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Implement liftover requests#105

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jennifer-bowser merged 21 commits into
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issue-104-implement-liftover-requests
Jun 26, 2026
Merged

Implement liftover requests#105
jennifer-bowser merged 21 commits into
mainfrom
issue-104-implement-liftover-requests

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@jennifer-bowser

@jennifer-bowser jennifer-bowser commented May 28, 2026

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closes #104

@jennifer-bowser jennifer-bowser self-assigned this May 28, 2026
@jennifer-bowser jennifer-bowser added the priority:high High priority label May 28, 2026
@jennifer-bowser jennifer-bowser marked this pull request as ready for review June 17, 2026 19:47
@jennifer-bowser jennifer-bowser requested a review from a team as a code owner June 17, 2026 19:47
@korikuzma

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Was curious about this after reading weekly report out. Took a quick glance and it looks like there's still some todos left in the source code. Do you plan to address in this PR?

Comment thread src/anyvlm/utils/types.py Outdated

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I am not sure I'm done reading through this, but I gotta go home so I wanted to just put in what I have now and I'll circle back

Comment thread src/anyvlm/functions/get_caf.py Outdated
Comment thread src/anyvlm/functions/get_caf.py Outdated
Comment thread src/anyvlm/functions/get_caf.py Outdated
)

for caf in cafs:
if isinstance(caf.focusAllele, iriReference):

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is this necessary? it should always be one type, right?

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This was part of the original get_caf function. I don't think we prevent people from submitting Alleles with iriReferences, so I think we need this to make sure we catch any of those?

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Ah interesting. I think these come directly from storage so they should always be IRIs, but if it's not new code then probably not worth figuring out

@jennifer-bowser

jennifer-bowser commented Jun 24, 2026

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Was curious about this after reading weekly report out. Took a quick glance and it looks like there's still some todos left in the source code. Do you plan to address in this PR?

Welp no @korikuzma I totally forgot about the TODOs! I'll resolve them now

@jennifer-bowser jennifer-bowser merged commit 6f1ae64 into main Jun 26, 2026
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@jennifer-bowser jennifer-bowser deleted the issue-104-implement-liftover-requests branch June 26, 2026 17:33
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Implement VLM-required liftover capabilities in GET /variant_counts

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