Skip to content

Conversation

@alyssadai
Copy link
Contributor

@alyssadai alyssadai commented Dec 16, 2025

Changes proposed in this pull request:

  • Add new page "Preparing the dataset description"
  • Update example CLI commands to use new --dataset-description arg
  • Add mkdocs-madlibs plugin (and required stylesheet) for templated dataset description code snippets

Checklist

Please leave checkboxes empty for PR reviewers

  • PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF]) see our Contributing Guidelines for more info)
  • PR links to GitHub issue with mention Closes #XXXX
  • Checks pass
  • If an existing page was renamed or deleted, redirects have been added to the mkdocs.yml config

@netlify
Copy link

netlify bot commented Dec 16, 2025

Deploy Preview for neurobagel-documentation ready!

Name Link
🔨 Latest commit 357aaf8
🔍 Latest deploy log https://app.netlify.com/projects/neurobagel-documentation/deploys/696001bec7476900087779d0
😎 Deploy Preview https://deploy-preview-351--neurobagel-documentation.netlify.app
📱 Preview on mobile
Toggle QR Code...

QR Code

Use your smartphone camera to open QR code link.

To edit notification comments on pull requests, go to your Netlify project configuration.

Copy link
Contributor

@surchs surchs left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks @alyssadai for writing the docs! Reads well and clear!

I have some high level suggestions that I think would make this easier to digest for a new user:

  1. Put the example of the file at the very top, right after a (brief) explainer. Shows the user what we're dealing with
  2. Have the "editable template" second. Gets the user going immediately and avoids having to sift through text that may or may not be relevant.
  3. Add a downloadable template file as well - parallel to the template text box. Lets user go direct to their text editor if wanted and avoids additional step of "create new text file first".
  4. Turn the BIDS / not-BIDS part into just an admonition. Avoids overlap and cognitive load for user to parse the difference between sections. Main message: "you may have this file already from BIDS, in this case just add the keys you don't have from the template as needed" - this should be easy because a BIDS dataset_description.json is valid for us (reverse not, but that's not a real worry because if they didn't have a dataset_description.json to begin with, then their BIDS dataset was never valid).

@alyssadai
Copy link
Contributor Author

@surchs, thanks for your suggestions! I implemented them all, but there's one that probably needs another look:

Add a downloadable template file as well - parallel to the template text box. Lets user go direct to their text editor if wanted and avoids additional step of "create new text file first".

So because JSON can be rendered directly in the browser, I don't actually think (or haven't found a way) to force a direct file download for a JSON file using either markdown attributes or HTML tags - for me at least, it always opens in a separate tab as plaintext. The only workaround I could find was to zip the file first, which I've done in the latest commit. Is that fine do you think?

@alyssadai alyssadai requested a review from surchs December 22, 2025 16:53
@surchs
Copy link
Contributor

surchs commented Dec 22, 2025

Hey @alyssadai

The only workaround I could find was to zip the file first

Interesting, I hadn't expected this. I'm not sure what to do here. First of all: great solution. But the reason I suggested the file is to make it easier on the user to use our template. Seems to me that unzipping a file is not a lot easier than either saving a JSON file from a browser tab or copy-pasting the template directly.

So I'd say in order of preference for me:

  1. Remove the downloadable link completely since it doesn't work as expected and just ask users to copy-paste our template from the docs
  2. Leave the download link as is as a JSON and mention to users that they'll have to save the file after it opens in a new tab. Not ideal, some users may get confused and save this as a different file format / mix it up, etc. But maybe still easier
  3. Make the file zipped and explain to users how to unzip it. Least preferred, depending on system may require other programs, not simple for non-technical users to do on a Linux machine etc.

Copy link
Contributor

@surchs surchs left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks @alyssadai, I think this now reads very clear and straightforward. I also like the position of the "I have a file from BIDS dataset" info box - I was spotting that exactly when I was wondering about that question (i.e. after reading the editable box). Very cool.

🧑‍🍳

@surchs surchs merged commit b2f262f into main Jan 8, 2026
9 checks passed
@surchs surchs deleted the document-dataset-description branch January 8, 2026 19:14
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

Document use of dataset_description.json

3 participants