chore: bump dependencies

Cargo.toml

@@ -15,12 +15,12 @@ clap-verbosity-flag = "2.2"
 clap = { version = "4.5", features = ["derive", "help", "env"] }
 console = "0.15"
 csv = "1.3"
-derive_more = "0.99"
-env_logger = "0.10"
+derive_more = { version = "1.0", features = ["full"] }
+env_logger = "0.11"
 fastobo = "0.15.2"
 fastrand = "2.1"
 flate2 = "1.0"
-hpo = "0.8"
+hpo = "0.11"
 indexmap = { version = "2.6", features = ["serde"] }
 indicatif = { version = "0.17", features = ["rayon"] }
 itertools = "0.13"
@@ -36,13 +36,13 @@ serde_with = { version = "3.9", features=["alloc", "macros", "indexmap_2"], defa
 shellexpand = "3.0"
 strum_macros = "0.26"
 strum = { version = "0.26", features = ["strum_macros", "derive"] }
-tantivy = "0.21.1"
-tempdir = "0.3.7"
+tantivy = "0.22"
+tempdir = "0.3"
 thiserror = "2.0"
 tracing = "0.1"
 tracing-subscriber = "0.3"
-utoipa-swagger-ui = { version = "7.1.0", features = ["actix-web"] }
-utoipa = { version = "4.2", features = ["actix_extras", "chrono", "indexmap", "preserve_order", "yaml"] }
+utoipa-swagger-ui = { version = "8.0", features = ["actix-web"] }
+utoipa = { version = "5.2", features = ["actix_extras", "chrono", "indexmap", "preserve_order", "yaml"] }
 
 [build-dependencies]
 anyhow = "1.0"

src/algos/phenomizer.rs

@@ -47,7 +47,11 @@ fn score_dir(qs: &HpoGroup, ds: &HpoGroup, o: &Ontology, s: &impl Similarity) ->
 #[cfg(test)]
 mod test {
     use super::*;
-    use hpo::{annotations::OmimDiseaseId, term::HpoGroup, HpoTermId, Ontology};
+    use hpo::{
+        annotations::{Disease as _, OmimDiseaseId},
+        term::HpoGroup,
+        HpoTermId, Ontology,
+    };
 
     fn load_hpo() -> Result<Ontology, anyhow::Error> {
         Ok(Ontology::from_standard("tests/data/hpo")?)
@@ -84,7 +88,7 @@ mod test {
 
         let score = score(&prepare(query), &hpo_marfan, &hpo);
 
-        assert!((score - 1.757_194).abs() < 0.00001, "score = {score}");
+        assert!((score - 1.756_347).abs() < 0.00001, "score = {score}");
 
         Ok(())
     }

src/common.rs

@@ -66,10 +66,10 @@
 pub enum IcBasedOn {
     /// Compute information content based on gene.
     #[default]
-    #[display(fmt = "gene")]
+    #[display("gene")]
     Gene,
     /// Compute information content based on OMIM disease.
-    #[display(fmt = "omim")]
+    #[display("omim")]
     Omim,
 }
 
@@ -105,29 +105,29 @@
 #[serde(rename_all = "kebab-case")]
 pub enum SimilarityMethod {
     /// "Distance" similarity.
-    #[display(fmt = "distance")]
+    #[display("distance")]
     DistanceGene,
     /// Graph IC similarity.
-    #[display(fmt = "graph-ic")]
+    #[display("graph-ic")]
     GraphIc,
     /// Information coefficient similarity..
-    #[display(fmt = "information-coefficient")]
+    #[display("information-coefficient")]
     InformationCoefficient,
     /// Jiang & Conrath similarity.
-    #[display(fmt = "jc")]
+    #[display("jc")]
     Jc,
     /// Lin similarity..
-    #[display(fmt = "lin")]
+    #[display("lin")]
     Lin,
     /// "Mutation" similarity.
-    #[display(fmt = "mutation")]
+    #[display("mutation")]
     Mutation,
     /// "Relevance" similarity.
-    #[display(fmt = "relevance")]
+    #[display("relevance")]
     Relevance,
     /// Resnik similarity..
     #[default]
-    #[display(fmt = "resnik")]
+    #[display("resnik")]
     Resnik,
 }
 
@@ -182,13 +182,13 @@
 pub enum ScoreCombiner {
     /// funSimAvg algborithm.
     #[default]
-    #[display(fmt = "fun-sim-avg")]
+    #[display("fun-sim-avg")]
     FunSimAvg,
     /// funSimMax algorithm.
-    #[display(fmt = "fun-sim-max")]
+    #[display("fun-sim-max")]
     FunSimMax,
     /// BMA algorithm.
-    #[display(fmt = "bma")]
+    #[display("bma")]
     Bma,
 }
 
@@ -197,7 +197,7 @@
         match val {
             ScoreCombiner::FunSimAvg => StandardCombiner::FunSimAvg,
             ScoreCombiner::FunSimMax => StandardCombiner::FunSimMax,
-            ScoreCombiner::Bma => StandardCombiner::Bwa,
+            ScoreCombiner::Bma => StandardCombiner::Bma,
         }
     }
 }

src/convert/mod.rs

@@ -29,14 +29,9 @@
     tracing::info!("args_common = {:?}", &args_common);
     tracing::info!("args = {:?}", &args);
 
-    if let Some(level) = args_common.verbose.log_level() {
-        match level {
-            log::Level::Trace | log::Level::Debug => {
-                std::env::set_var("RUST_LOG", "debug");
-                env_logger::init_from_env(env_logger::Env::new().default_filter_or("info"));
-            }
-            _ => (),
-        }
+    if let Some(log::Level::Trace | log::Level::Debug) = args_common.verbose.log_level() {
+        std::env::set_var("RUST_LOG", "debug");
+        env_logger::init_from_env(env_logger::Env::new().default_filter_or("info"));
     }
 
     tracing::info!("Loading HPO...");

src/index.rs

@@ -98,7 +98,7 @@ impl Index {
             .iter()
             .filter_map(fastobo::ast::EntityFrame::as_term)
         {
-            let mut doc = tantivy::Document::default();
+            let mut doc = tantivy::TantivyDocument::default();
 
             doc.add_field_value(
                 schema.get_field("term_id")?,

src/query/mod.rs

@@ -52,7 +52,15 @@
 
     /// Struct for storing gene information in the result.
     #[derive(
-        serde::Serialize, serde::Deserialize, PartialEq, Eq, PartialOrd, Ord, Debug, Clone,
+        PartialEq,
+        Eq,
+        PartialOrd,
+        Ord,
+        Debug,
+        Clone,
+        serde::Serialize,
+        serde::Deserialize,
+        utoipa::ToSchema,
     )]
     #[serde_with::skip_serializing_none]
     pub struct Gene {
@@ -65,7 +73,7 @@
     }
 
     /// The performed query.
-    #[derive(serde::Serialize, serde::Deserialize, utoipa::ToSchema, Debug, Clone)]
+    #[derive(Debug, Clone, serde::Serialize, serde::Deserialize, utoipa::ToSchema)]
     #[schema(title = "HpoSimTermGeneQuery")]
     pub struct Query {
         /// The query HPO terms.
@@ -75,7 +83,7 @@
     }
 
     /// Result container data structure.
-    #[derive(serde::Serialize, serde::Deserialize, utoipa::ToSchema, Debug, Clone)]
+    #[derive(Debug, Clone, serde::Serialize, serde::Deserialize, utoipa::ToSchema)]
     #[schema(title = "HpoSimTermGeneResult")]
     pub struct Result {
         /// Version information.
@@ -87,7 +95,7 @@
     }
 
     /// Store score for a record with information on individual terms.
-    #[derive(serde::Serialize, serde::Deserialize, utoipa::ToSchema, Debug, Clone)]
+    #[derive(Debug, Clone, serde::Serialize, serde::Deserialize, utoipa::ToSchema)]
     #[schema(title = "HpoSimTermGeneResultEntry")]
     pub struct ResultEntry {
         /// The gene symbol.
@@ -100,7 +108,7 @@
     }
 
     /// Detailed term scores.
-    #[derive(serde::Serialize, serde::Deserialize, utoipa::ToSchema, Debug, Clone)]
+    #[derive(Debug, Clone, serde::Serialize, serde::Deserialize, utoipa::ToSchema)]
     #[schema(title = "HpoSimTermGeneTermDetails")]
     pub struct TermDetails {
         /// The query HPO term.
@@ -258,14 +266,9 @@
     tracing::info!("args_common = {:?}", &args_common);
     tracing::info!("args = {:?}", &args);
 
-    if let Some(level) = args_common.verbose.log_level() {
-        match level {
-            log::Level::Trace | log::Level::Debug => {
-                std::env::set_var("RUST_LOG", "debug");
-                env_logger::init_from_env(env_logger::Env::new().default_filter_or("info"));
-            }
-            _ => (),
-        }
+    if let Some(log::Level::Trace | log::Level::Debug) = args_common.verbose.log_level() {
+        std::env::set_var("RUST_LOG", "debug");
+        env_logger::init_from_env(env_logger::Env::new().default_filter_or("info"));
     }
 
     tracing::info!("Loading HPO...");

src/server/run/hpo_genes.rs

@@ -5,7 +5,6 @@ use std::{collections::HashMap, sync::Arc};
 use actix_web::{
     get,
     web::{self, Data, Json, Path},
-    Responder,
 };
 use hpo::{
     annotations::{AnnotationId, Gene, GeneId},
@@ -143,7 +142,7 @@ async fn handle(
     data: Data<Arc<WebServerData>>,
     _path: Path<()>,
     query: web::Query<Query>,
-) -> actix_web::Result<impl Responder, CustomError> {
+) -> actix_web::Result<Json<Result>, CustomError> {
     let ontology = &data.ontology;
     let match_ = query.match_.unwrap_or_default();
     let mut result: Vec<ResultEntry> = Vec::new();

src/server/run/hpo_omims.rs

@@ -5,10 +5,9 @@ use std::sync::Arc;
 use actix_web::{
     get,
     web::{self, Data, Json, Path},
-    Responder,
 };
 use hpo::{
-    annotations::{OmimDisease, OmimDiseaseId},
+    annotations::{Disease as _, OmimDisease, OmimDiseaseId},
     term::HpoGroup,
     Ontology,
 };
@@ -178,7 +177,7 @@ async fn handle(
     data: Data<Arc<WebServerData>>,
     _path: Path<()>,
     query: web::Query<Query>,
-) -> actix_web::Result<impl Responder, CustomError> {
+) -> actix_web::Result<Json<Result>, CustomError> {
     let ontology = &data.ontology;
     let match_ = query.match_.unwrap_or_default();
     let mut result: Vec<ResultEntry> = Vec::new();

src/server/run/hpo_sim/term_gene.rs

@@ -6,13 +6,15 @@
 use actix_web::{
     get,
     web::{self, Data, Json, Path},
-    Responder,
 };
 
 use hpo::{annotations::GeneId, term::HpoGroup, HpoTermId, Ontology};
 
 use super::super::CustomError;
-use crate::{query, server::run::WebServerData};
+use crate::{
+    query::{self, query_result},
+    server::run::WebServerData,
+};
 
 /// Parameters for `handle`.
 ///
@@ -52,15 +54,15 @@
     operation_id = "hpo_sim_term_gene",
     params(Query),
     responses(
-        (status = 200, description = "The query was successful.", body = Result),
+        (status = 200, description = "The query was successful.", body = query_result::Result),
     )
 )]
 #[get("/hpo/sim/term-gene")]
 async fn handle(
     data: Data<Arc<WebServerData>>,
     _path: Path<()>,
     query: web::Query<Query>,
-) -> actix_web::Result<impl Responder, CustomError> {
+) -> actix_web::Result<Json<query_result::Result>, CustomError> {
     let hpo: &Ontology = &data.ontology;
 
     // Translate strings from the query into an `HpoGroup`.

src/server/run/hpo_sim/term_term.rs

@@ -6,7 +6,6 @@ use std::sync::Arc;
 use actix_web::{
     get,
     web::{self, Data, Json, Path},
-    Responder,
 };
 use hpo::{
     similarity::{Builtins, Similarity},
@@ -116,7 +115,7 @@ async fn handle(
     data: Data<Arc<WebServerData>>,
     _path: Path<()>,
     query: web::Query<RequestQuery>,
-) -> actix_web::Result<impl Responder, CustomError> {
+) -> actix_web::Result<Json<Result>, CustomError> {
     let ontology: &Ontology = &data.ontology;
     let mut result = Vec::new();