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[ENH] Have a jsonschema serialization of our data models #150

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surchs opened this issue Jun 10, 2023 · 4 comments
Closed
1 task done
Tracked by #64

[ENH] Have a jsonschema serialization of our data models #150

surchs opened this issue Jun 10, 2023 · 4 comments
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feedback:feature request Request for a new functionality or for an enhancement. _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again

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@surchs
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surchs commented Jun 10, 2023

Is there an existing issue for this?

  • I have searched the existing issues

New feature

When looking at a data dictionary I would like to get a quick idea if it is valid according to our current data model or not.
Right now I need to either make a schema from the data dictionary model classes myself or run the bagel pheno command on the file. It would be much faster if I had a jsonschema that I could use with any validator.

We could even look into whether https://linkml.io/ can help us with that.
The other place to look for inspiration for is, as usual: https://github.com/dandi/dandi-schema and how they auto-populate https://github.com/dandi/schema/tree/master/releases

Unclear documentation

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@surchs surchs added the feedback:feature request Request for a new functionality or for an enhancement. label Jun 10, 2023
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We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 30 days.
We have applied the stale-issue label to indicate that this issue should be reviewed again and then either prioritized or closed.

@github-actions github-actions bot added the _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again label Jul 11, 2023
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We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 30 days.
We have applied the stale-issue label to indicate that this issue should be reviewed again and then either prioritized or closed.

@alyssadai
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@surchs, can we close this now that we have this guy https://github.com/neurobagel/bagelschema/blob/main/neurobagel_data_dictionary.schema.json?

@surchs
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surchs commented Dec 5, 2023

thanks @alyssadai, agreed!

@surchs surchs closed this as completed Dec 5, 2023
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Labels
feedback:feature request Request for a new functionality or for an enhancement. _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again
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