wip

src/gnomad_nuclear/cli/query.rs

@@ -101,7 +101,7 @@ pub fn open_rocksdb_from_args(
 fn print_record(
     out_writer: &mut Box<dyn std::io::Write>,
     output_format: common::cli::OutputFormat,
-    value: &Box<dyn SerializeRecordTrait>,
+    value: &dyn SerializeRecordTrait,
 ) -> Result<(), anyhow::Error> {
     match output_format {
         common::cli::OutputFormat::Jsonl => {
@@ -179,7 +179,7 @@ pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error>
             _ => unreachable!("unhandled gnomAD version: {}", &meta.gnomad_version),
         };
         if let Some(record) = query_result {
-            print_record(&mut out_writer, args.out_format, &record)?
+            print_record(&mut out_writer, args.out_format, record.as_ref())?
         } else {
             tracing::info!("no record found for variant {:?}", &variant);
         }
@@ -244,7 +244,7 @@ pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error>
                         '4' => Box::new(pbs::gnomad::gnomad4::Record::decode(&mut cursor)?),
                         _ => unreachable!("unhandled gnomAD version: {}", &meta.gnomad_version),
                     };
-                print_record(&mut out_writer, args.out_format, &record)?;
+                print_record(&mut out_writer, args.out_format, record.as_ref())?;
                 iter.next();
             } else {
                 break;

src/server/actix_server/annos_variant.rs

@@ -153,11 +153,31 @@ async fn handle(
                 data.annos[genome_release][anno_db]
                     .as_ref()
                     .map(|db| {
-                        fetch_var_protobuf::<crate::pbs::gnomad::gnomad2::Record>(
-                            db,
-                            anno_db.cf_name(),
-                            query.clone().into_inner().into(),
-                        )
+                        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_var_protobuf::<crate::pbs::gnomad::gnomad2::Record>(
+                                db,
+                                anno_db.cf_name(),
+                                query.clone().into_inner().into(),
+                            )
+                        } else if db_version.starts_with("4.") {
+                            fetch_var_protobuf::<crate::pbs::gnomad::gnomad4::Record>(
+                                db,
+                                anno_db.cf_name(),
+                                query.clone().into_inner().into(),
+                            )
+                        } else {
+                            Err(CustomError::new(anyhow::anyhow!(
+                                "don't know how to tread gnomAD version {}",
+                                db_version
+                            )))
+                        }
                     })
                     .transpose()?
                     .map(|v| annotations.insert(anno_db, v));
@@ -184,6 +204,12 @@ async fn handle(
                                 anno_db.cf_name(),
                                 query.clone().into_inner().into(),
                             )
+                        } else if db_version.starts_with("4.") {
+                            fetch_var_protobuf::<crate::pbs::gnomad::gnomad4::Record>(
+                                db,
+                                anno_db.cf_name(),
+                                query.clone().into_inner().into(),
+                            )
                         } else {
                             Err(CustomError::new(anyhow::anyhow!(
                                 "don't know how to tread gnomAD version {}",