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Clinical-Genomics / preClinVar

A ClinVar API submission helper written in FastAPI
MIT License
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ClinVar upload issues.. #114

Closed dnil closed 7 months ago

dnil commented 7 months ago

From cust002: image

dnil commented 7 months ago

Looks like the newish MultipleConditions thing; possibly something on the list is from before that update, I guess, or we have a new uncovered change. Lets see!

northwestwitch commented 7 months ago

Good, some form of feedback for the many changes done lately is good. I can work on a fix f you haven't started @dnil

northwestwitch commented 7 months ago

Checking that submission. I see something weird, but not the cause of this issue:

image
northwestwitch commented 7 months ago

AIs ❤️

image
dnil commented 7 months ago

Hihi, it got the gist of it, though the suggested code would not be exactly as suggested ("HP:HP:0001510" ought to bug out later..)

northwestwitch commented 7 months ago

Hihi, it got the gist of it, though the suggested code would not be exactly as suggested ("HP:HP:0001510" ought to bug out later..)

Ah I didn't try the validation of the whole submission in chatGPT because the schema is too long, but for that you can use other tools like this one: https://www.jsonschemavalidator.net/

And also the suggestion on the small part that is failing is not super correct. It got the lowercase error right, but condition is supposed to be a list, I double checked again on ClinVar:

image

But it was useful!

northwestwitch commented 7 months ago

The multipleConditionExplanation field parsing is fixed now and the new release or PreClinVar is deployed on prod. After fixing the submission content (see my comment here), submission via API should work