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Christina-J-Diaz
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RobertJCarroll,
allisonheath,
awarkow,
calkinsh and
chris-s-friedman
RobertJCarroll
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RobertJCarroll
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Hi Christina. It looks like you haven't been able to test this yet. I think the github action for running the build may have not triggered as it was converted from a draft, but I'm not sure. Happy to help get that set up, You won't need copier, but the other prerequisites here should get you started:
https://github.com/dalito/linkml-project-copier?tab=readme-ov-file#prerequisites
I tested locally, and the build is failing. One part that stood out is that the slot definitions should all happen in the slot section (ie, line 637 and beyond in your version). Looking at your yaml, none of the information about descriptions should appear there, for example, this description is already present (broadly) in the slot definition here. We also want to use slot_usage as infrequently as possible. IE, where the names, titles, types, and descriptions can reasonably be the same, we want to preserve that. It looks like you might be trying to define everything within the classes, which is understandable, but not the "linkml way". Slot_usage would mainly be to specify something as the unique key of a class/table or to set something as required in that specific class/table's context.
To get this building, I would recommend starting by moving all of these "slot definition details", eg, the descriptions nested in the class slots section and the other definitions in the class slot_usage section into the high level slots. You'd then only have the names of those slots in the class, eg, like DOI and it's slots do_id and bibliographic_reference.
We can dig a bit deeper on the field-level specifics once it's building- I see some duplicate slots in here, and it'll be easier to review when they are cleaned up. Please let me know if you need more guidance on the "how".
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Adding modeling for a files access model and assay access model. still WIP