ode".format(ode_id))
xpp.xpp2sbml(xpp_file=xpp_file, sbml_file=sbml_file)
Nall_res, Nerr_res, Nwarn_res = validation.check_sbml(sbml_file,
ucheck=False)
assert Nall_res == Nall
assert Nerr_res == Nerr
assert Nwarn_res == Nwarn
force_lower = True
results = []
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()
#!/usr/bin/env python # coding: utf-8 # # SBML converters # `sbmlutils` provides functionality for converting formats to SBML and SBML to some formats. # In[1]: from sbmlutils.report import sbmlreport # ## XPP to SBML # In this example a given xpp model is converted to SBML. # In[2]: from sbmlutils.converters import xpp from sbmlutils import validation # convert to SBML xpp.xpp2sbml(xpp_file="./xpp/SkM_AP_KCa.ode", sbml_file="./xpp/SkM_AP_KCa.xml")