[Bug]: Populated metadata overwritten

[jkalayan]

Bug Report

When topology, trajectory and logfile are provided to the metadata extractor, the metadata extracted from the logfile is overwritten by the metadata extracted from the topology/trjectory files.

---

To Reproduce

    mapping_path = engine_mappings_path()
    biosim_path = schema_yaml_path()

    populator = MetadataPopulator(
        schema_path=mapping_path,
        top_file=top_file,
        traj_file=[traj_file],
        log_file=log_file,
        engine="gromacs",
        store_file_metadata=True,
    )

    result = populator.populate()
    populator.validate(result, biosimschema_path=biosim_path)