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sujaypatil96 / ga4gh-va

LinkML schema for GA4GH variant annotation
https://sujaypatil96.github.io/ga4gh-va/
MIT License
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Incorrect links being generated in LinkML #2

Open gaurav opened 2 years ago

gaurav commented 2 years ago

I made a PR to quickly generate from Markdown from this schema (PR #1) and ran into a bug in one of the generated links. I'm not sure if this is a bug in LinkML or in this model, so I'm reporting it here first.

Steps to reproduce:

  1. Generate the documentation with make docserve
  2. Navigate to http://127.0.0.1:8000/ga4gh-va-spec/gene/ (you can also see this online at https://www.ggvaidya.com/ga4gh-va-spec/gene/)
  3. Look for the line "GeneticCondition GeneticCondition➞gene 0..* Gene" in the "Referenced by Class" section.

Expected:

  1. The final word "Gene" should be a link to this page, https://www.ggvaidya.com/ga4gh-va-spec/gene/, or alternately should be a bold non-link since we're already on that page.

Observed:

  1. That word is instead linked to https://www.ggvaidya.com/ga4gh-va-spec/gene/Gene.md, which is a page that does not exist.

I suspect that this is caused by the term "gene" being both a class and a slot in this model, but I'm not sure. I can reproduce this issue with both gen-markdown as well as gen-docs.

cmungall commented 2 years ago

https://github.com/linkml/linkml/issues/632

gaurav commented 2 years ago

Aha, thanks @cmungall! That's very useful.