[MNT] Add example scripts for creating data dictionary + graph data JSON schema

[alyssadai]

Changes proposed in this pull request:

• Add standalone Python scripts for creating JSON schema from our Pydantic models

Checklist

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• Tests have been added

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Summary by Sourcery

New Features:

• Add standalone Python scripts for creating JSON schema from Pydantic models.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request introduces two new scripts that generate JSON schemas for the Neurobagel data dictionary and graph data models. These scripts use the Pydantic models to create the schemas and output them to JSON files.

Sequence diagram for JSON schema generation

sequenceDiagram
    participant Script
    participant PydanticModel
    participant FileSystem
    Script->>PydanticModel: model_json_schema()
    PydanticModel-->>Script: JSON schema
    Script->>FileSystem: Write schema to file
    Note over Script,FileSystem: Writes formatted JSON with indent=2

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Flow diagram for JSON schema generation process

graph TD
    A[Pydantic Models] --> B[generate_dictionary_jsonschema.py]
    A --> C[generate_graphdata_jsonschema.py]
    B --> D[neurobagel_datadictionary.schema.json]
    C --> E[neurobagel_graphdata.schema.json]
    subgraph Models
    F[DataDictionary Model] -.-> A
    G[Dataset Model] -.-> A
    end

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File-Level Changes

Change	Details	Files
Added a script to generate a JSON schema for the Neurobagel graph data model.	Created a new Python script. Imported the necessary libraries. Used the Dataset model to generate the JSON schema. Output the schema to a JSON file.	generate_graphdata_jsonschema.py
Added a script to generate a JSON schema for the Neurobagel data dictionary model.	Created a new Python script. Imported the necessary libraries. Used the DataDictionary model to generate the JSON schema. Output the schema to a JSON file.	generate_dictionary_jsonschema.py

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.55%. Comparing base (62cbad8) to head (92e00f5).
Report is 3 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #427   +/-   ##
=======================================
  Coverage   98.55%   98.55%           
=======================================
  Files          18       18           
  Lines        1109     1109           
=======================================
  Hits         1093     1093           
  Misses         16       16           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[surchs]

looks good @alyssadai. I'm wondering though: should we group these scripts up a bit? Either in a /helperscript or similar directory, or even in a single script with basic argparse to switch between the modes (or even generate all schemata every time the single script is run)?

🧑‍🍳

[surchs]

Hey @alyssadai, while you're at it with grouping the scripts, take a look at #412 and see if that would be an easy fix. I'm assuming that no, but wanted to point out

[alyssadai]

Hey @surchs, thanks for the ping. I agree that #412 is not a quick fix and would be better addressed separately! For now, I've organized all helper scripts into a directory as suggested.