structured version

src/common.rs

@@ -240,3 +240,27 @@ impl FromStr for ScoreCombiner {
             .ok_or(anyhow::anyhow!("unknown score combiner: {}", s))
     }
 }
+
+/// The version of `viguno` package.
+pub const VERSION: &str = env!("CARGO_PKG_VERSION");
+
+/// Version information that is returned by the HTTP server.
+#[derive(serde::Serialize, serde::Deserialize, Default, Debug, Clone)]
+pub struct Version {
+    /// Version of the HPO.
+    pub hpo: String,
+    /// Version of the `viguno` package.
+    pub viguno: String,
+}
+
+impl Version {
+    /// Construct a new version.
+    ///
+    /// The viguno version is filed automatically.
+    pub fn new(hpo: &str) -> Self {
+        Self {
+            hpo: hpo.to_string(),
+            viguno: VERSION.to_string(),
+        }
+    }
+}

src/query/mod.rs

@@ -12,7 +12,6 @@ use hpo::{annotations::AnnotationId, term::HpoGroup, HpoTermId, Ontology};
 use crate::algos::phenomizer;
 use crate::pbs::simulation::SimulationResults;
 use crate::query::query_result::TermDetails;
-use crate::simulate::VERSION;
 
 /// Command line arguments for `query` command.
 #[derive(Parser, Debug)]
@@ -52,7 +51,9 @@ pub mod query_result {
     use super::HpoTerm;
 
     /// Struct for storing gene information in the result.
-    #[derive(serde::Serialize, serde::Deserialize, PartialEq, Eq, PartialOrd, Ord, Debug, Clone)]
+    #[derive(
+        serde::Serialize, serde::Deserialize, PartialEq, Eq, PartialOrd, Ord, Debug, Clone,
+    )]
     pub struct Gene {
         /// The NCBI gene ID.
         pub entrez_id: u32,
@@ -72,10 +73,8 @@ pub mod query_result {
     /// Result container data structure.
     #[derive(serde::Serialize, serde::Deserialize, Debug, Clone)]
     pub struct Container {
-        /// Version of the HPO.
-        pub hpo_version: String,
-        /// Version of the `viguno` package.
-        pub viguno_version: String,
+        /// Version information.
+        pub version: crate::common::Version,
         /// The original query records.
         pub query: Query,
         /// The resulting records for the scored genes.
@@ -131,6 +130,7 @@ pub mod query_result {
 /// In the case that a term or database lookup fails.
 #[allow(clippy::cast_possible_truncation)]
 #[allow(clippy::cast_precision_loss)]
+#[allow(clippy::too_many_lines)]
 pub fn run_query(
     patient: &HpoGroup,
     genes: &Vec<&hpo::annotations::Gene>,
@@ -144,20 +144,19 @@ pub fn run_query(
     let num_terms = std::cmp::min(10, patient.len());
     let query = query_result::Query {
         terms: patient
-        .iter()
-        .map(|t| {
-            let term = hpo.hpo(t).expect("could not resolve HPO term");
-            HpoTerm {
-                term_id: term.id().to_string(),
-                term_name: Some(term.name().to_string()),
-            }
-        })
-        .collect(),
+            .iter()
+            .map(|t| {
+                let term = hpo.hpo(t).expect("could not resolve HPO term");
+                HpoTerm {
+                    term_id: term.id().to_string(),
+                    term_name: Some(term.name().to_string()),
+                }
+            })
+            .collect(),
         genes: Vec::new(),
     };
     let mut result = query_result::Container {
-        hpo_version: hpo.hpo_version(),
-        viguno_version: VERSION.to_string(),
+        version: crate::common::Version::new(&hpo.hpo_version()),
         query,
         result: Vec::new(),
     };

src/server/actix_server/hpo_sim/snapshots/viguno__server__actix_server__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_gene_ids.snap

@@ -2,8 +2,9 @@
 source: src/server/actix_server/hpo_sim/term_gene.rs
 expression: "&run_query(\"/hpo/sim/term-gene?terms=HP:0010442,HP:0000347&gene_ids=23483,7273\").await?"
 ---
-hpo_version: 2023-04-05
-viguno_version: 0.1.0
+version:
+  hpo: 2023-04-05
+  viguno: 0.1.0
 query:
   terms:
     - term_id: "HP:0000347"

src/server/actix_server/hpo_sim/snapshots/viguno__server__actix_server__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_symbols.snap

@@ -2,8 +2,9 @@
 source: src/server/actix_server/hpo_sim/term_gene.rs
 expression: "&run_query(\"/hpo/sim/term-gene?terms=HP:0010442,HP:0000347&gene_symbols=TGDS,TTN\").await?"
 ---
-hpo_version: 2023-04-05
-viguno_version: 0.1.0
+version:
+  hpo: 2023-04-05
+  viguno: 0.1.0
 query:
   terms:
     - term_id: "HP:0000347"

src/server/actix_server/hpo_sim/snapshots/viguno__server__actix_server__hpo_sim__term_term__test__hpo_sim_term_term_one_one.snap

@@ -2,8 +2,9 @@
 source: src/server/actix_server/hpo_sim/term_term.rs
 expression: "&run_query(\"/hpo/sim/term-term?lhs=HP:0010442&rhs=HP:0001780\").await?"
 ---
-hpo_version: 2023-04-05
-viguno_version: 0.1.0
+version:
+  hpo: 2023-04-05
+  viguno: 0.1.0
 query:
   lhs:
     - "HP:0010442"

src/server/actix_server/hpo_sim/snapshots/viguno__server__actix_server__hpo_sim__term_term__test__hpo_sim_term_term_two_two.snap

@@ -2,8 +2,9 @@
 source: src/server/actix_server/hpo_sim/term_term.rs
 expression: "&run_query(\"/hpo/sim/term-term?lhs=HP:0010442,HP:0000347&rhs=HP:0001780,HP:0000252\").await?"
 ---
-hpo_version: 2023-04-05
-viguno_version: 0.1.0
+version:
+  hpo: 2023-04-05
+  viguno: 0.1.0
 query:
   lhs:
     - "HP:0010442"

src/server/actix_server/hpo_sim/term_term.rs

@@ -12,11 +12,8 @@ use hpo::{
 };
 use itertools::Itertools;
 
+use crate::common::{to_pairwise_sim, IcBasedOn, ScoreCombiner, SimilarityMethod};
 use crate::server::{actix_server::CustomError, WebServerData};
-use crate::{
-    common::{to_pairwise_sim, IcBasedOn, ScoreCombiner, SimilarityMethod},
-    simulate::VERSION,
-};
 
 /// Parameters for `handle`.
 ///
@@ -66,10 +63,8 @@ pub struct ResponseQuery {
 /// Result container.
 #[derive(serde::Serialize, serde::Deserialize, Default, Debug, Clone)]
 pub struct Container {
-    /// Version of the HPO.
-    pub hpo_version: String,
-    /// Version of the `viguno` package.
-    pub viguno_version: String,
+    /// Version information.
+    pub version: crate::common::Version,
     /// The original query records.
     pub query: ResponseQuery,
     /// The resulting records for the scored genes.
@@ -146,8 +141,7 @@ async fn handle(
     } = query.into_inner();
 
     let result = Container {
-        hpo_version: data.ontology.hpo_version().to_string(),
-        viguno_version: VERSION.to_string(),
+        version: crate::common::Version::new(&data.ontology.hpo_version()),
         query: ResponseQuery {
             lhs,
             rhs,

src/simulate/mod.rs

@@ -20,9 +20,6 @@ use crate::{
     pbs::simulation::SimulationResults,
 };
 
-/// The version of `viguno` package.
-pub const VERSION: &str = env!("CARGO_PKG_VERSION");
-
 /// Command line arguments for Viguno.
 #[derive(Parser, Debug)]
 #[command(author, version, about = "Prepare values for Viguno", long_about = None)]
@@ -247,7 +244,7 @@ pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow:
         .cf_handle("meta")
         .ok_or(anyhow::anyhow!("column family meta not found"))?;
     db.put_cf(&cf_meta, "hpo-version", ontology.hpo_version())?;
-    db.put_cf(&cf_meta, "app-version", VERSION)?;
+    db.put_cf(&cf_meta, "app-version", crate::common::VERSION)?;
     tracing::info!("...done opening RocksDB in {:?}", before_rocksdb.elapsed());
 
     tracing::info!("Running simulations...");