Source code for sbmltoodejax.parse

import libsbml
import os
import sbmltoodepy
from tempfile import NamedTemporaryFile

[docs] def ParseSBMLFile(file: str): """ Wrapper of SBMLtoODEpy's ``ParseSBMLFile`` function. This function extract the SBML modelโ€™s elements using libSBML, and returns an instance ModelData which is intended to be then passed to the :func:`~sbmltoodejax.modulegeneration.GenerateModel`. See Also: This function buils upon SBMLtoODEpy ``ParseSBMLFile`` function, see their documentation at Note: Here, at the difference of the original SBMLtoODEpy's function, ``ParseSBMLFile``: - takes as input a string which can be a filepath but also directly a string containing the content of the file (allows to directly parse online-hosted SBML files, see Example) - raises an error if the SBML model contains Events (not handled yet neither in SBMLtoODEpy nor in SBMLtoODEjax) Args: file (str): can be either the filepath of the SBML model to be parsed or a string with the content of the file Returns: modelData (sbmltoodepy.dataclasses.ModelData): An sbmltoodepy object containing the modelโ€™s components and their properties Raises: ValueError: if there is an error during LibSBML reading of the file NotImplementedError: if the SBML model contains events Example: .. code-block:: python from sbmltoodejax.parse import ParseSBMLFile from urllib.request import urlopen model_idx = 647 model_url = f"{model_idx:010d}.2?filename=BIOMD{model_idx:010d}_url.xml" with urlopen(model_url) as response: model_xml_body ="utf-8") model_data = ParseSBMLFile(model_xml_body) """ if os.path.exists(file): filePath = file libsbml.readSBML(filePath) doc = libsbml.readSBML(file) else: tmp_sbml_file = NamedTemporaryFile(suffix=".xml") with open(, 'w') as f: f.write(file) doc = libsbml.readSBMLFromString(file) filePath = # Raise an Error if SBML error if doc.getNumErrors() > 0: raise ValueError("LibSBML read error") # Raise an Error if the model contains events as they are not handled by SBMLtoODEpy model = doc.getModel() if model.getNumEvents() > 0: raise NotImplementedError("Events are not handled") modelData = sbmltoodepy.parse.ParseSBMLFile(filePath) return modelData