perf: cache mappers, avoid allocations, codons are arrays (#172)

* fix: use array instead of Vec for Codon representation

* don't allocate until necessary

* reduce usage of lazy_static, use consts instead where possible, copy instead of reference lookup tables

* cache calls to alignment::Mapper::new

* rely on seqrepo-rs with cloneable Error

* fmt

* implement data_version and schema_version for mock Provider in tests

* update seqrepo to v0.10.2

* shorter Arc::new error wrapping

* clippy lints

* clippy lints

* do not run doctests for sequence.rs generators

* workaround ignore in doctest by using stringify, see rust-lang/rust/issues/87586

Cargo.toml

@@ -27,13 +27,14 @@ postgres = { version = "0.19", features = ["with-chrono-0_4"] }
 quick_cache = "0.5"
 regex = "1.7"
 rustc-hash = "1.1"
-seqrepo = { version = "0.10", features = ["cached"] }
+seqrepo = { version = "0.10.2", features = ["cached"] }
 serde_json = "1.0"
 serde = { version = "1.0", features = ["derive"] }
 thiserror = "1.0"
 indexmap = { version = "2", features = ["serde"] }
 biocommons-bioutils = "0.1.0"
 ahash = "0.8.11"
+cached = "0.50.0"
 
 [dev-dependencies]
 anyhow = "1.0"

src/data/cdot/json.rs

@@ -766,13 +766,9 @@ impl TxProvider {
                 .as_ref()
                 .expect("cannot happen; genes without map_location are not imported")
                 .clone(),
-            descr: gene
-                .description
-                .as_ref()
-                .map(Clone::clone)
-                .unwrap_or_default(),
-            summary: gene.summary.as_ref().map(Clone::clone).unwrap_or_default(),
-            aliases: gene.aliases.as_ref().map(Clone::clone).unwrap_or_default(),
+            descr: gene.description.clone().unwrap_or_default(),
+            summary: gene.summary.clone().unwrap_or_default(),
+            aliases: gene.aliases.clone().unwrap_or_default(),
             added: NaiveDateTime::default(),
         })
     }

src/data/error.rs

@@ -1,12 +1,13 @@
 //! Error type definition.
 
+use std::sync::Arc;
 use thiserror::Error;
 
 /// Error type for data.
-#[derive(Error, Debug)]
+#[derive(Error, Debug, Clone)]
 pub enum Error {
     #[error("UTA Postgres access error")]
-    UtaPostgresError(#[from] postgres::Error),
+    UtaPostgresError(#[from] Arc<postgres::Error>),
     #[error("sequence operation failed")]
     SequenceOperationFailed(#[from] crate::sequences::Error),
     #[error("problem with seqrepo access")]

src/data/uta.rs

@@ -6,7 +6,7 @@ use indexmap::IndexMap;
 use postgres::{Client, NoTls, Row};
 use quick_cache::sync::Cache;
 use std::fmt::Debug;
-use std::sync::Mutex;
+use std::sync::{Arc, Mutex};
 
 use crate::sequences::{seq_md5, TranslationTable};
 use biocommons_bioutils::assemblies::{Assembly, ASSEMBLY_INFOS};
@@ -42,15 +42,15 @@ impl TryFrom<Row> for GeneInfoRecord {
     type Error = Error;
 
     fn try_from(row: Row) -> Result<Self, Self::Error> {
-        let aliases: String = row.try_get("aliases")?;
+        let aliases: String = row.try_get("aliases").map_err(Arc::new)?;
         let aliases = aliases.split(',').map(|s| s.to_owned()).collect::<Vec<_>>();
         Ok(Self {
-            hgnc: row.try_get("hgnc")?,
-            maploc: row.try_get("maploc")?,
-            descr: row.try_get("descr")?,
-            summary: row.try_get("summary")?,
+            hgnc: row.try_get("hgnc").map_err(Arc::new)?,
+            maploc: row.try_get("maploc").map_err(Arc::new)?,
+            descr: row.try_get("descr").map_err(Arc::new)?,
+            summary: row.try_get("summary").map_err(Arc::new)?,
             aliases,
-            added: row.try_get("added")?,
+            added: row.try_get("added").map_err(Arc::new)?,
         })
     }
 }
@@ -60,8 +60,8 @@ impl TryFrom<Row> for TxSimilarityRecord {
 
     fn try_from(row: Row) -> Result<Self, Self::Error> {
         Ok(Self {
-            tx_ac1: row.try_get("tx_ac1")?,
-            tx_ac2: row.try_get("tx_ac2")?,
+            tx_ac1: row.try_get("tx_ac1").map_err(Arc::new)?,
+            tx_ac2: row.try_get("tx_ac2").map_err(Arc::new)?,
             hgnc_eq: row.try_get("hgnc_eq").unwrap_or(false),
             cds_eq: row.try_get("cds_eq").unwrap_or(false),
             es_fp_eq: row.try_get("es_fp_eq").unwrap_or(false),
@@ -76,24 +76,24 @@ impl TryFrom<Row> for TxExonsRecord {
 
     fn try_from(row: Row) -> Result<Self, Self::Error> {
         Ok(Self {
-            hgnc: row.try_get("hgnc")?,
-            tx_ac: row.try_get("tx_ac")?,
-            alt_ac: row.try_get("alt_ac")?,
-            alt_aln_method: row.try_get("alt_aln_method")?,
-            alt_strand: row.try_get("alt_strand")?,
-            ord: row.try_get("ord")?,
-            tx_start_i: row.try_get("tx_start_i")?,
-            tx_end_i: row.try_get("tx_end_i")?,
-            alt_start_i: row.try_get("alt_start_i")?,
-            alt_end_i: row.try_get("alt_end_i")?,
-            cigar: row.try_get("cigar")?,
-            tx_aseq: row.try_get("tx_aseq")?,
-            alt_aseq: row.try_get("alt_aseq")?,
-            tx_exon_set_id: row.try_get("tx_exon_set_id")?,
-            alt_exon_set_id: row.try_get("alt_exon_set_id")?,
-            tx_exon_id: row.try_get("tx_exon_id")?,
-            alt_exon_id: row.try_get("alt_exon_id")?,
-            exon_aln_id: row.try_get("exon_aln_id")?,
+            hgnc: row.try_get("hgnc").map_err(Arc::new)?,
+            tx_ac: row.try_get("tx_ac").map_err(Arc::new)?,
+            alt_ac: row.try_get("alt_ac").map_err(Arc::new)?,
+            alt_aln_method: row.try_get("alt_aln_method").map_err(Arc::new)?,
+            alt_strand: row.try_get("alt_strand").map_err(Arc::new)?,
+            ord: row.try_get("ord").map_err(Arc::new)?,
+            tx_start_i: row.try_get("tx_start_i").map_err(Arc::new)?,
+            tx_end_i: row.try_get("tx_end_i").map_err(Arc::new)?,
+            alt_start_i: row.try_get("alt_start_i").map_err(Arc::new)?,
+            alt_end_i: row.try_get("alt_end_i").map_err(Arc::new)?,
+            cigar: row.try_get("cigar").map_err(Arc::new)?,
+            tx_aseq: row.try_get("tx_aseq").map_err(Arc::new)?,
+            alt_aseq: row.try_get("alt_aseq").map_err(Arc::new)?,
+            tx_exon_set_id: row.try_get("tx_exon_set_id").map_err(Arc::new)?,
+            alt_exon_set_id: row.try_get("alt_exon_set_id").map_err(Arc::new)?,
+            tx_exon_id: row.try_get("tx_exon_id").map_err(Arc::new)?,
+            alt_exon_id: row.try_get("alt_exon_id").map_err(Arc::new)?,
+            exon_aln_id: row.try_get("exon_aln_id").map_err(Arc::new)?,
         })
     }
 }
@@ -103,12 +103,12 @@ impl TryFrom<Row> for TxForRegionRecord {
 
     fn try_from(row: Row) -> Result<Self, Self::Error> {
         Ok(Self {
-            tx_ac: row.try_get("tx_ac")?,
-            alt_ac: row.try_get("alt_ac")?,
-            alt_strand: row.try_get("alt_strand")?,
-            alt_aln_method: row.try_get("alt_aln_method")?,
-            start_i: row.try_get("start_i")?,
-            end_i: row.try_get("end_i")?,
+            tx_ac: row.try_get("tx_ac").map_err(Arc::new)?,
+            alt_ac: row.try_get("alt_ac").map_err(Arc::new)?,
+            alt_strand: row.try_get("alt_strand").map_err(Arc::new)?,
+            alt_aln_method: row.try_get("alt_aln_method").map_err(Arc::new)?,
+            start_i: row.try_get("start_i").map_err(Arc::new)?,
+            end_i: row.try_get("end_i").map_err(Arc::new)?,
         })
     }
 }
@@ -126,15 +126,15 @@ impl TryFrom<Row> for TxIdentityInfo {
     type Error = Error;
 
     fn try_from(row: Row) -> Result<Self, Self::Error> {
-        let hgnc = row.try_get("hgnc")?;
+        let hgnc = row.try_get("hgnc").map_err(Arc::new)?;
         let is_selenoprotein = SELENOPROTEIN_SYMBOLS.contains(&hgnc);
         Ok(Self {
-            tx_ac: row.try_get("tx_ac")?,
-            alt_ac: row.try_get("alt_ac")?,
-            alt_aln_method: row.try_get("alt_aln_method")?,
-            cds_start_i: row.try_get("cds_start_i")?,
-            cds_end_i: row.try_get("cds_end_i")?,
-            lengths: row.try_get("lengths")?,
+            tx_ac: row.try_get("tx_ac").map_err(Arc::new)?,
+            alt_ac: row.try_get("alt_ac").map_err(Arc::new)?,
+            alt_aln_method: row.try_get("alt_aln_method").map_err(Arc::new)?,
+            cds_start_i: row.try_get("cds_start_i").map_err(Arc::new)?,
+            cds_end_i: row.try_get("cds_end_i").map_err(Arc::new)?,
+            lengths: row.try_get("lengths").map_err(Arc::new)?,
             hgnc: hgnc.to_string(),
             // UTA database does not support selenoproteins (yet).
             translation_table: if is_selenoprotein {
@@ -151,12 +151,12 @@ impl TryFrom<Row> for TxInfoRecord {
 
     fn try_from(row: Row) -> Result<Self, Self::Error> {
         Ok(Self {
-            hgnc: row.try_get("hgnc")?,
-            cds_start_i: row.try_get("cds_start_i")?,
-            cds_end_i: row.try_get("cds_end_i")?,
-            tx_ac: row.try_get("tx_ac")?,
-            alt_ac: row.try_get("alt_ac")?,
-            alt_aln_method: row.try_get("alt_aln_method")?,
+            hgnc: row.try_get("hgnc").map_err(Arc::new)?,
+            cds_start_i: row.try_get("cds_start_i").map_err(Arc::new)?,
+            cds_end_i: row.try_get("cds_end_i").map_err(Arc::new)?,
+            tx_ac: row.try_get("tx_ac").map_err(Arc::new)?,
+            alt_ac: row.try_get("alt_ac").map_err(Arc::new)?,
+            alt_aln_method: row.try_get("alt_aln_method").map_err(Arc::new)?,
         })
     }
 }
@@ -166,9 +166,9 @@ impl TryFrom<Row> for TxMappingOptionsRecord {
 
     fn try_from(row: Row) -> Result<Self, Self::Error> {
         Ok(Self {
-            tx_ac: row.try_get("tx_ac")?,
-            alt_ac: row.try_get("alt_ac")?,
-            alt_aln_method: row.try_get("alt_aln_method")?,
+            tx_ac: row.try_get("tx_ac").map_err(Arc::new)?,
+            alt_ac: row.try_get("alt_ac").map_err(Arc::new)?,
+            alt_aln_method: row.try_get("alt_aln_method").map_err(Arc::new)?,
         })
     }
 }
@@ -231,7 +231,7 @@ impl Debug for Provider {
 impl Provider {
     pub fn with_config(config: &Config) -> Result<Self, Error> {
         let config = config.clone();
-        let conn = Mutex::new(Client::connect(&config.db_url, NoTls)?);
+        let conn = Mutex::new(Client::connect(&config.db_url, NoTls).map_err(Arc::new)?);
         let schema_version = Self::fetch_schema_version(
             &mut conn.lock().expect("cannot obtain connection lock"),
             &config.db_schema,
@@ -246,7 +246,7 @@ impl Provider {
 
     fn fetch_schema_version(conn: &mut Client, db_schema: &str) -> Result<String, Error> {
         let sql = format!("select key, value from {db_schema}.meta where key = 'schema_version'");
-        let row = conn.query_one(&sql, &[])?;
+        let row = conn.query_one(&sql, &[]).map_err(Arc::new)?;
         Ok(row.get("value"))
     }
 }
@@ -282,7 +282,8 @@ impl interface::Provider for Provider {
             .conn
             .lock()
             .expect("cannot obtain connection lock")
-            .query_one(&sql, &[&hgnc])?
+            .query_one(&sql, &[&hgnc])
+            .map_err(Arc::new)?
             .try_into()?;
 
         self.caches
@@ -305,11 +306,12 @@ impl interface::Provider for Provider {
             .conn
             .lock()
             .expect("cannot obtain connection lock")
-            .query(&sql, &[&tx_ac])?)
+            .query(&sql, &[&tx_ac])
+            .map_err(Arc::new)?)
         .into_iter()
         .next()
         {
-            let result = Some(row.try_get("pro_ac")?);
+            let result = Some(row.try_get("pro_ac").map_err(Arc::new)?);
             self.caches
                 .get_pro_ac_for_tx_ac
                 .insert(tx_ac.to_string(), None);
@@ -337,8 +339,10 @@ impl interface::Provider for Provider {
             .conn
             .lock()
             .expect("cannot obtain connection lock")
-            .query_one(&sql, &[&ac])?
-            .try_get("seq_id")?;
+            .query_one(&sql, &[&ac])
+            .map_err(Arc::new)?
+            .try_get("seq_id")
+            .map_err(Arc::new)?;
 
         let sql = format!(
             "SELECT seq FROM {}.seq WHERE seq_id = $1",
@@ -348,8 +352,10 @@ impl interface::Provider for Provider {
             .conn
             .lock()
             .expect("cannot obtain connection lock")
-            .query_one(&sql, &[&seq_id])?
-            .try_get("seq")?;
+            .query_one(&sql, &[&seq_id])
+            .map_err(Arc::new)?
+            .try_get("seq")
+            .map_err(Arc::new)?;
 
         let begin = begin.unwrap_or_default();
         let end = end
@@ -373,7 +379,8 @@ impl interface::Provider for Provider {
             .conn
             .lock()
             .expect("cannot obtain connection lock")
-            .query(&sql, &[&md5])?
+            .query(&sql, &[&md5])
+            .map_err(Arc::new)?
         {
             result.push(row.get(0));
         }
@@ -402,7 +409,8 @@ impl interface::Provider for Provider {
             .conn
             .lock()
             .expect("cannot obtain connection lock")
-            .query(&sql, &[&tx_ac])?
+            .query(&sql, &[&tx_ac])
+            .map_err(Arc::new)?
         {
             result.push(row.try_into()?);
         }
@@ -439,7 +447,8 @@ impl interface::Provider for Provider {
             .conn
             .lock()
             .expect("cannot obtain connection lock")
-            .query(&sql, &[&tx_ac, &alt_ac, &alt_aln_method])?
+            .query(&sql, &[&tx_ac, &alt_ac, &alt_aln_method])
+            .map_err(Arc::new)?
         {
             result.push(row.try_into()?);
         }
@@ -473,7 +482,8 @@ impl interface::Provider for Provider {
             .conn
             .lock()
             .expect("cannot obtain connection lock")
-            .query(&sql, &[&gene])?
+            .query(&sql, &[&gene])
+            .map_err(Arc::new)?
         {
             result.push(row.try_into()?);
         }
@@ -517,7 +527,8 @@ impl interface::Provider for Provider {
             .conn
             .lock()
             .expect("cannot obtain connection lock")
-            .query(&sql, &[&alt_ac, &start_i, &end_i])?
+            .query(&sql, &[&alt_ac, &start_i, &end_i])
+            .map_err(Arc::new)?
         {
             let record: TxForRegionRecord = row.try_into()?;
             // NB: The original Python code did not use alt_aln_method in the query either.
@@ -547,7 +558,8 @@ impl interface::Provider for Provider {
             .conn
             .lock()
             .expect("cannot obtain connection lock")
-            .query_one(&sql, &[&tx_ac])?
+            .query_one(&sql, &[&tx_ac])
+            .map_err(Arc::new)?
             .try_into()?;
 
         self.caches
@@ -583,7 +595,8 @@ impl interface::Provider for Provider {
             .conn
             .lock()
             .expect("cannot obtain connection lock")
-            .query_one(&sql, &[&tx_ac, &alt_ac, &alt_aln_method])?
+            .query_one(&sql, &[&tx_ac, &alt_ac, &alt_aln_method])
+            .map_err(Arc::new)?
             .try_into()?;
 
         self.caches.get_tx_info.insert(key, result.clone());
@@ -607,7 +620,8 @@ impl interface::Provider for Provider {
             .conn
             .lock()
             .expect("cannot obtain connection lock")
-            .query(&sql, &[&tx_ac])?
+            .query(&sql, &[&tx_ac])
+            .map_err(Arc::new)?
         {
             result.push(row.try_into()?);
         }