wip

src/index.rs

@@ -96,7 +96,7 @@ impl Index {
         for term_frame in hpo_doc
             .entities()
             .iter()
-            .flat_map(fastobo::ast::EntityFrame::as_term)
+            .filter_map(fastobo::ast::EntityFrame::as_term)
         {
             let mut doc = tantivy::Document::default();
 
@@ -105,7 +105,11 @@ impl Index {
                 ident_to_string(term_frame.id().as_inner().as_ref()),
             );
 
-            for line in term_frame.clauses().iter().map(|l| l.as_inner()) {
+            for line in term_frame
+                .clauses()
+                .iter()
+                .map(fastobo::ast::Line::as_inner)
+            {
                 match line {
                     fastobo::ast::TermClause::Name(name) => {
                         doc.add_field_value(schema.get_field("name")?, name.as_str());

src/server/actix_server/hpo_genes.rs

@@ -86,7 +86,6 @@ impl ResultEntry {
                 .map(|term| ResultHpoTerm {
                     term_id: term.id().to_string(),
                     name: term.name().to_string(),
-                    ..Default::default()
                 })
                 .collect::<Vec<_>>();
             terms.sort();

src/server/actix_server/hpo_omims.rs

@@ -111,7 +111,6 @@ impl ResultEntry {
                     ResultHpoTerm {
                         term_id: term.id().to_string(),
                         name: term.name().to_string(),
-                        ..Default::default()
                     }
                 })
                 .collect::<Vec<_>>();

src/server/actix_server/hpo_terms.rs

@@ -137,12 +137,12 @@ impl ResultEntry {
 
         let definition = doc
             .get_all(field_def)
-            .flat_map(|f| f.as_text().map(|s| s.to_string()))
+            .filter_map(|f| f.as_text().map(std::string::ToString::to_string))
             .collect::<Vec<_>>();
-        let definition = definition.first().map(|s| s.clone());
+        let definition = definition.first().map(std::clone::Clone::clone);
         let synonyms = doc
             .get_all(field_synonym)
-            .flat_map(|f| f.as_text().map(|s| s.to_string()))
+            .filter_map(|f| f.as_text().map(std::string::ToString::to_string))
             .collect::<Vec<_>>();
         let synonyms = if synonyms.is_empty() {
             None
@@ -151,7 +151,7 @@ impl ResultEntry {
         };
         let xrefs = doc
             .get_all(field_xref)
-            .flat_map(|f| f.as_text().map(|s| s.to_string()))
+            .filter_map(|f| f.as_text().map(std::string::ToString::to_string))
             .collect::<Vec<_>>();
         let xrefs = if xrefs.is_empty() { None } else { Some(xrefs) };
 
@@ -199,6 +199,7 @@ struct Container {
 ///
 /// In the case that there is an error running the server.
 #[allow(clippy::unused_async)]
+#[allow(clippy::too_many_lines)]
 #[get("/hpo/terms")]
 async fn handle(
     data: Data<WebServerData>,
@@ -277,8 +278,8 @@ async fn handle(
             query_parser.set_field_fuzzy(field_synonym, true, 1, true);
             query_parser
         };
-        let index_query = query_parser.parse_query(&name).map_err(|e| {
-            eprintln!("{}", e);
+        let index_query = query_parser.parse_query(name).map_err(|e| {
+            eprintln!("{e}");
             CustomError::new(anyhow::anyhow!("Error parsing query: {}", e))
         })?;
         let top_docs = searcher

src/server/mod.rs

@@ -150,7 +150,7 @@ pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow:
 
     tracing::info!("Loading HPO OBO...");
     let before_load_obo = std::time::Instant::now();
-    let hpo_doc = fastobo::from_file(&format!("{}/{}", &args.path_hpo_dir, "hp.obo"))
+    let hpo_doc = fastobo::from_file(format!("{}/{}", &args.path_hpo_dir, "hp.obo"))
         .map_err(|e| anyhow::anyhow!("Error loading HPO OBO: {}", e))?;
     tracing::info!(
         "... done loading HPO OBO in {:?}",