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Ajout profils de taxons #941

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Oct 25, 2021
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Ajout profils de taxons #941

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58029d9
Création des profils d'espèces
DonovanMaillard Jun 17, 2020
e084b57
Complément doc fonctions pour profils
DonovanMaillard Jun 17, 2020
6309bcd
Update admin-manual.rst
DonovanMaillard Jun 17, 2020
e093dc2
Update admin-manual.rst
DonovanMaillard Jun 17, 2020
f20cce4
Mise en forme
DonovanMaillard Jun 17, 2020
42a4187
Suppression des vm et fonctions min_max_for_taxons
DonovanMaillard Jun 17, 2020
6365327
Create 2.4.0to2.4.1.sql
DonovanMaillard Jun 17, 2020
6f795ae
Update CHANGELOG.rst
DonovanMaillard Jun 17, 2020
2c98e84
Update CHANGELOG.rst
DonovanMaillard Jun 17, 2020
71b91e8
Update CHANGELOG.rst
DonovanMaillard Jun 17, 2020
9cd0187
Update CHANGELOG.rst
DonovanMaillard Jun 17, 2020
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314 changes: 314 additions & 0 deletions data/core/profiles.sql
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Original file line number Diff line number Diff line change
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----------
--SCHEMA--
----------
CREATE SCHEMA gn_profiles;

----------
--TABLES--
----------

CREATE TABLE gn_profiles.t_profiles_parameters(
id_profile_parameter serial NOT NULL,
id_organism int4 NULL,
profiles_parameter_name varchar(100) NOT NULL,
profiles_parameter_desc text NULL,
profiles_parameter_value text NOT NULL,
profiles_parameter_extra_value varchar(255) NULL
);


CREATE TABLE gn_profiles.cor_taxons_profiles_parameters(
cd_ref integer,
spatial_precision integer,
temporal_precision_days integer,
active_life_stage boolean DEFAULT false
);


CREATE TABLE gn_profiles.t_altitude_ranges(
id_altitude_range serial,
label_range character varying(50),
alt_min_range integer,
alt_max_range integer
);

---------------
--PRIMARY KEY--
---------------
ALTER TABLE ONLY gn_profiles.t_profiles_parameters ADD CONSTRAINT pk_profiles_parameters PRIMARY KEY (id_profile_parameter);

ALTER TABLE ONLY gn_profiles.t_profiles_parameters ADD CONSTRAINT fk_t_profiles_parameters_bib_organismes FOREIGN KEY (id_organism) REFERENCES utilisateurs.bib_organismes(id_organisme) ON UPDATE CASCADE;

ALTER TABLE ONLY gn_profiles.cor_taxons_profiles_parameters ADD CONSTRAINT pk_taxons_profiles_parameters PRIMARY KEY (cd_ref);

ALTER TABLE ONLY gn_profiles.t_altitude_ranges ADD CONSTRAINT pk_altitude_range PRIMARY KEY (id_altitude_range);


-----------------
-- CONSTRAINTS --
-----------------

ALTER TABLE gn_profiles.cor_taxons_profiles_parameters ADD CONSTRAINT check_t_param_profiles_cdref_is_valid CHECK (taxonomie.check_is_cd_ref(cd_ref)) NOT VALID;


------------------
-- DEFAULT DATA --
------------------

INSERT INTO gn_profiles.cor_taxons_profiles_parameters(cd_ref, spatial_precision, temporal_precision_days, active_life_stage)
SELECT
DISTINCT t.cd_ref,
2000,
10,
false
FROM taxonomie.taxref t
WHERE id_rang='KD';


INSERT INTO gn_profiles.t_altitude_ranges(label_range, alt_min_range, alt_max_range)
VALUES
('Etages planitiaires et collinéens',0,700),
('Etages montagnards et subalpins',701,2000),
('Etages alpins et nivaux',2001,4811);

-- Ajout d'un nouveau paramètre à GeoNature pour définir le niveau de validation des données à utiliser dans le calcul des profils
INSERT INTO gn_profiles.t_profiles_parameters(id_organism, profiles_parameter_name, profiles_parameter_desc, profiles_parameter_value)
SELECT
0,
'id_valid_status_for_profiles',
'Liste des id_nomenclature du statut de validation permettant de définir les données à prendre en compte dans le calcul des profils d''espèces. A renseigner sous forme de liste id1,id2,id3.',
string_agg(DISTINCT n.id_nomenclature::text, ','::text)
FROM ref_nomenclatures.t_nomenclatures n
WHERE n.id_type=(SELECT id_type FROM ref_nomenclatures.bib_nomenclatures_types bnt WHERE mnemonique='STATUT_VALID')
AND n.cd_nomenclature IN ('1','2') -- Commenter pour considérer l'ensemble des données;
;


-- Ajout d'un paramètre permettant de définir à partir de combien de données une phénologie est jugée valide/fiable
INSERT INTO gn_profiles.t_profiles_parameters(id_organism, profiles_parameter_name, profiles_parameter_desc, profiles_parameter_value)
VALUES (
0,
'min_occurrence_check_profile_phenology',
'Nombre minimal d''occurrences requis dans les profils d''espèces pour considérer une période phénologique comme valide',
1
);


-------------
--FUNCTIONS--
-------------

-- Fonctions dédiées à la comparaison des données avec leur profil d'espèce dans gn_profiles
CREATE OR REPLACE FUNCTION gn_profiles.get_profiles_parameters(mycdnom integer)
RETURNS TABLE (cd_ref integer, spatial_precision integer, temporal_precision_days integer, active_life_stage boolean, distance smallint)
LANGUAGE plpgsql
IMMUTABLE
AS $function$
-- fonction permettant de récupérer les paramètres les plus adaptés (définis au plus proche du taxon) pour calculer le profil d'un taxon donné
-- par exemple, s'il existe des paramètres pour les "Animalia" des paramètres pour le renard, les paramètres du renard surcoucheront les paramètres Animalia pour cette espèce
DECLARE
my_cd_ref integer := t.cd_ref FROM taxonomie.taxref t WHERE t.cd_nom=mycdnom;
BEGIN
RETURN QUERY
WITH all_parameters AS (
SELECT param.cd_ref, param.spatial_precision, param.temporal_precision_days, param.active_life_stage, parents.distance
FROM gn_profiles.cor_taxons_profiles_parameters param
JOIN taxonomie.find_all_taxons_parents(my_cd_ref) parents ON parents.cd_nom=param.cd_ref)
SELECT * FROM all_parameters all_param WHERE all_param.distance=(SELECT min(all_param2.distance) FROM all_parameters all_param2)
;
END;
$function$
;


CREATE OR REPLACE FUNCTION gn_profiles.check_profile_distribution(myidsynthese integer)
RETURNS boolean
LANGUAGE plpgsql
IMMUTABLE
AS $function$
--fonction permettant de vérifier la cohérence d'une donnée d'occurrence en s'assurant que sa localisation est totalement incluse dans l'aire d'occurrences valide définie par le profil du taxon en question
DECLARE
mycdref integer := t.cd_ref FROM taxonomie.taxref t JOIN gn_synthese.synthese s ON s.cd_nom=t.cd_nom WHERE s.id_synthese=myidsynthese;
valid_geom geometry := vp.valid_distribution FROM gn_profiles.vm_valid_profiles vp WHERE vp.cd_ref=mycdref;
check_geom geometry := s.the_geom_local FROM gn_synthese.synthese s WHERE s.id_synthese=myidsynthese ;
BEGIN
IF ST_Contains(valid_geom, check_geom)
THEN
RETURN true;
ELSE
RETURN false;
END IF;
END;
$function$
;


CREATE OR REPLACE FUNCTION gn_profiles.check_profile_phenology(myidsynthese integer)
RETURNS boolean
LANGUAGE plpgsql
IMMUTABLE
AS $function$
--fonction permettant de vérifier la cohérence d'une donnée d'occurrence en s'assurant que sa phénologie (dates, altitude, stade de vie selon les paramètres)
--correspond bien à la phénologie valide définie par le profil du taxon en question
--La fonction renvoie 'false' pour les données trop imprécises (durée d'observation supérieure à la précision temporelle définie dans les paramètres des profils).
DECLARE
valid_count integer;
BEGIN
valid_count:=
(WITH myphenology AS (
SELECT DISTINCT
t.cd_ref AS cd_ref,
unnest(ARRAY[ceiling(EXTRACT(DOY FROM s.date_min)/p.temporal_precision_days)::integer, ceiling(EXTRACT(DOY FROM s.date_max)/p.temporal_precision_days)::integer]) AS period,
CASE
WHEN p.active_life_stage=true THEN s.id_nomenclature_life_stage
ELSE NULL
END AS id_nomenclature_life_stage,
tar.id_altitude_range AS id_altitude_range
FROM gn_synthese.synthese s
LEFT JOIN taxonomie.taxref t ON s.cd_nom=t.cd_nom
LEFT JOIN gn_profiles.t_altitude_ranges tar ON s.altitude_min <= tar.alt_max_range AND s.altitude_max >= tar.alt_min_range
CROSS JOIN gn_profiles.get_profiles_parameters(s.cd_nom) p
WHERE s.id_synthese=myidsynthese
AND p.temporal_precision_days IS NOT NULL
AND p.spatial_precision IS NOT NULL
AND p.active_life_stage IS NOT NULL
AND DATE_part('day', s.date_max-s.date_min)<p.temporal_precision_days
AND ST_MaxDistance(ST_centroid(s.the_geom_local), s.the_geom_local)<p.spatial_precision
GROUP BY t.cd_ref, period, CASE WHEN p.active_life_stage=true THEN s.id_nomenclature_life_stage ELSE NULL END ,id_altitude_range)

SELECT max(ctp.count_valid_data)
FROM gn_profiles.vm_cor_taxon_phenology ctp, myphenology
WHERE ctp.cd_ref=myphenology.cd_ref
AND ctp.period=myphenology.period
AND (ctp.id_nomenclature_life_stage=myphenology.id_nomenclature_life_stage OR (ctp.id_nomenclature_life_stage IS NULL AND myphenology.id_nomenclature_life_stage IS NULL))
AND ctp.id_altitude_range=myphenology.id_altitude_range);

IF valid_count>=(SELECT profiles_parameter_value::integer FROM gn_profiles.t_profiles_parameters WHERE profiles_parameter_name='min_occurrence_check_profile_phenology')
THEN
RETURN true;
ELSE
RETURN false;
END IF;
END;
$function$
;


CREATE OR REPLACE FUNCTION gn_profiles.check_profile_altitudes(myidsynthese integer)
RETURNS boolean
LANGUAGE plpgsql
IMMUTABLE
AS $function$
--fonction permettant de vérifier la cohérence d'une donnée d'occurrence en s'assurant que son altitude se trouve entièrement comprise dans la fourchette altitudinale valide du taxon en question
DECLARE
mycdref integer := t.cd_ref FROM taxonomie.taxref t JOIN gn_synthese.synthese s ON s.cd_nom=t.cd_nom WHERE s.id_synthese=myidsynthese;
BEGIN
IF (SELECT altitude_min FROM gn_synthese.synthese WHERE id_synthese=myidsynthese)>=(SELECT altitude_min FROM gn_profiles.vm_valid_profiles WHERE cd_ref=mycdref)
AND (SELECT altitude_max FROM gn_synthese.synthese WHERE id_synthese=myidsynthese)<=(SELECT altitude_max FROM gn_profiles.vm_valid_profiles WHERE cd_ref=mycdref)
THEN
RETURN true;
ELSE
RETURN false;
END IF;
END;
$function$
;


CREATE OR REPLACE FUNCTION gn_profiles.get_profile_score(myidsynthese integer)
RETURNS integer
LANGUAGE plpgsql
IMMUTABLE
AS $function$
--fonction permettant de vérifier la cohérence d'une donnée d'occurrence en s'assurant que sa localisation est totalement incluse dans l'aire d'occurrences valide définie par le profil du taxon en question
DECLARE
score integer
BEGIN
SELECT INTO score gn_profiles.check_profile_distribution(myidsynthese)::int + gn_profiles.check_profile_phenology(myidsynthese)::int + gn_profiles.check_profile_altitudes(myidsynthese)::int;
RETURN score;
END;
$function$
;

----------------------------------
-- VIEWS AND MATERIALIZED VIEWS --
----------------------------------
CREATE MATERIALIZED VIEW gn_profiles.vm_valid_profiles AS
SELECT DISTINCT
t.cd_ref AS cd_ref,
st_union(st_buffer(s.the_geom_local, COALESCE(p.spatial_precision, 1))) AS valid_distribution,
min(s.altitude_min) AS altitude_min,
max(s.altitude_max) AS altitude_max,
min(s.date_min) AS first_valid_data,
max(s.date_max) AS last_valid_data,
count(s.*) AS count_valid_data
FROM gn_synthese.synthese s
LEFT JOIN taxonomie.taxref t ON s.cd_nom=t.cd_nom
CROSS JOIN gn_profiles.get_profiles_parameters(s.cd_nom) p
WHERE p.spatial_precision IS NOT NULL AND ST_MaxDistance(ST_centroid(s.the_geom_local), s.the_geom_local)<p.spatial_precision
AND s.id_nomenclature_valid_status IN (SELECT regexp_split_to_table(profiles_parameter_value, ',')::integer FROM gn_profiles.t_profiles_parameters WHERE profiles_parameter_name='id_valid_status_for_profiles')
GROUP BY t.cd_ref;


CREATE MATERIALIZED VIEW gn_profiles.vm_cor_taxon_phenology AS
SELECT DISTINCT
t.cd_ref AS cd_ref,
unnest(ARRAY[ceiling(EXTRACT(DOY FROM s.date_min)/p.temporal_precision_days)::integer, ceiling(EXTRACT(DOY FROM s.date_max)/p.temporal_precision_days)::integer]) AS period,
CASE
WHEN p.active_life_stage=true THEN s.id_nomenclature_life_stage
ELSE NULL
END AS id_nomenclature_life_stage,
tar.id_altitude_range AS id_altitude_range,
count(s.*) AS count_valid_data
FROM gn_synthese.synthese s
LEFT JOIN taxonomie.taxref t ON s.cd_nom=t.cd_nom
LEFT JOIN gn_profiles.t_altitude_ranges tar ON s.altitude_min <= tar.alt_max_range AND s.altitude_max >= tar.alt_min_range
CROSS JOIN gn_profiles.get_profiles_parameters(s.cd_nom) p
WHERE p.temporal_precision_days IS NOT NULL
AND p.spatial_precision IS NOT NULL
AND p.active_life_stage IS NOT NULL
AND DATE_part('day', s.date_max-s.date_min)<p.temporal_precision_days
AND ST_MaxDistance(ST_centroid(s.the_geom_local), s.the_geom_local)<p.spatial_precision
AND s.id_nomenclature_valid_status IN (SELECT regexp_split_to_table(profiles_parameter_value, ',')::integer FROM gn_profiles.t_profiles_parameters WHERE profiles_parameter_name='id_valid_status_for_profiles')
AND s.altitude_min IS NOT NULL
AND s.altitude_max IS NOT NULL
GROUP BY t.cd_ref, period, CASE WHEN p.active_life_stage=true THEN s.id_nomenclature_life_stage ELSE NULL END ,id_altitude_range;


CREATE VIEW gn_profiles.v_checks_consistancy_data_profiles AS
SELECT
s.id_synthese AS id_synthese,
s.unique_id_sinp AS id_sinp,
t.cd_ref AS cd_ref,
t.lb_nom AS nom_taxon,
gn_profiles.check_profile_distribution(id_synthese) AS valid_distribution,
gn_profiles.check_profile_phenology(id_synthese) AS valid_phenology,
gn_profiles.check_profile_altitudes(id_synthese) AS valid_altitude,
gn_profiles.get_profile_score(id_synthese) AS score,
n.label_default AS valid_status
FROM gn_synthese.synthese s
LEFT JOIN ref_nomenclatures.t_nomenclatures n ON s.id_nomenclature_valid_status = n.id_nomenclature
LEFT JOIN taxonomie.taxref t ON s.cd_nom=t.cd_nom;


CREATE VIEW gn_profiles.v_decode_profiles_parameters AS
SELECT
p.cd_ref,
t.lb_nom,
t.id_rang,
p.spatial_precision,
p.temporal_precision_days,
p.active_life_stage
FROM gn_profiles.cor_taxons_profiles_parameters p
LEFT JOIN taxonomie.taxref t ON p.cd_ref=t.cd_ref;


-----------
-- INDEX --
-----------

CREATE INDEX index_vm_valid_profiles_cd_ref
ON gn_profiles.vm_valid_profiles (cd_ref);

CREATE INDEX index_vm_cor_taxon_phenology_cd_ref
ON gn_profiles.vm_cor_taxon_phenology (cd_ref);
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