"""
Execute a COMBINE archive.
"""
from pathlib import Path
from sbmlsim.combine.examples import execute_sedml
from tests import DATA_DIR
[docs]def run_repressilator():
repressilator_omex = DATA_DIR / "omex" / "tellurium" / "repressilator.omex"
working_dir = Path(__file__).parent / "results" / "repressilator_omex"
working_dir.mkdir(exist_ok=True)
execute_sedml(path=repressilator_omex, working_dir=working_dir)
[docs]def run_omex(omex_path: Path):
# print(omex_path)
working_dir = Path(__file__).parent / "results" / omex_path.name
# print(working_dir)
working_dir.mkdir(parents=True, exist_ok=True)
execute_sedml(path=omex_path, working_dir=working_dir, output_path=working_dir)
if __name__ == "__main__":
[docs] biomodels_omex_base_path = DATA_DIR / "combine" / "omex" / "biomodels" / "omex"
biomodels_omex_paths = []
for path in Path(biomodels_omex_base_path).rglob("*.omex"):
biomodels_omex_paths.append(path)
biomodels_omex_paths = sorted(biomodels_omex_paths)
for omex_path in [biomodels_omex_base_path / "BIOMD0000000111_fi4_sedml.omex"]:
run_omex(omex_path)
# for omex_path in sorted(biomodels_omex_paths):
# run_biomodel_omex(omex_path)
"/home/mkoenig/git/sbmlsim/src/sbmlsim/tests/data/combine/omex/jws/omex/fraser2002_fig1a_1b_2a_2b.sedx"
"/home/mkoenig/git/sbmlsim/src/sbmlsim/tests/data/combine/omex/jws/omex/levering2012_fig2-user.sedx",
"/home/mkoenig/git/sbmlsim/src/sbmlsim/tests/data/combine/omex/jws/omex/levering2012_fig5-user.sedx",
"/home/mkoenig/git/sbmlsim/src/sbmlsim/tests/data/combine/omex/jws/omex/martins2016_fig4b.sedx"