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cancerDHC / ccdhmodel

CRDC-H model in LinkML, developed by the Center for Cancer Data Harmonization (CCDH)
https://cancerdhc.github.io/ccdhmodel/
BSD 3-Clause "New" or "Revised" License
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Fix links to LinkML types #22

Open gaurav opened 3 years ago

gaurav commented 3 years ago

We currently have CCDH types (such as ccdh_Decimal) in the model, which are child types of LinkML types (in this case, linkml:Decimal). Unfortunately, the links in the Markdown documentation from the CCDH type to the LinkML type is broken: instead of linking to https://cancerdhc.github.io/ccdhmodel/dev/types/Decimal/, it links to https://cancerdhc.github.io/ccdhmodel/dev/types/CcdhDecimal/types/Decimal.md instead, which does not work.

(The .md looks incorrect there, but if it wasn't for the duplicated /types/.../types in the URL, it would be resolved correctly and turned into a link to an index.html file.)

This is probably a bug in LinkML's Markdown generation, but it needs to be isolated and reported upstream.

gaurav commented 3 years ago

Note that this occurs because we import the LinkML types by specifying import:\n - linkml:types in the ccdhmodel.yaml file. I'm not sure where LinkML gets this file from -- it's probably worth tracing that so we know what we are dependent on.

nlharris commented 2 years ago

@monicacecilia was this one that you wanted @turbomam to take a look at?

gaurav commented 2 years ago

This will probably be more up @sujaypatil96's alley more than Mark's -- it'll require digging into LinkML Markdown generation to figure out why the URLs are being generated incorrectly.