fix: make /hpo/genes endpoint return HGNC ID (#16) (#17)

varfish-org · Jun 11, 2023 · 77bd9af · 77bd9af
1 parent f38a1bb
commit 77bd9af
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Showing 41 changed files with 127 additions and 47 deletions.
diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
@@ -82,12 +82,6 @@ jobs:
           version: 0.21.0
           args: "--all-features -- --test-threads 1"
 
-      - name: Build all examples
-        uses: actions-rs/cargo@v1
-        with:
-          command: build
-          args: --examples
-
       - name: Codecov
         uses: codecov/codecov-action@v3
         with:

diff --git a/src/common.rs b/src/common.rs
@@ -242,7 +242,18 @@ impl FromStr for ScoreCombiner {
 }
 
 /// The version of `viguno` package.
-pub const VERSION: &str = env!("CARGO_PKG_VERSION");
+#[cfg(not(test))]
+const VERSION: &str = env!("CARGO_PKG_VERSION");
+
+/// Returns the current version of `viguno`.
+///
+/// This allows us to override the version to `0.0.0` in tests.
+pub fn version() -> &'static str {
+    #[cfg(test)]
+    return "0.0.0";
+    #[cfg(not(test))]
+    return VERSION;
+}
 
 /// Version information that is returned by the HTTP server.
 #[derive(serde::Serialize, serde::Deserialize, Default, Debug, Clone)]
@@ -260,7 +271,7 @@ impl Version {
     pub fn new(hpo: &str) -> Self {
         Self {
             hpo: hpo.to_string(),
-            viguno: VERSION.to_string(),
+            viguno: version().to_string(),
         }
     }
 }

diff --git a/src/server/actix_server/hpo_genes.rs b/src/server/actix_server/hpo_genes.rs
@@ -1,5 +1,7 @@
 //! Implementation of `/hpo/genes`.
 
+use std::collections::HashMap;
+
 use actix_web::{
     get,
     web::{self, Data, Json, Path},
@@ -56,18 +58,26 @@ fn _default_hpo_terms() -> bool {
 
 /// Result entry for `handle`.
 #[derive(serde::Serialize, serde::Deserialize, Debug, Clone, Eq, PartialEq, Ord, PartialOrd)]
+#[serde_with::skip_serializing_none]
 struct ResultEntry {
     /// The gene's NCBI ID.
     pub gene_ncbi_id: u32,
     /// The gene's HGNC symbol.
     pub gene_symbol: String,
+    /// The gene's HGNC ID.
+    pub hgnc_id: Option<String>,
     /// The gene's associated HPO terms.
     #[serde(default = "Option::default", skip_serializing_if = "Option::is_none")]
     pub hpo_terms: Option<Vec<ResultHpoTerm>>,
 }
 
 impl ResultEntry {
-    pub fn from_gene_with_ontology(gene: &Gene, ontology: &Ontology, hpo_terms: bool) -> Self {
+    pub fn from_gene_with_ontology(
+        gene: &Gene,
+        ontology: &Ontology,
+        hpo_terms: bool,
+        ncbi_to_hgnc: &HashMap<u32, String>,
+    ) -> Self {
         let hpo_terms = if hpo_terms {
             let mut terms = gene
                 .to_hpo_set(ontology)
@@ -86,6 +96,7 @@ impl ResultEntry {
         ResultEntry {
             gene_ncbi_id: gene.id().as_u32(),
             gene_symbol: gene.name().to_string(),
+            hgnc_id: ncbi_to_hgnc.get(&gene.id().as_u32()).cloned(),
             hpo_terms,
         }
     }
@@ -134,6 +145,7 @@ async fn handle(
                 gene,
                 ontology,
                 query.hpo_terms,
+                &data.ncbi_to_hgnc,
             ));
         }
     } else if let Some(gene_symbol) = &query.gene_symbol {
@@ -152,6 +164,7 @@ async fn handle(
                     gene.expect("checked above"),
                     ontology,
                     query.hpo_terms,
+                    &data.ncbi_to_hgnc,
                 ));
             }
 

diff --git a/...erver__actix_server__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_hgnc_gene_ids.snap b/...erver__actix_server__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_hgnc_gene_ids.snap
@@ -4,7 +4,7 @@ expression: "&run_query(\"/hpo/sim/term-gene?terms=HP:0010442,HP:0000347&gene_id
 ---
 version:
   hpo: 2023-04-05
-  viguno: 0.1.0
+  viguno: 0.0.0
 query:
   terms:
     - term_id: "HP:0000347"

diff --git a/...erver__actix_server__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_ncbi_gene_ids.snap b/...erver__actix_server__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_ncbi_gene_ids.snap
@@ -4,7 +4,7 @@ expression: "&run_query(\"/hpo/sim/term-gene?terms=HP:0010442,HP:0000347&gene_id
 ---
 version:
   hpo: 2023-04-05
-  viguno: 0.1.0
+  viguno: 0.0.0
 query:
   terms:
     - term_id: "HP:0000347"

diff --git a/...uno__server__actix_server__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_symbols.snap b/...uno__server__actix_server__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_symbols.snap
@@ -4,7 +4,7 @@ expression: "&run_query(\"/hpo/sim/term-gene?terms=HP:0010442,HP:0000347&gene_sy
 ---
 version:
   hpo: 2023-04-05
-  viguno: 0.1.0
+  viguno: 0.0.0
 query:
   terms:
     - term_id: "HP:0000347"

diff --git a/...ts/viguno__server__actix_server__hpo_sim__term_term__test__hpo_sim_term_term_one_one.snap b/...ts/viguno__server__actix_server__hpo_sim__term_term__test__hpo_sim_term_term_one_one.snap
@@ -4,7 +4,7 @@ expression: "&run_query(\"/hpo/sim/term-term?lhs=HP:0010442&rhs=HP:0001780\").aw
 ---
 version:
   hpo: 2023-04-05
-  viguno: 0.1.0
+  viguno: 0.0.0
 query:
   lhs:
     - "HP:0010442"

diff --git a/...ts/viguno__server__actix_server__hpo_sim__term_term__test__hpo_sim_term_term_two_two.snap b/...ts/viguno__server__actix_server__hpo_sim__term_term__test__hpo_sim_term_term_two_two.snap
@@ -4,7 +4,7 @@ expression: "&run_query(\"/hpo/sim/term-term?lhs=HP:0010442,HP:0000347&rhs=HP:00
 ---
 version:
   hpo: 2023-04-05
-  viguno: 0.1.0
+  viguno: 0.0.0
 query:
   lhs:
     - "HP:0010442"

diff --git a/...__server__actix_server__hpo_genes__test__hpo_genes_gene_symbol_contains_no_hpo_terms.snap b/...__server__actix_server__hpo_genes__test__hpo_genes_gene_symbol_contains_no_hpo_terms.snap
@@ -4,7 +4,7 @@ expression: "&run_query(\"/hpo/genes?gene_symbol=GD&match=contains\").await?"
 ---
 version:
   hpo: 2023-04-05
-  viguno: 0.1.0
+  viguno: 0.0.0
 query:
   gene_id: ~
   gene_symbol: GD
@@ -14,54 +14,80 @@ query:
 result:
   - gene_ncbi_id: 396
     gene_symbol: ARHGDIA
+    hgnc_id: "HGNC:678"
   - gene_ncbi_id: 1421
     gene_symbol: CRYGD
+    hgnc_id: "HGNC:2411"
   - gene_ncbi_id: 2245
     gene_symbol: FGD1
+    hgnc_id: "HGNC:3663"
   - gene_ncbi_id: 2657
     gene_symbol: GDF1
+    hgnc_id: "HGNC:4214"
   - gene_ncbi_id: 2658
     gene_symbol: GDF2
+    hgnc_id: "HGNC:4217"
   - gene_ncbi_id: 2661
     gene_symbol: GDF9
+    hgnc_id: "HGNC:4224"
   - gene_ncbi_id: 2664
     gene_symbol: GDI1
+    hgnc_id: "HGNC:4226"
   - gene_ncbi_id: 2668
     gene_symbol: GDNF
+    hgnc_id: "HGNC:4232"
   - gene_ncbi_id: 3081
     gene_symbol: HGD
+    hgnc_id: "HGNC:4892"
   - gene_ncbi_id: 3248
     gene_symbol: HPGD
+    hgnc_id: "HGNC:5154"
   - gene_ncbi_id: 4967
     gene_symbol: OGDH
+    hgnc_id: "HGNC:8124"
   - gene_ncbi_id: 7358
     gene_symbol: UGDH
+    hgnc_id: "HGNC:12525"
   - gene_ncbi_id: 8200
     gene_symbol: GDF5
+    hgnc_id: "HGNC:4220"
   - gene_ncbi_id: 9573
     gene_symbol: GDF3
+    hgnc_id: "HGNC:4218"
   - gene_ncbi_id: 10220
     gene_symbol: GDF11
+    hgnc_id: "HGNC:4216"
   - gene_ncbi_id: 23483
     gene_symbol: TGDS
+    hgnc_id: "HGNC:20324"
   - gene_ncbi_id: 26227
     gene_symbol: PHGDH
+    hgnc_id: "HGNC:8923"
   - gene_ncbi_id: 29958
     gene_symbol: DMGDH
+    hgnc_id: "HGNC:24475"
   - gene_ncbi_id: 54332
     gene_symbol: GDAP1
+    hgnc_id: "HGNC:15968"
   - gene_ncbi_id: 54834
     gene_symbol: GDAP2
+    hgnc_id: "HGNC:18010"
   - gene_ncbi_id: 55753
     gene_symbol: OGDHL
+    hgnc_id: "HGNC:25590"
   - gene_ncbi_id: 79641
     gene_symbol: ROGDI
+    hgnc_id: "HGNC:29478"
   - gene_ncbi_id: 79944
     gene_symbol: L2HGDH
+    hgnc_id: "HGNC:20499"
   - gene_ncbi_id: 121512
     gene_symbol: FGD4
+    hgnc_id: "HGNC:19125"
   - gene_ncbi_id: 392255
     gene_symbol: GDF6
+    hgnc_id: "HGNC:4221"
   - gene_ncbi_id: 728294
     gene_symbol: D2HGDH
+    hgnc_id: "HGNC:28358"