Request for a Python Variant of JS bids-validator

[hjbockholt]

Our team frequently utilizes the JS bids-validator and appreciates its robust capabilities.

Given the increasing adoption of Python in the neuroimaging community and some challenges we face using the Node-based validator, we wonder if there's any consideration or roadmap for a Python-centric version of the bids-validator.

Specifically:

• We find the process of installing node, executing it as a child process, and subsequently handling its results to be less than seamless.
• The current validation mechanism in pybids, while functional, doesn't quite capture all intricacies, leading to issues when utilizing certain BIDS-apps.

While we're keen on the idea of a py-bids-validator, our team's resources might be stretched to take the lead. However, we're enthusiastic about contributing if such a project is initiated.

Thank you for considering this feedback.

[Remi-Gau]

Just to make sure it is mentioned.

There is already a python library that can help do a "superficial" validation of bids filenames:

https://github.com/bids-standard/bids-validator/tree/master/bids-validator#python-library

https://pypi.org/project/bids-validator/

Also if Node installation is source of trouble but docker is not, consider using the docker image of the validator:

https://hub.docker.com/r/bids/validator

[effigies]

We also have the start of a validator in the BIDS specification repository: https://github.com/bids-standard/bids-specification/blob/master/tools/schemacode/bidsschematools/validator.py

This is installed with the Python package bidsschematools. Right now, it's just a Python interface, and it only does filename validation. It's been written toward the DANDI archive's use for BIDS validation, so the API may need refinement to fit other use cases.

[effigies]

Note that I've started scoping out a design in this doc:

https://demo.hedgedoc.org/s/yvkCVA3kh#

[kabilar]

Thank you, @effigies. Looking forward to this tool. Please let me know if you need help with testing, brainstorming, etc.

[effigies]

Please see https://github.com/bids-standard/python-validator, which has been moved out of this repository.

Contributions are more than welcome, and I've begun fleshing out some more of the validator structures in https://github.com/bids-standard/python-validator/pull/2. It is currently a side-project for me, as the javascript validator is the most critical goal. I would be happy to discuss and hand off work with someone if they have the time and energy to put into it.

[Remi-Gau]

Please see https://github.com/bids-standard/python-validator, which has been moved out of this repository.

Contributions are more than welcome, and I've begun fleshing out some more of the validator structures in bids-standard/python-validator#2. It is currently a side-project for me, as the javascript validator is the most critical goal. I would be happy to discuss and hand off work with someone if they have the time and energy to put into it.

probably worth making an "announcement" about this

[effigies]

Sure. Where? bids-discussion? Or update the README?

[Remi-Gau]

update the README

Let's start with this but I was thinking of a mini-blog post on the new bids website that we could then advertise in the mailing list, neurostars and social medias.

Maybe something that reminds people of the deno validator?

[effigies]

Yeah, a blog post sounds good. It would be good to walk through the overall schema world:

v1.14.6

graph LR;
    subgraph bids-specification;
        markdown ---> specification
        schema --> bidsschematools --> specification & schema.json
    end
    subgraph "bids-validator @ v1.14.6";
        regex["filename patterns"] --> Node.js & python
        deno
    end

    specification -. interpreted .-> regex
    schema.json --> deno

v1.14.7

graph LR;
    subgraph bids-specification;
        markdown ---> specification
        schema --> bidsschematools --> specification & schema.json
    end
    subgraph "bids-validator @ v1.14.7";
        regex["filename patterns"] --> Node.js
        deno
        python
    end

    specification -. interpreted .-> regex
    schema.json --> deno
    bidsschematools --> python

v1.14.8+

graph LR;
    subgraph bids-specification;
        markdown ---> specification
        schema --> bidsschematools --> specification & schema.json
    end
    subgraph "bids-validator > v1.14.7";
        regex["filename patterns"] --> Node.js
        deno
    end
    subgraph "python-validator > v1.14.7";
        python
    end

    specification -. interpreted .-> regex
    schema.json --> deno
    bidsschematools ---> python