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Improve taxon search box #557

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286fa35
feat: improve taxons search (unaccent, better display)
jpm-cbna May 2, 2024
d6deb5e
Merge branch 'develop' into feat/taxons-search
jpm-cbna May 20, 2024
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2 changes: 1 addition & 1 deletion atlas/atlasAPI.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)

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1 change: 1 addition & 0 deletions atlas/modeles/entities/vmSearchTaxon.py
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Expand Up @@ -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,
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26 changes: 13 additions & 13 deletions atlas/modeles/repositories/vmSearchTaxonRepository.py
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Expand Up @@ -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
Expand All @@ -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]
84 changes: 56 additions & 28 deletions data/atlas/5.atlas.vm_search_taxon.sql
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@@ -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
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Avec SRING_TO_TABLE on ne pourra plus rechercher sur tous les noms vernaculaires, je pense que c'est dommage. Il me semble que que le split n'était fait que sur la fiche espèce, pour de l'affichage

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oups j'avais pas vu la différence entre search_name et display_name

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Normalement, c'est fonctionnel. J'ai mis en prod cette PR sur les 2 Atlas des SINP PACA et AURA, si tu veux vérifier certains points : https://nature.silene.eu/ et https://atlas.biodiversite-auvergne-rhone-alpes.fr/

Est ce que tu penses que j'ai loupé quelque chose ?

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);
69 changes: 69 additions & 0 deletions data/update/update_1.6.1to1.6.2.sql
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Expand Up @@ -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
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Il est également nécessaire de donner les droits à l'utilisateur en lecture seule de l'Atlas (habituellement geonatatlas) :

GRANT SELECT ON TABLE atlas.vm_search_taxon TO geonatatlas;

Vue que le nom de cet utilisateur est configurable et que l'accès au paramètre de config n'est pas possible, comment doit-on procéder ?

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Je mettrais une note spécifique dans le changelog, indiquant la commande à lancer manuellement

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Je mettrais une note spécifique dans le changelog, indiquant la commande à lancer manuellement

Tu veux dire que je peux modifier le fichier https://github.com/PnX-SI/GeoNature-atlas/blob/master/docs/changelog.rst ? Ou c'est à faire uniquement lors de la création de la nouvelle release ?

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Oui c'est bien de compléter le Changelog au fur et à mesure dans les PR, ça rend les merge un peu plus complexe, mais on s'en charge.

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);
18 changes: 18 additions & 0 deletions docs/changelog.rst
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Expand Up @@ -2,6 +2,24 @@
CHANGELOG
=========

[Unreleased]
------------------

🐛 **Optimisations**

- Amélioration de la "recherche par espèces" (#532 par @jpm-cbna)


⚠️ **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)
------------------

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