PnX-SI · jpm-cbna · Mar 23, 2022 · Jun 22, 2023
diff --git a/atlas/configuration/settings.ini.sample b/atlas/configuration/settings.ini.sample
@@ -35,11 +35,11 @@ owner_atlas_pass=monpassachanger
 geonature_source=true
 
 # L'atlas est-il en lien avec le référentiel géographique de GeoNature (ref_geo) ?
-# ATTENTION : Doit être égal à true si geonature_source=true, 
+# ATTENTION : Doit être égal à true si geonature_source=true,
 # ATTENTION : Doit être égal à false si geonature_source=false
 use_ref_geo_gn2=true
 
-# Souhaitez-vous installer le schéma taxonomie de TaxHub dans la BDD de GeoNature-atlas ? 
+# Souhaitez-vous installer le schéma taxonomie de TaxHub dans la BDD de GeoNature-atlas ?
 # false si vous souhaitez utiliser celui de GeoNature en FDW
 # ATTENTION : Doit être true si geonature_source=false
 install_taxonomie=false
@@ -61,6 +61,10 @@ db_source_port=5432
 # Nom de la BDD GeoNature source
 db_source_name=geonature2db
 
+# Taille du nombre d'éléments à récupérer à la fois pour Foreign Data Wrapper (défaut 100)
+# Note : utiliser 1000000 pour une table synthese avec plusieurs millions d'observations.
+db_source_fetch_size=100
+
 # Nom de l'utilisateur atlas dans la BDD GeoNature source (lecture seule)
 atlas_source_user=geonatatlas
 

diff --git a/data/atlas/14.grant.sql b/data/atlas/14.grant.sql
@@ -20,6 +20,7 @@ GRANT ALL ON TABLE spatial_ref_sys TO my_reader_user;*/
 
 GRANT USAGE ON SCHEMA atlas TO my_reader_user;
 
+GRANT SELECT ON TABLE synthese.vm_cor_synthese_area TO my_reader_user
 GRANT SELECT ON TABLE atlas.vm_altitudes TO my_reader_user;
 GRANT SELECT ON TABLE atlas.vm_communes TO my_reader_user;
 GRANT SELECT ON TABLE atlas.vm_observations TO my_reader_user;

diff --git a/data/atlas/2.atlas.vm_observations.sql b/data/atlas/2.atlas.vm_observations.sql
@@ -10,7 +10,8 @@ CREATE MATERIALIZED VIEW atlas.vm_observations AS
         s.the_geom_point,
         s.effectif_total,
         tx.cd_ref,
-        st_asgeojson(st_transform(s.the_geom_point, 4326)) as geojson_point,
+        st_asgeojson(s.the_geom_point) as geojson_point,
+        s.sensitivity,
         s.diffusion_level,
         s.id_dataset
     FROM synthese.syntheseff s

diff --git a/data/atlas/atlas.refresh_materialized_view_data.sql b/data/atlas/atlas.refresh_materialized_view_data.sql
@@ -23,6 +23,8 @@ CREATE OR REPLACE FUNCTION atlas.refresh_materialized_view_data()
 RETURNS VOID AS $$
 BEGIN
 
+  REFRESH MATERIALIZED VIEW CONCURRENTLY synthese.vm_cor_synthese_area;
+
   REFRESH MATERIALIZED VIEW CONCURRENTLY atlas.vm_observations;
   REFRESH MATERIALIZED VIEW CONCURRENTLY atlas.vm_observations_mailles;
   REFRESH MATERIALIZED VIEW CONCURRENTLY atlas.vm_cor_taxon_organism;

diff --git a/data/atlas/without_geonature.sql b/data/atlas/without_geonature.sql
@@ -1,6 +1,6 @@
 CREATE TABLE synthese.syntheseff(
     id_synthese serial PRIMARY KEY,
-    id_organism integer DEFAULT 2, 
+    id_organism integer DEFAULT 2,
     id_dataset integer,
     cd_nom integer,
     insee character(5),
@@ -10,15 +10,16 @@ CREATE TABLE synthese.syntheseff(
     supprime boolean DEFAULT false,
     the_geom_point geometry('POINT',4326),
     effectif_total integer,
-    diffusion_level integer
+    diffusion_level integer,
+    sensitivity integer
 );
 
 INSERT INTO synthese.syntheseff
-(cd_nom, insee, observateurs, altitude_retenue, the_geom_point, effectif_total, diffusion_level)
-VALUES (67111, 05122, 'Mon observateur', 1254, ST_SetSRID( ST_Point( 6, 42.315), 4326), 3, 5);
+(cd_nom, insee, observateurs, altitude_retenue, the_geom_point, effectif_total, diffusion_level, sensitivity)
+VALUES (67111, 05122, 'Mon observateur', 1254, ST_SetSRID( ST_Point( 6, 42.315), 4326), 3, 5, 0);
 INSERT INTO synthese.syntheseff
-(cd_nom, insee, observateurs, altitude_retenue, the_geom_point, effectif_total, diffusion_level)
-VALUES (67111, 05122, 'Mon observateur 3', 940, ST_SetSRID( ST_Point( 6.1, 42.315), 4326), 2, 5);
+(cd_nom, insee, observateurs, altitude_retenue, the_geom_point, effectif_total, diffusion_level, sensitivity)
+VALUES (67111, 05122, 'Mon observateur 3', 940, ST_SetSRID( ST_Point( 6.1, 42.315), 4326), 2, 5, 0);
 
 
 CREATE TABLE gn_meta.cor_dataset_actor (

diff --git a/data/gn2/atlas_synthese.sql b/data/gn2/atlas_synthese.sql
@@ -1,50 +1,90 @@
 -- Creation d'une vue permettant de reproduire le contenu de la table du même nom dans les versions précédentes
 
-CREATE VIEW synthese.syntheseff AS
-WITH areas AS (
+CREATE MATERIALIZED VIEW synthese.vm_cor_synthese_area
+TABLESPACE pg_default
+AS
 	SELECT DISTINCT ON (sa.id_synthese, t.type_code)
-          sa.id_synthese, 
-          sa.id_area, 
-          a.centroid, 
-          st_transform(centroid, 4326) as centroid_4326, 
-          t.type_code
-	FROM synthese.cor_area_synthese sa
-	JOIN ref_geo.l_areas a ON sa.id_area = a.id_area
-	JOIN ref_geo.bib_areas_types t ON a.id_type = t.id_type
-	WHERE type_code IN ('M10', 'COM', 'DEP')
- ),  obs_data AS (
-	SELECT s.id_synthese,
-	    s.cd_nom,
-		s.id_dataset,
-	    s.date_min AS dateobs,
-	    s.observers AS observateurs,
-	    (s.altitude_min + s.altitude_max) / 2 AS altitude_retenue,
-	    CASE
-		WHEN dl.cd_nomenclature = '1' THEN
-			(SELECT centroid_4326 FROM areas a WHERE a.id_synthese = s.id_synthese AND type_code = 'COM' LIMIT 1)
-		WHEN dl.cd_nomenclature = '2' THEN
-			(SELECT centroid_4326 FROM areas a WHERE a.id_synthese = s.id_synthese AND type_code = 'M10' LIMIT 1)
-		WHEN dl.cd_nomenclature = '3' THEN
-			(SELECT centroid_4326 FROM areas a WHERE a.id_synthese = s.id_synthese AND type_code = 'DEP' LIMIT 1)
+		sa.id_synthese,
+		sa.id_area,
+		st_transform(a.centroid, 4326) AS centroid_4326,
+		t.type_code,
+		a.area_code
+	FROM synthese.cor_area_synthese AS sa
+		 JOIN ref_geo.l_areas AS a
+		 	ON (sa.id_area = a.id_area)
+		 JOIN ref_geo.bib_areas_types AS t
+		 	ON (a.id_type = t.id_type)
+	WHERE t.type_code IN ('M10', 'COM', 'DEP')
+WITH DATA;
+
+-- View indexes:
+CREATE UNIQUE INDEX ON synthese.vm_cor_synthese_area (id_synthese, id_area);
+CREATE INDEX ON synthese.vm_cor_synthese_area (type_code);
+
+
+VACUUM ANALYSE synthese.vm_cor_synthese_area;
+
+
+CREATE OR REPLACE FUNCTION atlas.get_blurring_centroid_geom_by_code(code CHARACTER VARYING, idSynthese INTEGER)
+ RETURNS geometry
+ LANGUAGE plpgsql
+ IMMUTABLE
+AS $function$
+	-- Function which return the centroid for a sensitivity or diffusion_level code and a synthese id
+	DECLARE centroid public.geometry;
+
+	BEGIN
+		SELECT INTO centroid csa.centroid_4326
+		FROM synthese.vm_cor_synthese_area AS csa
+		WHERE csa.id_synthese = idSynthese
+			AND csa.type_code = (CASE WHEN code = '1' THEN 'COM' WHEN code = '2' THEN 'M10' WHEN code = '3' THEN 'DEP' END)
+		LIMIT 1 ;
+
+		RETURN centroid ;
+	END;
+$function$
+;
+
+CREATE VIEW synthese.syntheseff AS
+SELECT
+	s.id_synthese,
+	s.id_dataset,
+	s.cd_nom,
+	s.date_min AS dateobs,
+	s.observers AS observateurs,
+	(s.altitude_min + s.altitude_max) / 2 AS altitude_retenue,
+	CASE
+		WHEN (sens.cd_nomenclature::INT >= 1 AND sens.cd_nomenclature::INT <= 3 AND dl.cd_nomenclature::INT >= 1 AND dl.cd_nomenclature::INT <= 3) THEN
+			CASE
+				WHEN (sens.cd_nomenclature::INT >= dl.cd_nomenclature::INT) THEN (
+					atlas.get_blurring_centroid_geom_by_code(sens.cd_nomenclature, s.id_synthese)
+				)
+				WHEN (sens.cd_nomenclature::INT < dl.cd_nomenclature::INT) THEN (
+					atlas.get_blurring_centroid_geom_by_code(dl.cd_nomenclature, s.id_synthese)
+				)
+			END
+		WHEN (sens.cd_nomenclature::INT >= 1 AND sens.cd_nomenclature::INT <= 3) AND (dl.cd_nomenclature::INT < 1 OR dl.cd_nomenclature::INT > 3) THEN (
+			atlas.get_blurring_centroid_geom_by_code(sens.cd_nomenclature, s.id_synthese)
+		)
+		WHEN (dl.cd_nomenclature::INT >= 1 AND dl.cd_nomenclature::INT <= 3) AND (sens.cd_nomenclature::INT < 1 OR sens.cd_nomenclature::INT > 3) THEN (
+			atlas.get_blurring_centroid_geom_by_code(dl.cd_nomenclature, s.id_synthese)
+		)
 		ELSE st_transform(s.the_geom_point, 4326)
-	    END AS the_geom_point,
-	    s.count_min AS effectif_total,
-	    dl.cd_nomenclature::int as diffusion_level
-	   FROM synthese.synthese s
-	   LEFT OUTER JOIN synthese.t_nomenclatures dl ON s.id_nomenclature_diffusion_level = dl.id_nomenclature
-	   LEFT OUTER JOIN synthese.t_nomenclatures st ON s.id_nomenclature_observation_status = st.id_nomenclature
-	  WHERE (NOT dl.cd_nomenclature = '4'::text OR id_nomenclature_diffusion_level IS NULL)   -- Filtre données non diffusable code "4" ou pas de diffusion spécifiée
-		AND st.cd_nomenclature = 'Pr'-- seulement les données présentes (status_observation = )
-)
- SELECT d.id_synthese,
-    d.id_dataset,
-    d.cd_nom,
-    d.dateobs,
-    d.observateurs,
-    d.altitude_retenue,
-    d.the_geom_point,
-    d.effectif_total,
-    c.insee,
-    diffusion_level
-FROM obs_data d
-JOIN atlas.l_communes c ON st_intersects(d.the_geom_point, c.the_geom);
+	END AS the_geom_point,
+	s.count_min AS effectif_total,
+	areas.area_code AS insee,
+	sens.cd_nomenclature AS sensitivity,
+	dl.cd_nomenclature AS diffusion_level
+FROM synthese.synthese s
+	JOIN synthese.vm_cor_synthese_area AS areas
+		ON (s.id_synthese = areas.id_synthese)
+	LEFT JOIN synthese.t_nomenclatures AS sens
+		ON (s.id_nomenclature_sensitivity = sens.id_nomenclature)
+	LEFT JOIN synthese.t_nomenclatures AS dl
+		ON (s.id_nomenclature_diffusion_level = dl.id_nomenclature)
+	LEFT JOIN synthese.t_nomenclatures AS st
+		ON (s.id_nomenclature_observation_status = st.id_nomenclature)
+WHERE areas.type_code = 'COM'
+	AND ( NOT dl.cd_nomenclature = '4' OR s.id_nomenclature_diffusion_level IS NULL )
+	AND ( NOT sens.cd_nomenclature = '4' OR s.id_nomenclature_sensitivity IS NULL )
+	AND st.cd_nomenclature = 'Pr' ;
diff --git a/data/update/update_synthese.sql b/data/update/update_synthese.sql
@@ -0,0 +1,134 @@
+BEGIN;
+
+DROP MATERIALIZED VIEW IF EXISTS synthese.vm_cor_synthese_area;
+
+CREATE MATERIALIZED VIEW synthese.vm_cor_synthese_area
+TABLESPACE pg_default
+AS
+	SELECT DISTINCT ON (sa.id_synthese, t.type_code)
+		sa.id_synthese,
+		sa.id_area,
+		st_transform(a.centroid, 4326) AS centroid_4326,
+		t.type_code,
+		a.area_code
+	FROM synthese.cor_area_synthese AS sa
+		 JOIN ref_geo.l_areas AS a
+		 	ON (sa.id_area = a.id_area)
+		 JOIN ref_geo.bib_areas_types AS t
+		 	ON (a.id_type = t.id_type)
+	WHERE t.type_code IN ('M10', 'COM', 'DEP')
+WITH DATA;
+
+GRANT SELECT ON TABLE synthese.vm_cor_synthese_area TO geonatatlas;
+
+-- View indexes:
+CREATE UNIQUE INDEX ON synthese.vm_cor_synthese_area (id_synthese, id_area);
+CREATE INDEX ON synthese.vm_cor_synthese_area (type_code);
+
+
+CREATE OR REPLACE FUNCTION atlas.get_blurring_centroid_geom_by_code(code CHARACTER VARYING, idSynthese INTEGER)
+ RETURNS geometry
+ LANGUAGE plpgsql
+ IMMUTABLE
+AS $function$
+	-- Function which return the centroid for a sensitivity or diffusion_level code and a synthese id
+	DECLARE centroid geometry;
+
+	BEGIN
+		SELECT INTO centroid csa.centroid_4326
+		FROM synthese.vm_cor_synthese_area AS csa
+		WHERE csa.id_synthese = idSynthese
+			AND csa.type_code = (CASE WHEN code = '1' THEN 'COM' WHEN code = '2' THEN 'M10' WHEN code = '3' THEN 'DEP' END)
+		LIMIT 1 ;
+
+		RETURN centroid ;
+	END;
+$function$
+;
+
+
+DROP VIEW IF EXISTS synthese.syntheseff;
+
+
+CREATE VIEW synthese.syntheseff AS
+SELECT
+	s.id_synthese,
+	s.id_dataset,
+	s.cd_nom,
+	s.date_min AS dateobs,
+	s.observers AS observateurs,
+	(s.altitude_min + s.altitude_max) / 2 AS altitude_retenue,
+	CASE
+		WHEN (sens.cd_nomenclature::INT >= 1 AND sens.cd_nomenclature::INT <= 3 AND dl.cd_nomenclature::INT >= 1 AND dl.cd_nomenclature::INT <= 3) THEN
+			CASE
+				WHEN (sens.cd_nomenclature::INT >= dl.cd_nomenclature::INT) THEN (
+					atlas.get_blurring_centroid_geom_by_code(sens.cd_nomenclature, s.id_synthese)
+				)
+				WHEN (sens.cd_nomenclature::INT < dl.cd_nomenclature::INT) THEN (
+					atlas.get_blurring_centroid_geom_by_code(dl.cd_nomenclature, s.id_synthese)
+				)
+			END
+		WHEN (sens.cd_nomenclature::INT >= 1 AND sens.cd_nomenclature::INT <= 3) AND (dl.cd_nomenclature::INT < 1 OR dl.cd_nomenclature::INT > 3) THEN (
+			atlas.get_blurring_centroid_geom_by_code(sens.cd_nomenclature, s.id_synthese)
+		)
+		WHEN (dl.cd_nomenclature::INT >= 1 AND dl.cd_nomenclature::INT <= 3) AND (sens.cd_nomenclature::INT < 1 OR sens.cd_nomenclature::INT > 3) THEN (
+			atlas.get_blurring_centroid_geom_by_code(dl.cd_nomenclature, s.id_synthese)
+		)
+		ELSE st_transform(s.the_geom_point, 4326)
+	END AS the_geom_point,
+	s.count_min AS effectif_total,
+	areas.area_code AS insee,
+	sens.cd_nomenclature AS sensitivity,
+	dl.cd_nomenclature AS diffusion_level
+FROM synthese.synthese s
+	JOIN synthese.vm_cor_synthese_area AS areas
+		ON (s.id_synthese = areas.id_synthese)
+	LEFT JOIN synthese.t_nomenclatures AS sens
+		ON (s.id_nomenclature_sensitivity = sens.id_nomenclature)
+	LEFT JOIN synthese.t_nomenclatures AS dl
+		ON (s.id_nomenclature_diffusion_level = dl.id_nomenclature)
+	LEFT JOIN synthese.t_nomenclatures AS st
+		ON (s.id_nomenclature_observation_status = st.id_nomenclature)
+WHERE areas.type_code = 'COM'
+	AND ( NOT dl.cd_nomenclature = '4' OR s.id_nomenclature_diffusion_level IS NULL )
+	AND ( NOT sens.cd_nomenclature = '4' OR s.id_nomenclature_sensitivity IS NULL )
+	AND st.cd_nomenclature = 'Pr' ;
+
+
+-- Rafraichissement des vues contenant les données de l'atlas
+CREATE OR REPLACE FUNCTION atlas.refresh_materialized_view_data()
+RETURNS VOID AS $$
+BEGIN
+
+  REFRESH MATERIALIZED VIEW CONCURRENTLY synthese.vm_cor_synthese_area;
+
+  REFRESH MATERIALIZED VIEW CONCURRENTLY atlas.vm_observations;
+  REFRESH MATERIALIZED VIEW CONCURRENTLY atlas.vm_observations_mailles;
+  REFRESH MATERIALIZED VIEW CONCURRENTLY atlas.vm_mois;
+
+  REFRESH MATERIALIZED VIEW CONCURRENTLY atlas.vm_altitudes;
+
+  REFRESH MATERIALIZED VIEW CONCURRENTLY atlas.vm_taxons;
+  REFRESH MATERIALIZED VIEW CONCURRENTLY atlas.vm_cor_taxon_attribut;
+  REFRESH MATERIALIZED VIEW CONCURRENTLY atlas.vm_search_taxon;
+  REFRESH MATERIALIZED VIEW CONCURRENTLY atlas.vm_medias;
+  REFRESH MATERIALIZED VIEW CONCURRENTLY atlas.vm_taxons_plus_observes;
+
+END
+$$ LANGUAGE plpgsql;
+
+
+-- TODO: ajouter au CHANGELOG la nécessité d'executer la commande SQL suivante
+-- où il faut remplacer <my_reader_user> par la bonne valeur :
+-- GRANT SELECT ON TABLE synthese.vm_cor_synthese_area TO <my_reader_user>;
+-- Par défaut, ce script associe les droits à geonatatlas ligne 22.
+
+-- TODO: ajouter au CHANGELOG la possiblité d'ajouter l'option FDW fetch_size
+-- dans le cas des bases avec plusieurs millions d'obs dans la synthese :
+-- ALTER SERVER geonaturedbserver OPTIONS (ADD fetch_size '1000000');
+
+-- TODO: ajouter au CHANGELOG la nécessité de lancer le script : data/update/update_vm_observations.sql
+-- pour prendre en compte le nouveau champ "sensitivity" de la vm_observations.
+-- Ce champ n'est pas encore utilisé par l'interface...
+
+COMMIT;
diff --git a/install_db.sh b/install_db.sh
@@ -95,7 +95,7 @@ if ! database_exists $db_name
             then
                 echo "Adding FDW and connection to the GeoNature parent DB"
                 sudo -u postgres -s psql -d $db_name -c "CREATE EXTENSION IF NOT EXISTS postgres_fdw;"  &>> log/install_db.log
-                sudo -u postgres -s psql -d $db_name -c "CREATE SERVER geonaturedbserver FOREIGN DATA WRAPPER postgres_fdw OPTIONS (host '$db_source_host', dbname '$db_source_name', port '$db_source_port');"  &>> log/install_db.log
+                sudo -u postgres -s psql -d $db_name -c "CREATE SERVER geonaturedbserver FOREIGN DATA WRAPPER postgres_fdw OPTIONS (host '$db_source_host', dbname '$db_source_name', port '$db_source_port', fetch_size '$db_source_fetch_size');"  &>> log/install_db.log
                 sudo -u postgres -s psql -d $db_name -c "ALTER SERVER geonaturedbserver OWNER TO $owner_atlas;"  &>> log/install_db.log
                 sudo -u postgres -s psql -d $db_name -c "CREATE USER MAPPING FOR $owner_atlas SERVER geonaturedbserver OPTIONS (user '$atlas_source_user', password '$atlas_source_pass') ;"  &>> log/install_db.log
         fi