SBML Heta Cases

The package is designed to test different aspects of Heta formats on SBML Test Suite.

1. Conversion of cases into Heta code and JSON format
2. Load models in SBML format and make simulations in

File content

• SBML Test Suite cases in cases_path = "./cases/semantic". The original Matlab models were converted to Julia with Heta compiler. Julia code for each model is stored in ./cases/semantic/<case_num>/julia, while models' settings and tags are stored in cases_db = "./cases.json".
• API (documented in the Usage section) to upload cases_db, run simulations, save results to output_path = "./cases/output" and update status in results_db = "./results.json". A simulation can end with one of the three status: success indicates the output file has passed tolerance test, failure signifies that tolerance test for a given simulation was not passed and error stands for any error during the simulation (error message is printed to the message field in results_db).

Usage

SBML Heta Cases exports the following functions:

    upload_cases(;db_path::AbstractString=cases_db)

Upload cases from `cases_db`.

    add_cases(;
        cases_path::AbstractString=cases_path,
        cases_db::AbstractString=cases_db
    )

Add new cases from `cases_path` to `cases_db`.

    update_results(
        case::AbstractString,
        cases_dict::AbstractDict=upload_cases(db_path=results_db);
        cases_path::AbstractString=cases_path,
        cases_db::AbstractString=cases_db,
        results_db::AbstractString=results_db,
        backend::DataType=default_backend,
        kwargs...
    )

Reads `results_db` to `cases_dict`, accesses the `case`,
solves it with the chosen `backend` solver and writes result to `results_db`.

    update_results(
        cases_vec::Vector{String},
        cases_dict::AbstractDict=upload_cases(db_path=results_db);
        cases_path::AbstractString=cases_path,
        cases_db::AbstractString=cases_db,
        results_db::AbstractString=results_db,
        backend::DataType=default_backend,
        kwargs...
    )

Reads `results_db` to `cases_dict`, accesses the selected cases from `cases_vec`,
solves it with the chosen `backend` solver and writes results to `results_db`.

    update_results(
        cases_range::UnitRange,
        cases_dict::AbstractDict=upload_cases(db_path=results_db);
        cases_path::AbstractString=cases_path,
        cases_db::AbstractString=cases_db,
        results_db::AbstractString=results_db,
        backend::DataType=default_backend,
        kwargs...
    )

Reads `results_db` to `cases_dict`, accesses the selected cases from `cases_range`,
solves it with the chosen `backend` solver and writes results to `results_db`.

    update_results(
        cases_dict::AbstractDict=upload_cases(db_path=results_db);
        include_test_tags::Vector{String}=String[],
        include_component_tags::Vector{String}=String[],
        exclude_test_tags::Vector{String}=String[],
        exclude_component_tags::Vector{String}=String[],
        cases_path::AbstractString=cases_path,
        cases_db::AbstractString=cases_db,
        results_db::AbstractString=results_db,
        backend::DataType=default_backend,
        kwargs...
    )

Reads `results_db` to `cases_dict`, filters the cases according to `include` and `exclude` tags,
solves it with the chosen `backend` solver and writes results to `results_db`.