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@andrewelamb andrewelamb commented Dec 10, 2025

SYNPY-1698

Problem:

The documentation is missing how to create the data model CSV for Curator extension.

Solution:

An updated doc has been added.

https://synapsepythonclient--1292.org.readthedocs.build/en/1292/

@andrewelamb andrewelamb requested a review from a team as a code owner December 10, 2025 20:28
@andrewelamb andrewelamb marked this pull request as draft December 10, 2025 20:28
@andrewelamb andrewelamb changed the title first draft of data model tutorial [SYNPY-1698] Add CSV data model tutorial Dec 10, 2025
@andrewelamb andrewelamb marked this pull request as ready for review December 10, 2025 21:42
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🔥 Great document here outlining the context and all the columns to add and the relationships are very clear. Some minor comments

  1. change the title to "curator_data_model.md"
  2. Move this document into explanations folder as i think it falls under those guidelines better than the tutorial guidelines: https://github.com/Sage-Bionetworks/synapsePythonClient/blob/develop/docs/tutorials/README
  3. Add this page under Further reading section here: https://github.com/Sage-Bionetworks/synapsePythonClient/blob/develop/mkdocs.yml

Wait for it to build, then you can view the built page here: https://synapsepythonclient--1292.org.readthedocs.build/en/1292/. I think I will also Ask Jess V to review this, but if @linglp can provide a final review as well

@andrewelamb andrewelamb requested review from a team and removed request for a team December 11, 2025 02:34
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Hi @andrewelamb ! Thanks for your hard work. I think we're very close, but I have two concerns:

  • Shift between two data types: We alternate between "Patient" and "Person" in our examples. Should we standardize on one?
  • Attribute alignment: Some attributes in the "Person" examples seem misaligned and not truly Person-level properties. Could we revise those to use more appropriate person-level attributes?
  • I noticed a few things in the conditional dependencies example that we might want to adjust. See my comments below.

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Thanks for your hard work, Andrew! This is looking better. But you might want to consider regenerating the JSON Schema in the examples using the updated data model. See my comments below!

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Pull request overview

This PR adds comprehensive documentation for creating CSV data models for the Curator extension (formerly Schematic), addressing SYNPY-1698. The documentation explains how to structure data models in CSV format that can be converted to JSON Schemas for use in Curator.

  • Added new tutorial document explaining CSV data model structure and conversion to JSON Schema
  • Integrated the new documentation into the navigation structure
  • Provided extensive examples demonstrating each data model column and feature

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 12 comments.

File Description
mkdocs.yml Added "Curator Data model" entry to the Explanations section of the documentation navigation
docs/explanations/curator_data_model.md New comprehensive tutorial covering CSV data model structure, columns (Attribute, DependsOn, Description, Valid Values, Required, columnType, Format, Pattern, Minimum/Maximum), conditional dependencies, and multiple detailed examples with corresponding JSON Schema outputs

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@andrewelamb andrewelamb requested a review from linglp December 11, 2025 19:51
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LGTM! Just some minor comments.

@andrewelamb
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@thomasyu888 Should I merge this, or do you want to let Jess take a look first?

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🔥 LGTM! @andrewelamb let's merge and I'll ship this to Jess after the merge

@andrewelamb andrewelamb merged commit 6536f8a into develop Dec 11, 2025
15 of 21 checks passed
@andrewelamb andrewelamb deleted the SYNPY-1698 branch December 11, 2025 22:45
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4 participants