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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,132 @@ | ||
| //! Implementation of endpoint `/api/v1/seqvars/clinvar`. | ||
| //! | ||
| //! Also includes the implementation of the `/seqvars/clinvar` endpoint (deprecated). | ||
| use actix_web::{ | ||
| get, | ||
| web::{self, Data, Json, Path}, | ||
| }; | ||
|
|
||
| use crate::{annotate::seqvars::csq::VcfVariant, common::GenomeRelease}; | ||
|
|
||
| use super::{versions::VersionsInfoResponse, CustomError}; | ||
|
|
||
| /// Query parameters of the `/api/v1/seqvars/clinvar` endpoint. | ||
| #[derive( | ||
| Debug, Clone, serde::Serialize, serde::Deserialize, utoipa::IntoParams, utoipa::ToSchema, | ||
| )] | ||
| #[serde(rename_all = "snake_case")] | ||
| #[serde_with::skip_serializing_none] | ||
| pub(crate) struct ClinvarQuery { | ||
| /// The assembly. | ||
| pub genome_release: GenomeRelease, | ||
| /// SPDI sequence. | ||
| pub chromosome: String, | ||
| /// SPDI position. | ||
| pub position: u32, | ||
| /// SPDI deletion. | ||
| pub reference: String, | ||
| /// SPDI insertion. | ||
| pub alternative: String, | ||
| } | ||
|
|
||
| /// One entry in `ClinvarResponse`. | ||
| #[derive(Debug, Clone, serde::Serialize, serde::Deserialize, utoipa::ToSchema)] | ||
| pub(crate) struct ClinvarResultEntry { | ||
| pub clinvar_vcv: Vec<String>, | ||
| pub clinvar_germline_classification: Vec<String>, | ||
| } | ||
|
|
||
| /// Response of the `/api/v1/seqvars/clinvar` endpoint. | ||
| #[derive(Debug, Clone, serde::Serialize, serde::Deserialize, utoipa::ToSchema)] | ||
| pub(crate) struct ClinvarResponse { | ||
| /// Version information. | ||
| pub version: VersionsInfoResponse, | ||
|
|
||
| /// The original query records. | ||
| pub query: ClinvarQuery, | ||
|
|
||
| /// The resulting records for the scored genes. | ||
| pub result: Vec<ClinvarResultEntry>, | ||
| } | ||
|
|
||
| /// Implementation of endpoints. | ||
| async fn handle_impl( | ||
| data: Data<super::WebServerData>, | ||
| _path: Path<()>, | ||
| query: web::Query<ClinvarQuery>, | ||
| ) -> actix_web::Result<Json<ClinvarResponse>, super::CustomError> { | ||
| let ClinvarQuery { | ||
| genome_release, | ||
| chromosome, | ||
| position, | ||
| reference, | ||
| alternative, | ||
| } = query.clone().into_inner(); | ||
|
|
||
| let annotator = data | ||
| .clinvar_annotators | ||
| .get(&genome_release) | ||
| .ok_or_else(|| { | ||
| super::CustomError::new(anyhow::anyhow!( | ||
| "genome release not supported: {:?}", | ||
| &query.genome_release | ||
| )) | ||
| })?; | ||
|
|
||
| let mut result = Vec::new(); | ||
| let g_var = VcfVariant { | ||
| chromosome, | ||
| position: position as i32, | ||
| reference, | ||
| alternative, | ||
| }; | ||
| let annotations = annotator | ||
| .annotate_variant(&g_var) | ||
| .map_err(|e| super::CustomError::new(anyhow::anyhow!("annotation failed: {}", &e)))?; | ||
| if let Some(annotations) = annotations { | ||
| result.push(annotations); | ||
| } | ||
|
|
||
| let result = ClinvarResponse { | ||
| version: VersionsInfoResponse::from_web_server_data(data.into_inner().as_ref()) | ||
| .map_err(|e| CustomError::new(anyhow::anyhow!("Problem determining version: {}", e)))?, | ||
| query: query.into_inner(), | ||
| result, | ||
| }; | ||
|
|
||
| Ok(Json(result)) | ||
| } | ||
|
|
||
| /// Query for gnomAD frequencies of a variant. | ||
| #[allow(clippy::unused_async)] | ||
| #[get("/seqvars/clinvar")] | ||
| async fn handle( | ||
| data: Data<super::WebServerData>, | ||
| _path: Path<()>, | ||
| query: web::Query<ClinvarQuery>, | ||
| ) -> actix_web::Result<Json<ClinvarResponse>, super::CustomError> { | ||
| handle_impl(data, _path, query).await | ||
| } | ||
|
|
||
| /// Query for gnomAD frequencies of a variant. | ||
| #[allow(clippy::unused_async)] | ||
| #[utoipa::path( | ||
| get, | ||
| operation_id = "seqvarsClinvar", | ||
| params( | ||
| ClinvarQuery | ||
| ), | ||
| responses( | ||
| (status = 200, description = "Clinvar information.", body = ClinvarResponse), | ||
| (status = 500, description = "Internal server error.", body = CustomError) | ||
| ) | ||
| )] | ||
| #[get("/api/v1/seqvars/clinvar")] | ||
| async fn handle_with_openapi( | ||
| data: Data<super::WebServerData>, | ||
| _path: Path<()>, | ||
| query: web::Query<ClinvarQuery>, | ||
| ) -> actix_web::Result<Json<ClinvarResponse>, super::CustomError> { | ||
| handle_impl(data, _path, query).await | ||
| } |
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