def __init__(self, model_file, generate_network=False):
# check cvode library paths
if (conf.get("cvode_include") is None) or (conf.get("cvode_lib") is
None):
print(
"CVODE include and library paths are not set, compilation won't work"
)
# let's load the model first
if isinstance(model_file, str):
# load model file
self.model = bionetgen.bngmodel(model_file,
generate_network=generate_network)
elif isinstance(model_file, bionetgen.bngmodel):
# loaded model
self.model = model_file
cd = os.getcwd()
with tempfile.TemporaryDirectory() as tmpdirname:
os.chdir(tmpdirname)
self.model.actions.clear_actions()
self.model.write_model(f"{self.model.model_name}_cpy.bngl")
self.model = bionetgen.bngmodel(
f"{self.model.model_name}_cpy.bngl",
generate_network=generate_network,
)
os.chdir(cd)
else:
print(f"model format not recognized: {model_file}")
# set compiler
self.compiler = ccompiler.new_compiler()
self.compiler.add_include_dir(conf.get("cvode_include"))
self.compiler.add_library_dir(conf.get("cvode_lib"))
# compile shared library
self.compile_shared_lib()
# setup simulator
self.simulator = self.lib_file
def test_action_loading():
# tests a BNGL file containing all BNG actions
all_action_model = os.path.join(
*[tfold, "models", "actions", "all_actions.bngl"])
m1 = bng.bngmodel(all_action_model)
assert len(m1.actions) + len(m1.actions.before_model) == 31
no_action_model = os.path.join(
*[tfold, "models", "actions", "no_actions.bngl"])
m2 = bng.bngmodel(no_action_model)
assert len(m2.actions) == 0
def _get_pcoords(self):
# use bng api to get the model object
model = bionetgen.bngmodel(self.inp_file)
obs_arr = []
# get observable strings
for obs in model.observables:
obs_arr.append(str(obs))
return obs_arr
def generate_notebook(app):
"""
Uses BNGNotebook class to write a Jupyter notebook from a
given set of command line arguments
"""
args = app.pargs
if args.input is not None:
# we want to use the template to write a custom notebok
# TODO: Transition to BNGErrors and logging
assert args.input.endswith(
".bngl"), f"File {args.input} doesn't have bngl extension!"
try:
app.log.debug("Loading model", f"{__file__} : notebook()")
import bionetgen
m = bionetgen.bngmodel(args.input)
str(m)
except:
app.log.error("Failed to load model", f"{__file__} : notebook()")
raise RuntimeError(f"Couldn't import given model: {args.input}!")
notebook = BNGNotebook(
app.config["bionetgen"]["notebook"]["template"],
INPUT_ARG=args.input,
)
else:
# just use the basic notebook
notebook = BNGNotebook(app.config["bionetgen"]["notebook"]["path"])
# find our file name
if len(args.output) == 0:
fname = app.config["bionetgen"]["notebook"]["name"]
else:
fname = args.output
# write the notebook out
if os.path.isdir(fname):
if args.input is not None:
basename = os.path.basename(args.input)
mname = basename.replace(".bngl", "")
fname = mname + ".ipynb"
else:
mname = app.config["bionetgen"]["notebook"]["name"]
fname = os.path.join(args.output, mname)
app.log.debug(f"Writing notebook to file: {fname}",
f"{__file__} : notebook()")
notebook.write(fname)
# open the notebook with nbopen
# TODO: deal with stdout/err
app.log.debug(
f"Attempting to open notebook {fname} with nbopen",
f"{__file__} : notebook()",
)
stdout = getattr(subprocess, app.config["bionetgen"]["stdout"])
stderr = getattr(subprocess, app.config["bionetgen"]["stderr"])
if args.open:
command = ["nbopen", fname]
rc, _ = run_command(command)
def test_setup_simulator():
fpath = os.path.join(tfold, "test.bngl")
fpath = os.path.abspath(fpath)
try:
m = bng.bngmodel(fpath)
librr_simulator = m.setup_simulator()
res = librr_simulator.simulate(0, 1, 10)
except:
res = None
assert res is not None
def read_model(bngl_filename, filename):
model = None
errors = []
with StandardOutputErrorCapturer(level=StandardOutputErrorCapturerLevel.c,
relay=False) as captured:
try:
model = bionetgen.bngmodel(bngl_filename)
except Exception as exception:
errors.append([
'`{}` is not a valid BNGL or BGNL XML file.'.format(filename
or ''),
[[str(exception)]]
])
return model, errors, captured.get_text()
def test_bionetgen_all_model_loading():
# tests library model loading using many models
mpattern = os.path.join(tfold, "models") + os.sep + "*.bngl"
models = glob.glob(mpattern)
succ = []
fail = []
success = 0
fails = 0
for model in models:
try:
m = bng.bngmodel(model)
success += 1
mstr = str(m)
succ.append(model)
except:
print("can't load model {}".format(model))
fails += 1
fail.append(model)
print("succ: {}".format(success))
print(sorted(succ))
print("fail: {}".format(fails))
print(sorted(fail))
assert fails == 0
def _executable_BNGL_on_file(self):
# IMPORTANT!
# This assumes that the bngl file doesn't have any directives at the end!
# we have a bngl file
os.chdir("bngl_conf")
# Make specific BNGL files for a) generating network and then
# b) getting a starting gdat file
model = bionetgen.bngmodel(self.bngl_file)
model.add_action("generate_network", action_args={"overwrite": 1})
model.add_action(
"simulate", action_args={"method": "'ssa'", "t_end": 2, "n_steps": 2}
)
with open("init.bngl", "w") as f:
f.write(str(model))
r = bionetgen.run("init.bngl", "for_init")
shutil.copyfile(os.path.join("for_init", "init.net"), "init.net")
header_str = ""
for i in r[0].dtype.names:
header_str += " " + i
np.savetxt("init.gdat", r[0], header=header_str)
shutil.rmtree("for_init")
os.chdir(os.path.join(self.main_dir, self.sim_dir))
return model
import bionetgen as bng
import glob
models = glob.glob("*.bngl")
total = len(models)
succ = []
fail = []
success = 0
fails = 0
for model in models:
try:
m = bng.bngmodel(model)
success += 1
succ.append(model)
# mname = model.replace(".bngl","")
# with open("{}_loaded.bngl".format(mname), 'w') as f:
# f.write(str(m))
except:
print("can't do model {}".format(model))
fails += 1
fail.append(model)
print("succ: {}".format(success))
print(sorted(succ))
print("fail: {}".format(fails))
print(sorted(fail))
def test_bionetgen_model():
fpath = os.path.join(tfold, "test.bngl")
fpath = os.path.abspath(fpath)
m = bng.bngmodel(fpath)