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Merge pull request #21 from sybila/validation
Validation of SBML rules for MathML
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| Original file line number | Diff line number | Diff line change |
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| # Biodivine SBML (validation) | ||
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| Currently, the correctness of the implementation is ensured using two | ||
| mechanisms: | ||
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| - Unit tests. | ||
| - SBML syntactic test suite. | ||
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| ### Unit tests | ||
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| These are "straightforward" in the sense that they use standard `cargo` | ||
| functionality, and should be thus familiar to anyone testing in the | ||
| [Rust ecosystem](https://doc.rust-lang.org/book/ch11-01-writing-tests.html). | ||
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| ### SBML test suite | ||
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| For further validation, we compare our results to the | ||
| [SBML test suite](https://github.com/sbmlteam/sbml-test-suite/releases). | ||
| Specifically, we only use the `syntactic` subset of the test cases, | ||
| because the rest is concerned with simulation, which we do not support. | ||
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| This test suite is not part of the standard `cargo test` process. In fact, | ||
| it is present twice in the codebase. | ||
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| > Both cases expect that the latest version of the syntactic test suite | ||
| > is downloaded and extracted in the `./syntactic` folder (you can get | ||
| > the zip file in the release section of the repository linked above). | ||
| First, it is present as a "silent" test in `core::validation::test_suite` | ||
| module that is enabled by the `sbml_test_suite` feature. To run it, execute | ||
| `cargo test --all-features`. Here, we execute all the test cases in the suite, | ||
| but we don't check if the result is correct. This is mainly to (a) measure code | ||
| coverage, and (b) detect if the library outright fails on some of the examples. | ||
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| Second, a dedicated "example" binary (executed as | ||
| `cargo run --example test-suite-syntactic`) provides additional options to | ||
| tune the testing process. First, it prints additional info about the results | ||
| and actually checks that the results conform to the expected outputs. However, | ||
| you can request to only test a specific subset of rules by specifying their IDs | ||
| as the command line arguments (e.g. `cargo run --example test-suite-syntactic -- 10201 10202`). | ||
| This still runs all tests cases, but only shows | ||
| an error for the cases where an inconsistency is detected for one of the | ||
| requested rules. | ||
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| For the purposes of automated testing, we apply the list of rules in the | ||
| `validated-rules.txt` file. As such, if you extend the list of actually validated | ||
| rules, you have to also extend this file. |
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| use biodivine_lib_sbml::{Sbml, SbmlIssue}; | ||
| use biodivine_lib_sbml::Sbml; | ||
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| // To run this example, execute `cargo run --example basic_example`. | ||
| // If you want to add command line arguments, you can use | ||
| // `cargo run --example basic_example -- ARG_1 ARG_2`. | ||
| // Note the use of `--` to indicate that ARG_x values are meant as arguments | ||
| // for the example binary, not for `cargo` itself. | ||
| fn main() { | ||
| let doc = Sbml::read_path("test-inputs/COVID19_immunotherapy_Mathematical_Model.xml").unwrap(); | ||
| // let doc = Sbml::read_path("test-inputs/COVID19_immunotherapy_Mathematical_Model.xml").unwrap(); | ||
| // let doc = Sbml::read_path("test-inputs/cholesterol_metabolism_and_atherosclerosis.xml").unwrap(); | ||
| let doc = Sbml::read_path("test-inputs/Mukandavire2020.xml").unwrap(); | ||
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| // let model = doc.model().get().unwrap(); | ||
| // Print the whole document: | ||
| // println!("{}", model.read_doc().write_str().unwrap()); | ||
| let mut issues: Vec<SbmlIssue> = Vec::new(); | ||
| doc.validate(&mut issues); | ||
| let issues = doc.validate(); | ||
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| println!("No. of issues: {}", issues.len()); | ||
| println!("{:?}", issues); | ||
| for issue in issues { | ||
| println!("{:?}", issue); | ||
| } | ||
| // assert_eq!(issues.len(), 0); | ||
| } |
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