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biosimulations / biosimulations-physiome

Command-line application for publishing the Physiome model repository of physiological models to the BioSimulations repository for simulation projects
https://docs.biosimulations.org/repositories/physiome
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Folders are not preserved when adding files to COMBINE archives #21

Closed bilalshaikh42 closed 2 years ago

bilalshaikh42 commented 2 years ago

For example: https://run.biosimulations.dev/simulations/61cf538b7d88c1cd86aba290#tab=metadata

The simulation fails because the referenced file "Units/units.cellml" does not exist. This is because it has been moved to the top-level of the archive.

The code that adds the files is here: https://github.com/biosimulations/biosimulations-physiome/blob/21777442045ed5c571ad9be358d2c8cd1d719c7f/biosimulations_physiome/process_projects.py#L283

This is then passed to the COMBINEARCHIVE class with the root directory.

bilalshaikh42 commented 2 years ago

This is because files is a list of filenames without a path. 🤦🏾