return gene context info for genomic queries

[katiestahl]

It would be helpful to have gene context info for genomic queries so that tools like VarCat can use this data and display it to users

some potential considerations:

• return undefined/null if there is not an associated gene?
• should we return a list of genes if there are multiple genes associated?

[korikuzma]

@korikuzma TODO: Look into this issue more to see if @katiestahl is able to implement or if it's better to have her as a reviewer for the PR

[korikuzma]

I had forgotten that we removed returning gene context altogether when switching to draft VRS 2.0 in #512. It was not a need for downstream apps at the time, but since VarCat needs this we can add it back.

These comments are related in how we want to represent the response:
#529 (comment)
#529 (comment)
We could follow the approach in /gnomad_vcf_to_protein

It would probably be best for me to work on this since we'll probably make the scope more broad (return gene when we can regardless of molecule context). @wesleygoar when is this needed by?

[wesleygoar]

I had forgotten that we removed returning gene context altogether when switching to draft VRS 2.0 in #512. It was not a need for downstream apps at the time, but since VarCat needs this we can add it back.

These comments are related in how we want to represent the response: #529 (comment) #529 (comment) We could follow the approach in /gnomad_vcf_to_protein

It would probably be best for me to work on this since we'll probably make the scope more broad (return gene when we can regardless of molecule context). @wesleygoar when is this needed by?

Thanks @korikuzma. We definitely want this by MVP. Ideally, we could get this in by the end of the month, but I know you have a bunch of travel coming up. I will let you decide when the best time for you to tackle this issue is.

[korikuzma]

@katiestahl I can add you as a reviewer on this if you are interested

[korikuzma]

I'm pushing this back a sprint to focus on other priorities. A solution in the meantime is just getting this info from haus, which we already pull.

[korikuzma]

@wesleygoar Is it okay to do this for MANE as a first pass? See this gene-normalizer issue that I think will be needed in order to capture non-MANE genes.

[korikuzma]

@wesleygoar Or would you rather just work on gene-normalizer issue (which would be a heavy lift atm and would not be able to get something out fast)

[wesleygoar]

@wesleygoar Is it okay to do this for MANE as a first pass? See this gene-normalizer issue that I think will be needed in order to capture non-MANE genes.

Yes.

[github-actions]

This issue is stale because it has been open 135 days with no activity. This issue will be closed if no further activity occurs in 14 days.

[korikuzma]

Changing priority to low since we have what we need for VarCat.