re-enable searching by vernacular names

ARGA-Genomes · Jan 31, 2024 · 1a7a91b · 1a7a91b
1 parent e747f5e
commit 1a7a91b
Show file tree

Hide file tree

Showing 5 changed files with 20 additions and 10 deletions.
diff --git a/core/migrations/00000000003005_create_species_view/up.sql b/core/migrations/00000000003005_create_species_view/up.sql
@@ -13,7 +13,8 @@ SELECT
     summaries.specimens,
     summaries.other,
     summaries.total_genomic,
-    name_attributes.traits
+    name_attributes.traits,
+    vernacular_names.names AS vernacular_names
 FROM taxa
 JOIN (
   SELECT
@@ -41,4 +42,12 @@ LEFT JOIN (
   FROM name_attributes
   JOIN taxon_names ON taxon_names.name_id = name_attributes.name_id
   GROUP BY taxon_id
-) name_attributes ON taxa.id = name_attributes.taxon_id;
+) name_attributes ON taxa.id = name_attributes.taxon_id
+LEFT JOIN (
+  SELECT
+    taxon_id,
+    array_agg(vernacular_name) as names
+  FROM vernacular_names
+  JOIN taxon_names ON taxon_names.name_id = vernacular_names.name_id
+  GROUP BY taxon_id
+) vernacular_names ON taxa.id = vernacular_names.taxon_id;
diff --git a/core/src/models.rs b/core/src/models.rs
@@ -293,6 +293,7 @@ pub struct Species {
     pub total_genomic: i64,
 
     pub traits: Option<Vec<String>>,
+    pub vernacular_names: Option<Vec<String>>,
 }
 
 #[derive(Debug, Serialize, Deserialize, Default)]

diff --git a/core/src/schema_gnl.rs b/core/src/schema_gnl.rs
@@ -122,6 +122,7 @@ diesel::table! {
         other -> BigInt,
         total_genomic -> BigInt,
         traits -> Nullable<Array<Varchar>>,
+        vernacular_names -> Nullable<Array<Varchar>>,
     }
 }
 

diff --git a/tasks/src/search/mod.rs b/tasks/src/search/mod.rs
@@ -120,11 +120,11 @@ fn index_names(schema: &Schema, index: &Index) -> Result<(), Error> {
             //         doc.add_text(synonyms, name);
             //     }
             // }
-            // if let Some(names) = &species.vernacular_names {
-            //     for name in names {
-            //         doc.add_text(common_names, name);
-            //     }
-            // }
+            if let Some(names) = &species.vernacular_names {
+                for name in names {
+                    doc.add_text(common_names, name);
+                }
+            }
 
             if let Some(value) = &species.kingdom { doc.add_text(kingdom, value); }
             if let Some(value) = &species.phylum { doc.add_text(phylum, value); }

diff --git a/tasks/src/search/taxon.rs b/tasks/src/search/taxon.rs
@@ -26,7 +26,7 @@ pub struct SpeciesDoc {
     pub canonical_name: String,
     // pub subspecies: Option<Vec<String>>,
     // pub synonyms: Option<Vec<String>>,
-    // pub vernacular_names: Option<Vec<String>>,
+    pub vernacular_names: Option<Vec<String>>,
 
     pub kingdom: Option<String>,
     pub phylum: Option<String>,
@@ -50,15 +50,14 @@ pub fn get_species(pool: &PgPool) -> Result<Vec<SpeciesDoc>, Error> {
 
     let docs = species::table
         // .left_join(synonyms::table)
-        // .left_join(common_names::table)
         .select((
             species::id,
             species::status,
 
             species::canonical_name,
             // species::subspecies,
             // synonyms::names.nullable(),
-            // common_names::names.nullable(),
+            species::vernacular_names,
 
             sql::<Nullable<Varchar>>("classification->>'kingdom'"),
             sql::<Nullable<Varchar>>("classification->>'phylum'"),