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//! Code for `/annos/range`.
use actix_web::{
get,
web::{self, Data, Json, Path},
Responder,
};
use strum::IntoEnumIterator;
use crate::{
common::{keys, version},
server::{
run::fetch::{fetch_pos_protobuf, fetch_pos_tsv_json},
run::AnnoDb,
},
};
use super::{error::CustomError, WebServerData};
/// Parameters for `variant_annos::handle`.
#[serde_with::skip_serializing_none]
#[serde_with::serde_as]
#[derive(serde::Serialize, serde::Deserialize, Debug, Clone)]
#[serde(rename_all = "snake_case")]
struct Request {
/// Genome release version.
pub genome_release: String,
/// Chromosome name.
pub chromosome: String,
/// 1-based start position.
pub start: u32,
/// 1-based stop position.
pub stop: u32,
}
impl Request {
/// Conver to start `keys::Pos`.
pub fn start_pos(&self) -> keys::Pos {
keys::Pos {
chrom: self.chromosome.clone(),
pos: self.start as i32,
}
}
/// Conver to stop `keys::Pos`.
pub fn stop_pos(&self) -> keys::Pos {
keys::Pos {
chrom: self.chromosome.clone(),
pos: self.stop as i32,
}
}
}
/// Result for `handle`.
#[derive(serde::Serialize, serde::Deserialize, Debug, Clone)]
struct Result {
/// Version of the server code.
pub server_version: String,
/// Version of the builder code.
pub builder_version: String,
}
/// Result for `handle`.
#[derive(serde::Serialize, serde::Deserialize, Debug, Clone)]
#[serde_with::skip_serializing_none]
struct Container {
/// Version of the server code.
pub server_version: String,
/// The query parameters.
pub query: Request,
/// Annotations for the variant from each database.
pub result: std::collections::BTreeMap<AnnoDb, Option<serde_json::Value>>,
}
/// Query for annotations for one variant.
#[get("/annos/range")]
async fn handle(
data: Data<WebServerData>,
_path: Path<()>,
query: web::Query<Request>,
) -> actix_web::Result<impl Responder, CustomError> {
let genome_release =
query
.clone()
.into_inner()
.genome_release
.parse()
.map_err(|e: strum::ParseError| {
CustomError::new(anyhow::anyhow!("problem getting genome release: {}", e))
})?;
let mut annotations = std::collections::BTreeMap::default();
for anno_db in AnnoDb::iter() {
match anno_db {
AnnoDb::Other => (),
AnnoDb::Clinvar => {
data.annos[genome_release][anno_db]
.as_ref()
.map(|db| {
fetch_pos_protobuf::<crate::pbs::clinvar::minimal::ExtractedVcvRecordList>(
&db.data,
anno_db.cf_name(),
query.start_pos(),
query.stop_pos(),
)
})
.transpose()?
.map(|v| annotations.insert(anno_db, v));
}
AnnoDb::Cadd | AnnoDb::Dbnsfp | AnnoDb::Dbscsnv => {
data.annos[genome_release][anno_db]
.as_ref()
.map(|db| {
fetch_pos_tsv_json(
&db.data,
anno_db.cf_name(),
query.start_pos(),
query.stop_pos(),
)
})
.transpose()?
.map(|v| annotations.insert(anno_db, v));
}
AnnoDb::Dbsnp => {
data.annos[genome_release][anno_db]
.as_ref()
.map(|db| {
fetch_pos_protobuf::<crate::dbsnp::pbs::Record>(
&db.data,
anno_db.cf_name(),
query.start_pos(),
query.stop_pos(),
)
})
.transpose()?
.map(|v| annotations.insert(anno_db, v));
}
AnnoDb::Helixmtdb => {
data.annos[genome_release][anno_db]
.as_ref()
.map(|db| {
fetch_pos_protobuf::<crate::helixmtdb::pbs::Record>(
&db.data,
anno_db.cf_name(),
query.start_pos(),
query.stop_pos(),
)
})
.transpose()?
.map(|v| annotations.insert(anno_db, v));
}
AnnoDb::GnomadMtdna => {
data.annos[genome_release][anno_db]
.as_ref()
.map(|db| {
fetch_pos_protobuf::<crate::pbs::gnomad::mtdna::Record>(
&db.data,
anno_db.cf_name(),
query.start_pos(),
query.stop_pos(),
)
})
.transpose()?
.map(|v| annotations.insert(anno_db, v));
}
AnnoDb::GnomadExomes => {
data.annos[genome_release][anno_db]
.as_ref()
.map(|db| {
let db_version = data.db_infos[genome_release][anno_db]
.as_ref()
.expect("must have db info here")
.db_version
.as_ref()
.expect("gnomAD must have db version");
if db_version.starts_with("2.") {
fetch_pos_protobuf::<crate::pbs::gnomad::gnomad2::Record>(
&db.data,
anno_db.cf_name(),
query.start_pos(),
query.stop_pos(),
)
} else if db_version.starts_with("4.") {
fetch_pos_protobuf::<crate::pbs::gnomad::gnomad4::Record>(
&db.data,
anno_db.cf_name(),
query.start_pos(),
query.stop_pos(),
)
} else {
Err(CustomError::new(anyhow::anyhow!(
"don't know how to handle gnomAD version {}",
db_version
)))
}
})
.transpose()?
.map(|v| annotations.insert(anno_db, v));
}
AnnoDb::GnomadGenomes => {
data.annos[genome_release][anno_db]
.as_ref()
.map(|db| {
let db_version = data.db_infos[genome_release][anno_db]
.as_ref()
.expect("must have db info here")
.db_version
.as_ref()
.expect("gnomAD must have db version");
if db_version.starts_with("2.") {
fetch_pos_protobuf::<crate::pbs::gnomad::gnomad2::Record>(
&db.data,
anno_db.cf_name(),
query.start_pos(),
query.stop_pos(),
)
} else if db_version.starts_with("3.") {
fetch_pos_protobuf::<crate::pbs::gnomad::gnomad3::Record>(
&db.data,
anno_db.cf_name(),
query.start_pos(),
query.stop_pos(),
)
} else if db_version.starts_with("4.") {
fetch_pos_protobuf::<crate::pbs::gnomad::gnomad4::Record>(
&db.data,
anno_db.cf_name(),
query.start_pos(),
query.stop_pos(),
)
} else {
Err(CustomError::new(anyhow::anyhow!(
"don't know how to handle gnomAD version {}",
db_version
)))
}
})
.transpose()?
.map(|v| annotations.insert(anno_db, v));
}
AnnoDb::UcscConservation => {
data.annos[genome_release][anno_db]
.as_ref()
.map(|db| {
fetch_pos_protobuf::<crate::pbs::cons::RecordList>(
&db.data,
anno_db.cf_name(),
query.start_pos(),
query.stop_pos(),
)
})
.transpose()?
.map(|v| annotations.insert(anno_db, v));
}
}
}
let result = Container {
server_version: version().to_string(),
query: query.into_inner(),
result: annotations,
};
Ok(Json(result))
}