Source code for

"""COMBINE archive for PEtab problems."""

from pathlib import Path

import numpy as np
import petab
from petab import (
from pymetadata.omex import EntryFormat, ManifestEntry, Omex

[docs]def create_petab_omex( omex_file: Path, yaml_file: Path, ) -> None: """Create COMBINE archive for PETab.""" omex = Omex() # get relative path from yaml file base_dir: Path = yaml_file.parent yaml_config = petab.yaml.load_yaml(yaml_file) # "PEtab YAML file" omex.add_entry( entry_path=yaml_file, entry=ManifestEntry( location=f"./{yaml_file.relative_to(base_dir)}", format=EntryFormat.YAML, master=True, ), ) # Add parameter file(s) that describe a single parameter table. # Works for a single file name, or a list of file names. for parameter_subset_file in list(np.array(yaml_config[PARAMETER_FILE]).flat): omex.add_entry( entry_path=base_dir / parameter_subset_file, entry=ManifestEntry( location=parameter_subset_file, format=EntryFormat.TSV, master=True, ), ) for problem in yaml_config[PROBLEMS]: for sbml_file in problem[SBML_FILES]: omex.add_entry( entry_path=base_dir / sbml_file, entry=ManifestEntry( location=sbml_file, format=EntryFormat.SBML, master=True, ), ) for field in [ MEASUREMENT_FILES, OBSERVABLE_FILES, VISUALIZATION_FILES, CONDITION_FILES, ]: if field not in problem: continue for file in problem[field]: omex.add_entry( entry_path=base_dir / file, entry=ManifestEntry( location=file, format=EntryFormat.TSV, master=True, ), ) omex.to_omex(omex_file)
if __name__ == "__main__": from sbmlsim import RESOURCES_DIR
[docs] data_dir = RESOURCES_DIR / "testdata" / "petab" / "icg_example1"
print(data_dir, data_dir.exists()) create_petab_omex( omex_file=data_dir / "icg.omex", yaml_file=data_dir / "icg.yaml", )