VS Code Extension - SBML linting

[baconcheese113]

Thanks for all your work on this lib, I've published a VS Code extension that will validate sbml files as you write them.

https://marketplace.visualstudio.com/items/?itemName=joseph-yannessa.sbml-linter

[fbergmann]

@baconcheese113 thanks for letting us know, this seems quite interesting. It would be great if the extension would work on other systems as well. maybe a WASM version of sbml_validator would help, so it could run on all systems?

[baconcheese113]

@fbergmann I've been struggling to build a wasm-compatible .a archive from libsbml over the past couple days. If you get a chance, could you help ensure libSBML’s CMakeLists.txt supports static-only builds using Emscripten (via emcmake cmake) to produce an .a archive for linking into my wam project? Currently, even with -DBUILD_SHARED_LIBS=OFF, it seems the build still defaults to shared libraries. Or if you've already built this, could you provide the .a? https://github.com/baconcheese113/sbml-linter/blob/wasm-support/sbml_validator.cpp#L6

[fbergmann]

@baconcheese113 no problem, do you need it for a specific emscripten version?

[baconcheese113]

@fbergmann Thanks! I'm currently using emcc 4.0.8, however I'd be happy to downgrade if you run into any trouble building with emcc v4

[luciansmith]

@baconcheese113 : We put this together a few years back, but if it helps: https://github.com/sys-bio/libsbmljs

We'll be updating it to the latest version of libsbml soon; we need it for our other projects.

[baconcheese113]

@luciansmith I actually gave libsbmljs a try, but ran into a number of issues getting the Gradle build working. It seems to rely on several legacy tools and build assumptions from ~7 years ago, and I hit too many hurdles to get it building cleanly in a modern setup.

Instead, I opted to build native binaries directly for sbml-linter. Version 1.1.0 now includes support for Windows 11 and macOS 14/15. I started work on a Linux build too, but held off shipping it due to unresolved linking issues.

Looking forward to the upcoming libsbmljs update, I'd love to revisit this once it's refreshed!

[fbergmann]

I think it is actually for this project better not to use the full libsbml.js, and instead just go with the validation logic needed. I've compiled a version of the sbml_validator, though I needed to make some changes since we won't have direct access to the filesystem. So instead it exposes a method, that would validate a given sbml string and return the json string:

var validator = require('./sbml_validator.js');
var fs = require("fs");

validator().then((Module) => {

    // instantiate validator
    var instance = Module;

    // load a local file using the filesystem 
    var data = fs.readFileSync(process.argv[2], 'utf8');

    // print validation errors
    console.log(instance.validateSBMLString(data));

});

I've bundled all my changes as well as a build of an example for download here https://heibox.uni-heidelberg.de/d/a21b4a7c176041998a7a/