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fix: re-enable gnomad output for server #604

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merged 2 commits into from
Nov 22, 2024
Merged

fix: re-enable gnomad output for server #604

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031fbd8
fix: re-enable gnomad output for server
holtgrewe Nov 22, 2024
23afd38
wip
holtgrewe Nov 22, 2024
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100 changes: 97 additions & 3 deletions src/server/run/annos_variant.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -2924,8 +2924,103 @@ pub async fn handle_with_openapi(
.transpose()?
.flatten()
.map(Into::into),
// gnomad_exomes: Option<bool>,
// gnomad_genomes: Option<bool>,
gnomad_exomes: data.annos[genome_release][AnnoDb::GnomadExomes]
.as_ref()
.map(|db| {
let db_version = data.db_infos[genome_release][AnnoDb::GnomadExomes]
.as_ref()
.expect("must have db info here")
.db_version
.as_ref()
.expect("gnomAD must have db version");
if db_version.starts_with("2.") {
Ok(fetch_var_protobuf::<crate::pbs::gnomad::gnomad2::Record>(
&db.data,
AnnoDb::GnomadExomes.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("3.") {
Ok(fetch_var_protobuf::<crate::pbs::gnomad::gnomad3::Record>(
&db.data,
AnnoDb::GnomadExomes.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.") {
Ok(fetch_var_protobuf::<crate::pbs::gnomad::gnomad4::Record>(
&db.data,
AnnoDb::GnomadExomes.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
)))
}
})
.transpose()?
.flatten(),
gnomad_genomes: data.annos[genome_release][AnnoDb::GnomadGenomes]
.as_ref()
.map(|db| {
let db_version = data.db_infos[genome_release][AnnoDb::GnomadGenomes]
.as_ref()
.expect("must have db info here")
.db_version
.as_ref()
.expect("gnomAD must have db version");

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
)))
}
Comment on lines +2991 to +3020
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⚠️ Potential issue

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.

})
.transpose()?
.flatten(),
helixmtdb: data.annos[genome_release][AnnoDb::Helixmtdb]
.as_ref()
.map(|db| {
Expand Down Expand Up @@ -2973,7 +3068,6 @@ pub async fn handle_with_openapi(
})
.transpose()?
.flatten(),
..Default::default()
};

Ok(Json(SeqvarsAnnosResponse { result }))
Expand Down
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