more changes

Author: psnairne

Cargo.toml

@@ -1,16 +1,18 @@
 [package]
-authors = ["Peter Robinson, Rouven Router, Patrick Nairne"]
-description = "A Rust library for shared tools between different Phenopacket extraction programs."
+authors = ["Patrick Nairne, Rouven Reuter"]
+description = "A Rust library for retrieving data from the VariantValidator and HGNC APIs for Phenopackets."
 edition = "2024"
 homepage = "https://robinsongroup.github.io/"
-license = "MIT"
-name = "pivot"
-version = "0.1.4"
+license-file = "LICENSE"
+name = "pivotal"
+version = "0.1.6"
+keywords = ["variant", "validator", "hgnc", "hgvs", "phenopacket"]
+readme = "README.md"
+repository = "https://github.com/psnairne/PIVOT"
 
 
 [dependencies]
 phenopackets = { version = "0.2.2-post1", features = ["serde"] }
-rstest = "0.26.1"
 serde = "1.0.228"
 thiserror = "2.0.17"
 ratelimit = "0.10.0"

README.md

@@ -1,5 +1,5 @@
 ## PIVOT
-A Rust library for getting data from VariantValidator.
+A Rust library for getting data from VariantValidator and HGNC.
 
 ## License
 This project is licensed under MIT.

src/hgnc/error.rs

@@ -32,4 +32,8 @@ pub enum HGNCError {
     Request(#[from] reqwest::Error),
     #[error("Something went wrong when using Mutex: {0}")]
     MutexError(String),
+    #[error("HGNC fetch request for {gene} failed. Error: {err}.")]
+    FetchRequest { gene: String, err: String },
+    #[error("HgncAPI returned an error on {attempts} attempts to retrieve data about gene {gene}")]
+    HgncAPI { gene: String, attempts: usize },
 }

src/hgnc/hgnc_client.rs

@@ -5,38 +5,62 @@ use crate::hgnc::traits::HGNCData;
 use ratelimit::Ratelimiter;
 use reqwest::blocking::Client;
 use std::fmt::{Debug, Formatter};
+use std::sync::OnceLock;
 use std::thread::sleep;
 use std::time::Duration;
 
+static HGNC_RATE_LIMITER: OnceLock<Ratelimiter> = OnceLock::new();
+
+fn hgnc_rate_limiter() -> &'static Ratelimiter {
+    HGNC_RATE_LIMITER.get_or_init(|| {
+        Ratelimiter::builder(10, Duration::from_millis(1100))
+            .max_tokens(10)
+            .build()
+            .expect("Building rate limiter failed")
+    })
+}
+
 pub struct HGNCClient {
-    rate_limiter: Ratelimiter,
+    attempts: usize,
     api_url: String,
     client: Client,
 }
 
 impl HGNCClient {
-    pub fn new(rate_limiter: Ratelimiter, api_url: String) -> Self {
+    pub fn new(attempts: usize, api_url: String) -> Self {
         HGNCClient {
-            rate_limiter,
+            attempts,
             api_url,
             client: Client::new(),
         }
     }
 
-    fn fetch_request(&self, url: &str) -> Result<Vec<GeneDoc>, HGNCError> {
-        if let Err(duration) = self.rate_limiter.try_wait() {
-            sleep(duration);
+    fn fetch_request(&self, url: &str, query: &GeneQuery) -> Result<Vec<GeneDoc>, HGNCError> {
+        for _ in 0..self.attempts {
+            if let Err(duration) = hgnc_rate_limiter().try_wait() {
+                sleep(duration);
+            }
+            let response = self
+                .client
+                .get(url)
+                .header("User-Agent", "PIVOT")
+                .header("Accept", "application/json")
+                .send()
+                .map_err(|err| HGNCError::FetchRequest {
+                    gene: query.inner().to_string(),
+                    err: err.to_string(),
+                })?;
+
+            if response.status().is_success() {
+                let gene_response = response.json::<GeneResponse>()?;
+                return Ok(gene_response.response.docs);
+            }
         }
-        let response = self
-            .client
-            .get(url)
-            .header("User-Agent", "PIVOT")
-            .header("Accept", "application/json")
-            .send()?;
 
-        let gene_response = response.json::<GeneResponse>()?;
-
-        Ok(gene_response.response.docs)
+        Err(HGNCError::HgncAPI {
+            gene: query.inner().to_string(),
+            attempts: self.attempts,
+        })
     }
 }
 
@@ -46,7 +70,7 @@ impl HGNCData for HGNCClient {
             GeneQuery::Symbol(symbol) => format!("{}fetch/symbol/{}", self.api_url, symbol),
             GeneQuery::HgncId(id) => format!("{}fetch/hgnc_id/{}", self.api_url, id),
         };
-        let docs = self.fetch_request(&fetch_url)?;
+        let docs = self.fetch_request(&fetch_url, &query)?;
 
         if docs.len() == 1 {
             Ok(docs.first().unwrap().clone())
@@ -62,12 +86,7 @@ impl HGNCData for HGNCClient {
 
 impl Default for HGNCClient {
     fn default() -> Self {
-        let rate_limiter = Ratelimiter::builder(10, Duration::from_secs(1))
-            .max_tokens(10)
-            .build()
-            .expect("Building rate limiter failed");
-
-        HGNCClient::new(rate_limiter, "https://rest.genenames.org/".to_string())
+        HGNCClient::new(3, "https://rest.genenames.org/".to_string())
     }
 }
 

src/hgvs/hgvs_client.rs

@@ -11,13 +11,24 @@ use reqwest::blocking::Client;
 use serde_json::Value;
 use std::fmt::Debug;
 use std::string::ToString;
+use std::sync::OnceLock;
 use std::thread::sleep;
 use std::time::Duration;
 
 const ALLOWED_FLAGS: [&str; 2] = ["gene_variant", "mitochondrial"];
 
+static HGVS_RATE_LIMITER: OnceLock<Ratelimiter> = OnceLock::new();
+
+fn hgvs_rate_limiter() -> &'static Ratelimiter {
+    HGVS_RATE_LIMITER.get_or_init(|| {
+        Ratelimiter::builder(2, Duration::from_millis(1250))
+            .max_tokens(2)
+            .build()
+            .expect("Building rate limiter failed")
+    })
+}
+
 pub struct HGVSClient {
-    rate_limiter: Ratelimiter,
     attempts: usize,
     api_url: String,
     client: Client,
@@ -26,19 +37,9 @@ pub struct HGVSClient {
 
 impl Default for HGVSClient {
     fn default() -> Self {
-        let rate_limiter = Ratelimiter::builder(2, Duration::from_millis(1180))
-            .max_tokens(2)
-            .build()
-            .expect("Building rate limiter failed");
         let api_url =
             "https://rest.variantvalidator.org/VariantValidator/variantvalidator/".to_string();
-        HGVSClient::new(
-            rate_limiter,
-            3,
-            api_url.to_string(),
-            Client::new(),
-            GenomeAssembly::Hg38,
-        )
+        HGVSClient::new(3, api_url.to_string(), Client::new(), GenomeAssembly::Hg38)
     }
 }
 
@@ -55,14 +56,12 @@ impl Debug for HGVSClient {
 
 impl HGVSClient {
     pub fn new(
-        rate_limiter: Ratelimiter,
         attempts: usize,
         api_url: String,
         client: Client,
         genome_assembly: GenomeAssembly,
     ) -> Self {
         HGVSClient {
-            rate_limiter,
             attempts,
             api_url,
             client,
@@ -83,7 +82,7 @@ impl HGVSClient {
         unvalidated_hgvs: &str,
     ) -> Result<VariantValidatorResponse, HGVSError> {
         for _ in 0..self.attempts {
-            if let Err(duration) = self.rate_limiter.try_wait() {
+            if let Err(duration) = hgvs_rate_limiter().try_wait() {
                 sleep(duration);
             }
 
@@ -245,49 +244,48 @@ mod tests {
     use crate::hgvs::traits::HGVSData;
     use rstest::{fixture, rstest};
 
-    // this forces tests to run sequentially
-    #[rstest]
-    fn hgvs_client_tests() {
-        let client = HGVSClient::default();
-        test_request_and_validate_hgvs_c_autosomal(&client);
-        test_request_and_validate_hgvs_c_x(&client);
-        test_request_and_validate_hgvs_n(&client);
-        test_request_and_validate_hgvs_m(&client);
-        test_request_and_validate_hgvs_wrong_reference_base_err(&client);
-        test_request_and_validate_hgvs_not_c_or_n_hgvs_err(&client);
+    #[fixture]
+    fn client() -> HGVSClient {
+        HGVSClient::default()
     }
 
-    fn test_request_and_validate_hgvs_c_autosomal(client: &HGVSClient) {
+    #[rstest]
+    fn test_request_and_validate_hgvs_c_autosomal(client: HGVSClient) {
         let unvalidated_hgvs = "NM_001173464.1:c.2860C>T";
         let validated_hgvs = client.request_and_validate_hgvs(unvalidated_hgvs).unwrap();
         assert_eq!(validated_hgvs.transcript_hgvs(), unvalidated_hgvs);
     }
 
-    fn test_request_and_validate_hgvs_c_x(client: &HGVSClient) {
+    #[rstest]
+    fn test_request_and_validate_hgvs_c_x(client: HGVSClient) {
         let unvalidated_hgvs = "NM_000132.4:c.3637A>T";
         let validated_hgvs = client.request_and_validate_hgvs(unvalidated_hgvs).unwrap();
         assert_eq!(validated_hgvs.transcript_hgvs(), unvalidated_hgvs);
     }
 
-    fn test_request_and_validate_hgvs_n(client: &HGVSClient) {
+    #[rstest]
+    fn test_request_and_validate_hgvs_n(client: HGVSClient) {
         let unvalidated_hgvs = "NR_002196.1:n.601G>T";
         let validated_hgvs = client.request_and_validate_hgvs(unvalidated_hgvs).unwrap();
         assert_eq!(validated_hgvs.transcript_hgvs(), unvalidated_hgvs);
     }
 
-    fn test_request_and_validate_hgvs_m(client: &HGVSClient) {
+    #[rstest]
+    fn test_request_and_validate_hgvs_m(client: HGVSClient) {
         let unvalidated_hgvs = "NC_012920.1:m.616T>C";
         let validated_hgvs = client.request_and_validate_hgvs(unvalidated_hgvs).unwrap();
         assert_eq!(validated_hgvs.transcript_hgvs(), unvalidated_hgvs);
     }
 
-    fn test_request_and_validate_hgvs_wrong_reference_base_err(client: &HGVSClient) {
+    #[rstest]
+    fn test_request_and_validate_hgvs_wrong_reference_base_err(client: HGVSClient) {
         let unvalidated_hgvs = "NM_001173464.1:c.2860G>T";
         let result = client.request_and_validate_hgvs(unvalidated_hgvs);
         assert!(matches!(result, Err(HGVSError::InvalidHgvs { .. })));
     }
 
-    fn test_request_and_validate_hgvs_not_c_or_n_hgvs_err(client: &HGVSClient) {
+    #[rstest]
+    fn test_request_and_validate_hgvs_not_c_or_n_hgvs_err(client: HGVSClient) {
         let unvalidated_hgvs = "NC_000012.12:g.39332405G>A";
         let result = client.request_and_validate_hgvs(unvalidated_hgvs);
         assert!(matches!(

tests/hgnc_stress_test.rs

@@ -1,4 +1,4 @@
-use pivot::hgnc::{GeneQuery, HGNCClient, HGNCData};
+use pivotal::hgnc::{GeneQuery, HGNCClient, HGNCData};
 use rstest::{fixture, rstest};
 
 #[macro_export]
@@ -18,7 +18,7 @@ macro_rules! skip_in_ci {
 }
 
 // found here: https://www.genenames.org/download/statistics-and-files/
-// 319 genes
+// 274 genes
 #[fixture]
 fn genes() -> String {
     "A1BG
@@ -294,52 +294,7 @@ ADAMDEC1
 ADAMTS1
 ADAMTS2
 ADAMTS3
-ADAMTS4
-ADAMTS5
-ADAMTS6
-ADAMTS7
-ADAMTS8
-ADAMTS9
-ADAMTS10
-ADAMTS12
-ADAMTS13
-ADAMTS14
-ADAMTS15
-ADAMTS16
-ADAMTS17
-ADAMTS18
-ADAMTS19
-ADAMTS20
-ADAMTSL1
-ADAMTSL2
-ADAMTSL3
-ADAMTSL4
-ADAMTSL5
-ADAP1
-ADAP2
-ADAR
-ADARB1
-ADARB2
-ADAT1
-ADAT2
-ADAT3
-ADCK1
-ADCK2
-ADCK5
-ADCY1
-ADCY2
-ADCY3
-ADCY4
-ADCY5
-ADCY6
-ADCY7
-ADCY8
-ADCY9
-ADCY10
-ADCYAP1
-ADCYAP1R1
-ADD1
-ADD2"
+ADAMTS4"
         .to_string()
 }
 
@@ -350,7 +305,8 @@ fn hgnc_stress_test(genes: String) {
     let gene_vec = genes.lines().collect::<Vec<&str>>();
     for gene in gene_vec {
         let query = GeneQuery::Symbol(gene);
-        let gene_doc = client.request_gene_data(query).unwrap();
+        let gene_doc_result = client.request_gene_data(query);
+        let gene_doc = gene_doc_result.unwrap();
         assert_eq!(gene_doc.symbol.unwrap(), gene);
     }
 }

tests/hgvs_stress_test.rs

@@ -1,4 +1,4 @@
-use pivot::hgvs::{HGVSClient, HGVSData};
+use pivotal::hgvs::{HGVSClient, HGVSData};
 use rstest::{fixture, rstest};
 
 #[macro_export]
@@ -36,13 +36,13 @@ fn create_hgvs_variants_from_transcript(
 }
 
 // found here: https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=NUCID&DATA=1677538156
-//283 characters
+//270 characters
 #[fixture]
 fn kif21a_transcript_beginning() -> String {
     let str = "ATGTTGGGCGCCCCGGACGAGAGCTCCGTGCGGGTGGCTGTCAGAATAAGACCACAGCTTGCCAAAGAGA
 AGATTGAAGGATGCCATATTTGTACATCTGTCACACCAGGAGAGCCTCAGGTCTTCCTAGGGAAAGATAA
 GGCTTTTACTTTTGACTATGTATTTGACATTGACTCCCAGCAAGAGCAGATCTACATTCAATGTATAGAA
-AAACTAATTGAAGGTTGCTTTGAAGGATACAATGCTACAGTTTTTGCTTATGGACAAACTGGAGCTGGTA"
+AAACTAATTGAAGGTTGCTTTGAAGGATACAATGCTACAGTTTTTGCTTATGGACAA"
         .to_string();
     str.replace('\n', "")
 }