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feat: serving clinvar information through REST API #155

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merged 1 commit into from
Jul 27, 2023
Merged

feat: serving clinvar information through REST API #155

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14 changes: 14 additions & 0 deletions src/server/actix_server/annos_range.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -93,6 +93,20 @@ async fn handle(
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::clinvar_minimal::pbs::Record>(
db,
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()
Expand Down
13 changes: 13 additions & 0 deletions src/server/actix_server/annos_variant.rs
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Expand Up @@ -89,6 +89,19 @@ async fn handle(
for anno_db in AnnoDb::iter() {
match anno_db {
AnnoDb::Other => (),
AnnoDb::Clinvar => {
data.annos[genome_release][anno_db]
.as_ref()
.map(|db| {
fetch_var_protobuf::<crate::clinvar_minimal::pbs::Record>(
db,
anno_db.cf_name(),
query.clone().into_inner().into(),
)
})
.transpose()?
.map(|v| annotations.insert(anno_db, v));
}
AnnoDb::Cadd | AnnoDb::Dbnsfp | AnnoDb::Dbscsnv => {
data.annos[genome_release][anno_db]
.as_ref()
Expand Down
8 changes: 8 additions & 0 deletions src/server/mod.rs
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Expand Up @@ -52,6 +52,8 @@ pub enum AnnoDb {
Helixmtdb,
/// UCSC conservation annotations.
UcscConservation,
/// ClinVar with minimal data extracted.
Clinvar,
}

impl AnnoDb {
Expand All @@ -67,6 +69,7 @@ impl AnnoDb {
AnnoDb::GnomadGenomes => "gnomad_nuclear_data",
AnnoDb::Helixmtdb => "helixmtdb_data",
AnnoDb::UcscConservation => "ucsc_conservation",
AnnoDb::Clinvar => "clinvar",
AnnoDb::Other => panic!("cannot get CF name for 'Other'"),
}
}
Expand All @@ -83,6 +86,7 @@ impl AnnoDb {
AnnoDb::GnomadGenomes => Some("gnomad-version"),
AnnoDb::Helixmtdb => None,
AnnoDb::UcscConservation => None,
AnnoDb::Clinvar => None,
AnnoDb::Other => panic!("cannot get meta version name name for 'Other'"),
}
}
Expand Down Expand Up @@ -162,6 +166,9 @@ pub struct Args {
/// Path to genes database.
#[arg(long)]
pub path_genes: Option<String>,
/// ClinVar database(s), one for each release.
#[arg(long)]
pub path_clinvar: Vec<String>,
/// CADD database(s), one for each release.
#[arg(long)]
pub path_cadd: Vec<String>,
Expand Down Expand Up @@ -256,6 +263,7 @@ pub fn run(args_common: &common::cli::Args, args: &Args) -> Result<(), anyhow::E
}
// Argument lists from the command line with the corresponding database enum value.
let paths_db_pairs = vec![
(&args.path_clinvar, AnnoDb::Clinvar),
(&args.path_cadd, AnnoDb::Cadd),
(&args.path_dbnsfp, AnnoDb::Dbnsfp),
(&args.path_dbsnp, AnnoDb::Dbsnp),
Expand Down
10 changes: 8 additions & 2 deletions utils/docker/entrypoint.sh
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Expand Up @@ -12,6 +12,8 @@ set -euo pipefail
# HTTP_PORT -- port
# default: 8080
#
# PATH_DB_CLINVAR_37 -- path to ClinVar database for GRCh37, defaults to $PATH_DB_BAE/grch37/clinvar/rocksdb
# PATH_DB_CLINVAR_38 -- path to ClinVar database for GRCh37, defaults to $PATH_DB_BAE/grch38/clinvar/rocksdb
# PATH_DB_CADD_37 -- path to CADD database for GRCh37, defaults to $PATH_DB_BASE/grch37/cadd/rocksdb
# PATH_DB_CADD_38 -- path to CADD database for GRCh38, defaults to $PATH_DB_BASE/grch38/cadd/rocksdb
# PATH_DB_DBSNP_37 -- path to dbSNP database for GRCh37, defaults to $PATH_DB_BASE/grch37/dbsnp/rocksdb
Expand All @@ -37,6 +39,8 @@ PATH_DB_BASE=${PATH_HPO_DIR-/data/annonars}
HTTP_HOST=${HTTP_HOST-0.0.0.0}
HTTP_PORT=${HTTP_PORT-8080}

PATH_DB_CLINVAR_37=${PATH_DB_CLINVAR_37-$PATH_DB_BASE/grch37/clinvar/rocksdb}
PATH_DB_CLINVAR_38=${PATH_DB_CLINVAR_38-$PATH_DB_BASE/grch38/clinvar/rocksdb}
PATH_DB_CADD_37=${PATH_DB_CADD_37-$PATH_DB_BASE/grch37/cadd/rocksdb}
PATH_DB_CADD_38=${PATH_DB_CADD_38-$PATH_DB_BASE/grch38/cadd/rocksdb}
PATH_DB_DBSNP_37=${PATH_DB_DBSNP_37-$PATH_DB_BASE/grch37/dbsnp/rocksdb}
Expand Down Expand Up @@ -66,8 +70,10 @@ else
exec \
annonars \
run-server \
$(test -e $PATH_DB_CADD_37 && echo --path-cadd $PATH_DB_CADD_37) \
$(test -e $PATH_DB_CADD_38 && echo --path-cadd $PATH_DB_CADD_38) \
$(test -e $PATH_DB_CLINVAR_37 && echo --path-clinvar $PATH_DB_CLINVAR_37) \
$(test -e $PATH_DB_CLINVAR_38 && echo --path-clinvar $PATH_DB_CLINVAR_38) \
$(test -e $PATH_DB_CLINVAR_37 && echo --path-cadd $PATH_DB_CLINVAR_37) \
$(test -e $PATH_DB_CLINVAR_38 && echo --path-cadd $PATH_DB_CLINVAR_38) \
$(test -e $PATH_DB_DBSNP_37 && echo --path-dbsnp $PATH_DB_DBSNP_37) \
$(test -e $PATH_DB_DBSNP_38 && echo --path-dbsnp $PATH_DB_DBSNP_38) \
$(test -e $PATH_DB_DBNSFP_37 && echo --path-dbnsfp $PATH_DB_DBNSFP_37) \
Expand Down
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