Convert a Python Napistu SBML_dfs pathway representation into R tables. This will remove some attributes (identifiers and sources) and all the methods which are essential for the sbml_dfs to function as an SBML_dfs obbject but the core relational structure of the pathway can be more easily explored after this conversion.
Value
an S3 r_sbml_dfs object which is a list with one table for each of SBML_dfs' core attributes (compartments, species, compartmentalized_species, reactions, and reaction_species)
Examples
setup_napistu_list(create_napistu_config())
#>
#> ── Setting up Napistu environment ──────────────────────────────────────────────
#> No Python configuration specified, setting up conda environment
#> Using existing conda environment "napistu-env"
#> Python version 3.11 meets requirements
#> No assets configuration specified, loading bundled package data
#> ℹ Creating derived assets
#> ℹ Creating a table of species names to support lookups by name
#> ℹ Loading sbml_dfs from sbml_dfs.pkl
#> Error in value[[3L]](cond): Failed to load sbml_dfs from
#> /home/runner/work/_temp/Library/napistu.r/extdata/test_pathway/sbml_dfs.pkl:
#> ImportError: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: version `OPENSSL_3.3.0'
#> not found (required by
#> /usr/share/miniconda/envs/napistu-env/lib/python3.11/lib-dynload/_ssl.cpython-311-x86_64-linux-gnu.so)
#> Run `reticulate::py_last_error()` for details.
convert_sbml_dfs(napistu_list$sbml_dfs)
#> Error: object 'napistu_list' not found