fix: re-enable gnomad output for server #604
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WalkthroughThe pull request introduces significant updates to the Changes
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
src/server/run/annos_variant.rs (2)
2927-2979: Consider refactoring duplicate logic into a helper functionThe logic for handling gnomAD versions in both
gnomad_exomesandgnomad_genomesis very similar. Consider extracting this logic into a helper function to reduce code duplication and improve maintainability.
2981-3023: Consider refactoring duplicate logic into a helper functionAs with
gnomad_exomes, the version handling ingnomad_genomescan be refactored into a shared helper function to improve code clarity and reduce duplication.
| if db_version.starts_with("2.") { | ||
| Ok(fetch_var_protobuf::<crate::pbs::gnomad::gnomad2::Record>( | ||
| &db.data, | ||
| AnnoDb::GnomadGenomes.cf_name(), | ||
| query.clone().into_inner().into(), | ||
| )? | ||
| .map(|record| { | ||
| Ok(GnomadRecord::Gnomad2( | ||
| record.try_into().map_err(CustomError::new)?, | ||
| )) | ||
| }) | ||
| .transpose()?) | ||
| } else if db_version.starts_with("4.") { | ||
| Ok(fetch_var_protobuf::<crate::pbs::gnomad::gnomad4::Record>( | ||
| &db.data, | ||
| AnnoDb::GnomadGenomes.cf_name(), | ||
| query.clone().into_inner().into(), | ||
| )? | ||
| .map(|record| { | ||
| Ok(GnomadRecord::Gnomad4( | ||
| record.try_into().map_err(CustomError::new)?, | ||
| )) | ||
| }) | ||
| .transpose()?) | ||
| } else { | ||
| Err(CustomError::new(anyhow::anyhow!( | ||
| "don't know how to handle gnomAD version {}", | ||
| db_version | ||
| ))) | ||
| } |
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Missing handling for gnomAD Genomes version 3.x
The code does not handle gnomAD Genomes version 3.x in the gnomad_genomes block. This could lead to runtime errors if db_version starts with "3.".
Apply this diff to fix the issue:
if db_version.starts_with("2.") {
// existing code for version 2.x
+ } else if db_version.starts_with("3.") {
+ Ok(fetch_var_protobuf::<crate::pbs::gnomad::gnomad3::Record>(
+ &db.data,
+ AnnoDb::GnomadGenomes.cf_name(),
+ query.clone().into_inner().into(),
+ )?
+ .map(|record| {
+ Ok(GnomadRecord::Gnomad3(
+ record.try_into().map_err(CustomError::new)?,
+ ))
+ })
+ .transpose()?)
} else if db_version.starts_with("4.") {
// existing code for version 4.x
} else {
// existing error handling
}Committable suggestion skipped: line range outside the PR's diff.
Summary by CodeRabbit
New Features
Bug Fixes