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The docstrings and variable names for the batch_load_from_files function suggest that only json files are accepted as input, rather than both json and SBML.
The function currently checks whether the files in a batch are json or SBML by checking for a .json or .xml suffix--because people often use different extensions (e.g., modelname.sbml is common rather than modelname.xml), we should use the built-in error handling capabilities of cobrapy to determine whether the file type was correct. This will also enable the SBML parser to read compressed SBML files without any additional modification of Medusa code. We will need to add an additional argument to the function for the user to specify json or sbml, or have separate functions a la cobrapy (I favor an additional argument).
The text was updated successfully, but these errors were encountered:
gregmedlock
changed the title
clarify batch_load_from_files docstrings, variable names, and SBML.json checking
clarify batch_load_from_files docstrings, variable names, and SBML/json checking
Jan 6, 2020
The docstrings and variable names for the batch_load_from_files function suggest that only json files are accepted as input, rather than both json and SBML.
The function currently checks whether the files in a batch are json or SBML by checking for a .json or .xml suffix--because people often use different extensions (e.g., modelname.sbml is common rather than modelname.xml), we should use the built-in error handling capabilities of cobrapy to determine whether the file type was correct. This will also enable the SBML parser to read compressed SBML files without any additional modification of Medusa code. We will need to add an additional argument to the function for the user to specify json or sbml, or have separate functions a la cobrapy (I favor an additional argument).
The text was updated successfully, but these errors were encountered: