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| # SBML Heta Cases | ||
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| The package is designed to test different aspects of Heta formats on [SBML Test Suite](https://github.com/sbmlteam/sbml-test-suite). | ||
| The repository is designed to test different aspects of Heta formats on [SBML Test Suite](https://github.com/sbmlteam/sbml-test-suite). | ||
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| [](https://hetalang.github.io/) | ||
| [](https://insysbio.github.io/sbml-heta-cases/) | ||
| [](https://github.com/insysbio/sbml-heta-cases/actions/workflows/convert-to-heta.yml) | ||
| [](https://insysbio.github.io/sbml-heta-cases/) | ||
| [](https://GitHub.com/insysbio/sbml-heta-cases/issues/) | ||
| [](https://github.com/insysbio/sbml-heta-cases/blob/master/LICENSE) | ||
|
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| ## Summary | ||
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| 1. Conversion of cases into Heta code and JSON format | ||
| 2. Load models in SBML format and make simulations in | ||
| The GitHub Actions are utilized for the automatic testing. | ||
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| ## File content | ||
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| - [SBML Test Suite](https://github.com/sbmlteam/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](https://github.com/sbmlteam/sbml-test-suite/blob/master/cases/semantic/README.md#tolerances-and-errors-for-timecourse-tests), `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`). | ||
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| ## Usage | ||
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| SBML Heta Cases exports the following functions: | ||
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| ``` | ||
| upload_cases(;db_path::AbstractString=cases_db) | ||
| 1. Download SBML Test Suite v3.4.0 semantic cases from https://github.com/sbmlteam/sbml-test-suite. | ||
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| Upload cases from `cases_db`. | ||
| ``` | ||
| 2. Convert files of format SBML L2V5 and L3V2 (if presented) from semantic test suite to Heta format. | ||
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| ``` | ||
| add_cases(; | ||
| cases_path::AbstractString=cases_path, | ||
| cases_db::AbstractString=cases_db | ||
| ) | ||
| 3. Store the converted models and `summary.json` in the the `result` branch. | ||
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| Add new cases from `cases_path` to `cases_db`. | ||
| ``` | ||
| 4. The statistics of the conversion and result visualization can be seen in the https://insysbio.github.io/sbml-heta-cases/ | ||
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| ``` | ||
| 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`. | ||
| ``` | ||
|
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||
| ``` | ||
| 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... | ||
| ) | ||
| ## File content | ||
|
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||
| 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`. | ||
| ``` | ||
| - `.github/workflows` - GitHub Actions files. | ||
| - `bash` - bash scripts for the conversion. | ||
| - `result` (temporal) - the folder with the converted models and `summary.json`. | ||
| - `static` - the folder with the static files for the GitHub Pages. | ||
| - `README.md` - the current file. | ||
|
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| ``` | ||
| 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... | ||
| ) | ||
| ## Authors | ||
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| 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`. | ||
| ``` | ||
| - Evgeny Metelkin | ||
| - Ivan Borisov |
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| ## File content | ||
|
|
||
| - [SBML Test Suite](https://github.com/sbmlteam/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](https://github.com/sbmlteam/sbml-test-suite/blob/master/cases/semantic/README.md#tolerances-and-errors-for-timecourse-tests), `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`). | ||
|
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||
|
|
||
| ## 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`. | ||
| ``` |
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| .retCode_9 { | ||
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