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Genome builds have no unified format #408

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gromdimon opened this issue Mar 15, 2024 · 3 comments
Open

Genome builds have no unified format #408

gromdimon opened this issue Mar 15, 2024 · 3 comments
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@gromdimon
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Describe the bug
Currently genome builds have different "names"/"labels" in different APIs. For example:

https://reev.cubi.bihealth.org/internal/proxy/mehari/genes/txs?hgncId=HGNC:4806&genomeBuild=GENOME_BUILD_GRCH37&pageSize=1000

https://reev.cubi.bihealth.org/internal/proxy/mehari/seqvars/csq?genome_release=grch37&chromosome=6&position=24302274&reference=T&alternative=C

To Reproduce
N/A

Expected behavior
There should be one standard for genome builds across the mehari APIs.

Additional context
N/A

@gromdimon gromdimon added the bug Something isn't working label Mar 15, 2024
@xiamaz xiamaz closed this as completed Mar 25, 2024
@xiamaz xiamaz reopened this Mar 25, 2024
@xiamaz xiamaz assigned xiamaz and unassigned xiamaz Mar 28, 2024
@xiamaz
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xiamaz commented Mar 29, 2024

Issue is that currently the type definition for the seqvar/structvar endpoints are defined in rust, whereas the tx endpoint is directly defined in protobuf.

All exposed API endpoints should be defined consistently. Putting query definitions in protobuf might have the nice effect for allowing non-http APIs, but might be less easy to use in rust.

@xiamaz
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xiamaz commented Mar 29, 2024

Currently prost is used to interface with protobuf defined structures, whereas everything else uses serde. Both are unfortunately not compatible.

As a general design, moving everything i/o facing into protobuf might make sense.

@xiamaz
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xiamaz commented Mar 29, 2024

Action plan

  • define all request/response types for seqvar/structvar in protobuf
  • coordinate change with tools depending on proper mehari server functionality (currently reev and varfish)

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