feat: improve taxons search (unaccent, better display)

Resolve #532.
PnX-SI · May 14, 2024 · b65f025 · b65f025
1 parent 3978263
commit b65f025
Show file tree

Hide file tree

Showing 6 changed files with 153 additions and 42 deletions.
diff --git a/atlas/atlasAPI.py b/atlas/atlasAPI.py
@@ -20,7 +20,7 @@ def searchTaxonAPI():
     session = db.session
     search = request.args.get("search", "")
     limit = request.args.get("limit", 50)
-    results = vmSearchTaxonRepository.listeTaxonsSearch(session, search, limit)
+    results = vmSearchTaxonRepository.searchTaxons(session, search, limit)
     session.close()
     return jsonify(results)
 

diff --git a/atlas/modeles/entities/vmSearchTaxon.py b/atlas/modeles/entities/vmSearchTaxon.py
@@ -14,6 +14,7 @@ class VmSearchTaxon(Base):
         metadata,
         Column("cd_ref", Integer, primary_key=True, unique=True),
         Column("cd_nom", Integer),
+        Column("display_name", String),
         Column("search_name", String),
         schema="atlas",
         autoload=True,

diff --git a/atlas/modeles/repositories/vmSearchTaxonRepository.py b/atlas/modeles/repositories/vmSearchTaxonRepository.py
@@ -19,7 +19,7 @@ def listeTaxons(session):
     return taxonList
 
 
-def listeTaxonsSearch(session, search, limit=50):
+def searchTaxons(session, search, limit=50):
     """
     Recherche dans la VmSearchTaxon en ilike
     Utilisé pour l'autocomplétion de la recherche de taxon
@@ -34,20 +34,20 @@ def listeTaxonsSearch(session, search, limit=50):
         label = search_name
         value = cd_ref
     """
-
-    req = session.query(
-        VmSearchTaxon.search_name,
-        VmSearchTaxon.cd_ref,
-        func.similarity(VmSearchTaxon.search_name, search).label("idx_trgm"),
-    ).distinct()
-
-    search = search.replace(" ", "%")
-    req = (
-        req.filter(VmSearchTaxon.search_name.ilike("%" + search + "%"))
+    like_search = "%" + search.replace(" ", "%") + "%"
+
+    query = (
+        session.query(
+            VmSearchTaxon.display_name,
+            VmSearchTaxon.cd_ref,
+            func.similarity(VmSearchTaxon.search_name, search).label("idx_trgm"),
+        )
+        .distinct()
+        .filter(func.unaccent(VmSearchTaxon.search_name).ilike(func.unaccent(like_search)))
         .order_by(desc("idx_trgm"))
         .order_by(VmSearchTaxon.cd_ref == VmSearchTaxon.cd_nom)
         .limit(limit)
     )
-    data = req.all()
+    results = query.all()
 
-    return [{"label": d[0], "value": d[1]} for d in data]
+    return [{"label": r[0], "value": r[1]} for r in results]
diff --git a/data/atlas/5.atlas.vm_search_taxon.sql b/data/atlas/5.atlas.vm_search_taxon.sql
@@ -1,34 +1,62 @@
--- Taxons observés et de tous leurs synonymes (utilisés pour la recherche d'une espèce)
+CREATE MATERIALIZED VIEW atlas.vm_search_taxon AS
+	WITH verna_names AS (
+		SELECT DISTINCT
+			cd_nom,
+			lb_nom,
+		    cd_ref,
+		    STRING_TO_TABLE(nom_vern, ', ') AS nom_vern
+		FROM atlas.vm_taxref
+		WHERE nom_vern IS NOT NULL
+			AND cd_nom = cd_ref
+			AND nom_vern <> lb_nom
+	),
+	names AS (
+		-- Chosen scinames
+		SELECT
+			cd_nom,
+			cd_ref,
+			lb_nom AS search_name,
+		    CONCAT('<b>', REPLACE(nom_complet_html, lb_auteur, ''), '</b> ', lb_auteur) AS display_name
+		FROM atlas.vm_taxref
+		WHERE cd_nom = cd_ref
 
-CREATE MATERIALIZED VIEW atlas.vm_search_taxon AS 
-SELECT row_number() OVER (ORDER BY t.cd_nom,t.cd_ref,t.search_name)::integer AS fid,
-  t.cd_nom,
-  t.cd_ref,
-  t.search_name,
-  t.nom_valide,
-  t.lb_nom
-FROM (
-  SELECT t_1.cd_nom,
-        t_1.cd_ref,
-        concat(t_1.lb_nom, ' =  <i> ', t_1.nom_valide, '</i>') AS search_name,
-        t_1.nom_valide,
-        t_1.lb_nom
-  FROM atlas.vm_taxref t_1
+		UNION
 
-  UNION
-  SELECT t_1.cd_nom,
-        t_1.cd_ref,
-        concat(t_1.nom_vern, ' =  <i> ', t_1.nom_valide, '</i>' ) AS search_name,
-        t_1.nom_valide,
-        t_1.lb_nom
-  FROM atlas.vm_taxref t_1
-  WHERE t_1.nom_vern IS NOT NULL AND t_1.cd_nom = t_1.cd_ref
-) t
-JOIN atlas.vm_taxons taxons ON taxons.cd_ref = t.cd_ref;
+		-- Synonym scinames
+		SELECT
+			t1.cd_nom,
+			t1.cd_ref,
+			t1.lb_nom AS search_name,
+		    CONCAT(REPLACE(t1.nom_complet_html, t1.lb_auteur, ''), ' =  <b> ', REPLACE(t2.nom_complet_html, t2.lb_auteur, ''), '</b> ', t2.lb_auteur) AS display_name
+		FROM atlas.vm_taxref AS t1
+			JOIN atlas.vm_taxref AS t2
+				ON t1.cd_ref = t2.cd_nom
+		WHERE t1.cd_nom <> t1.cd_ref
+
+		UNION
+
+		-- Vernacular names
+		SELECT
+			v.cd_nom,
+		    v.cd_ref,
+		    v.nom_vern AS search_name,
+		    CONCAT(v.nom_vern, ' =  <b> ', REPLACE(t.nom_complet_html, t.lb_auteur, ''), '</b> ', t.lb_auteur) AS display_name
+		FROM verna_names AS v
+			JOIN atlas.vm_taxref AS t
+				ON t.cd_nom = v.cd_ref
+		WHERE v.nom_vern <> v.lb_nom
+	)
+	SELECT ROW_NUMBER() OVER (ORDER BY n.cd_nom, n.cd_ref, n.search_name)::integer AS fid,
+	  n.cd_nom,
+	  n.cd_ref,
+	  n.search_name,
+	  n.display_name
+	FROM atlas.vm_taxons AS t
+		JOIN names AS n
+			ON t.cd_ref = n.cd_ref ;
 
 CREATE UNIQUE INDEX ON atlas.vm_search_taxon(fid);
 CREATE INDEX ON atlas.vm_search_taxon(cd_nom);
-create INDEX ON atlas.vm_search_taxon(cd_ref);
-
+CREATE INDEX ON atlas.vm_search_taxon(cd_ref);
 CREATE INDEX trgm_idx ON atlas.vm_search_taxon USING GIST (search_name gist_trgm_ops);
-CREATE UNIQUE INDEX ON atlas.vm_search_taxon (cd_nom, search_name);
+CREATE UNIQUE INDEX ON atlas.vm_search_taxon (cd_nom, search_name);
diff --git a/data/update/update_1.6.1to1.6.2.sql b/data/update/update_1.6.1to1.6.2.sql
@@ -43,3 +43,72 @@ CREATE INDEX ON atlas.vm_observations_mailles
 
 CREATE INDEX ON atlas.vm_observations_mailles
     USING btree (id_maille, cd_ref);
+
+
+-- ISSUE #531 & #532
+CREATE EXTENSION IF NOT EXISTS unaccent SCHEMA "public";
+
+-- ISSUE #532
+DROP MATERIALIZED VIEW IF EXISTS atlas.vm_search_taxon ;
+CREATE MATERIALIZED VIEW atlas.vm_search_taxon AS
+	WITH verna_names AS (
+		SELECT DISTINCT
+			cd_nom,
+			lb_nom,
+		    cd_ref,
+		    STRING_TO_TABLE(nom_vern, ', ') AS nom_vern
+		FROM atlas.vm_taxref
+		WHERE nom_vern IS NOT NULL
+			AND cd_nom = cd_ref
+			AND nom_vern <> lb_nom
+	),
+	names AS (
+		-- Chosen scinames
+		SELECT
+			cd_nom,
+			cd_ref,
+			lb_nom AS search_name,
+		    CONCAT('<b>', REPLACE(nom_complet_html, lb_auteur, ''), '</b> ', lb_auteur) AS display_name
+		FROM atlas.vm_taxref
+		WHERE cd_nom = cd_ref
+
+		UNION
+
+		-- Synonym scinames
+		SELECT
+			t1.cd_nom,
+			t1.cd_ref,
+			t1.lb_nom AS search_name,
+		    CONCAT(REPLACE(t1.nom_complet_html, t1.lb_auteur, ''), ' =  <b> ', REPLACE(t2.nom_complet_html, t2.lb_auteur, ''), '</b> ', t2.lb_auteur) AS display_name
+		FROM atlas.vm_taxref AS t1
+			JOIN atlas.vm_taxref AS t2
+				ON t1.cd_ref = t2.cd_nom
+		WHERE t1.cd_nom <> t1.cd_ref
+
+		UNION
+
+		-- Vernacular names
+		SELECT
+			v.cd_nom,
+		    v.cd_ref,
+		    v.nom_vern AS search_name,
+		    CONCAT(v.nom_vern, ' =  <b> ', REPLACE(t.nom_complet_html, t.lb_auteur, ''), '</b> ', t.lb_auteur) AS display_name
+		FROM verna_names AS v
+			JOIN atlas.vm_taxref AS t
+				ON t.cd_nom = v.cd_ref
+		WHERE v.nom_vern <> v.lb_nom
+	)
+	SELECT ROW_NUMBER() OVER (ORDER BY n.cd_nom, n.cd_ref, n.search_name)::integer AS fid,
+	  n.cd_nom,
+	  n.cd_ref,
+	  n.search_name,
+	  n.display_name
+	FROM atlas.vm_taxons AS t
+		JOIN names AS n
+			ON t.cd_ref = n.cd_ref ;
+
+CREATE UNIQUE INDEX ON atlas.vm_search_taxon(fid);
+CREATE INDEX ON atlas.vm_search_taxon(cd_nom);
+CREATE INDEX ON atlas.vm_search_taxon(cd_ref);
+CREATE INDEX trgm_idx ON atlas.vm_search_taxon USING GIST (search_name gist_trgm_ops);
+CREATE UNIQUE INDEX ON atlas.vm_search_taxon (cd_nom, search_name);
diff --git a/docs/changelog.rst b/docs/changelog.rst
@@ -2,6 +2,19 @@
 CHANGELOG
 =========
 
+[Unreleased]
+------------------
+
+⚠️ **Notes de version**
+
+Si vous mettez à jour GeoNature-atlas :
+
+- Exécutez le script SQL de mise à jour de la BDD : https://github.com/PnX-SI/GeoNature-atlas/blob/master/data/update/update_1.6.1to1.6.2.sql
+- Donner les droits à l'utilisateur en lecture seule de l'Atlas (habituellement geonatatlas) :
+  ::
+    GRANT SELECT ON TABLE atlas.vm_search_taxon TO geonatatlas;
+
+
 1.6.1 (2023-10-16)
 ------------------