Update documentation to include assay models - #256
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Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Removed a duplicate Biospecimen Key entry from visiumRNALevel2's manifest and re-ran the valid-values sync so Study/shared data-use-code fields match the current DUO ontology IDs in duo.csv instead of stale short codes. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…ence Adds docs pages, download templates, and Standard Terms wiring for 24 models across modules: Biospecimen, Individual, Model, Imaging, NanoString GeoMx, Sequencing, 10x Visium. Reworks generate_linked_table() so each model's Full Field Reference is built from its live DependsOn list cross-checked against its JSON Schema export, sourced from the fully-collated mc2.model.csv rather than each module's own fragmentary CSV - this fixes missing/stale columns (e.g. Biospecimen was missing its foreign-key columns, Study still listed access-requirement fields already moved to governance). Reorganizes the Data Models nav into Sample, Administrative, Resource Sharing, and assay-specific subgroups. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
vpchung
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Love the new look!!!
I only checked the technical implementations (not the actual content updatess), and everything seems to be working as expected (reference creations, table linking, etc.) The only thing I couldn't actually check was the template download, but looking at the URLs, those should resolve successfully once we deploy.
Overall, LGTM!
| "Validation Rules", | ||
| "Column Type", | ||
| "Format", | ||
| "Pattern", |
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Should we render the title as "Regex Pattern" so that it's clear in the docs?
Or is it safe to assume that our users will know that we mean a regex pattern? 😅
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I would use "Regex Pattern" just to keep it clear
| link_prefix = f"../valid_values/{model}.md#attribute" | ||
| slug = attribute.lower().replace(" ", "-") | ||
| return f"[{attribute}]({link_prefix}-{slug})" | ||
| return f"[{text or attribute}]({link_prefix}-{slug})" |
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This isn't a nitpick or review comment.
Just flagging this to make sure we want to look at text first before looking at attribute, right?
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Changelog
Review needed for markdown files added to docs/models (biospecimen.md, etc.):
Next steps (ongoing in separate branch, https://github.com/mc2-center/data-models/tree/docs-with-mapping-updates):