Feat Synthese: add status, red lists filters

Improve display of form fields used.
Put taxonomic rank fields in a section.
Restore correct order for CorAreaSynthese.
Dynamic tree now avalaible in ngOnInit.
Use "bdc_statut_cor_text_area" name for variable linking tables between
ref_geo and taxonomie.
Use correct field names and css class.
Install Departements before Taxref.

Resolve #1492.

backend/geonature/core/gn_synthese/models.py

@@ -129,6 +129,16 @@ def filter_by_scope(self, scope, user=None):
         return self
 
 
+@serializable
+class CorAreaSynthese(DB.Model):
+    __tablename__ = "cor_area_synthese"
+    __table_args__ = {"schema": "gn_synthese", "extend_existing": True}
+    id_synthese = DB.Column(
+        DB.Integer, ForeignKey("gn_synthese.synthese.id_synthese"), primary_key=True
+    )
+    id_area = DB.Column(DB.Integer, ForeignKey("ref_geo.l_areas.id_area"), primary_key=True)
+
+
 @serializable
 @geoserializable(geoCol="the_geom_4326", idCol="id_synthese")
 @shapeserializable
@@ -335,16 +345,6 @@ def has_instance_permission(self, scope):
             return True
 
 
-@serializable
-class CorAreaSynthese(DB.Model):
-    __tablename__ = "cor_area_synthese"
-    __table_args__ = {"schema": "gn_synthese", "extend_existing": True}
-    id_synthese = DB.Column(
-        DB.Integer, ForeignKey("gn_synthese.synthese.id_synthese"), primary_key=True
-    )
-    id_area = DB.Column(DB.Integer, ForeignKey(LAreas.id_area), primary_key=True)
-
-
 @serializable
 class DefaultsNomenclaturesValue(DB.Model):
     __tablename__ = "defaults_nomenclatures_value"

backend/geonature/core/gn_synthese/routes.py

@@ -98,11 +98,13 @@ def get_observations_for_web(info_role):
 
     :param str info_role: Role used to get the associated filters, **TBC**
     :qparam str limit: Limit number of synthese returned. Defaults to NB_MAX_OBS_MAP.
+    :qparam str cd_ref_parent: filtre tous les taxons enfants d'un TAXREF cd_ref.
     :qparam str cd_ref: Filter by TAXREF cd_ref attribute
     :qparam str taxonomy_group2_inpn: Filter by TAXREF group2_inpn attribute
     :qparam str taxonomy_id_hab: Filter by TAXREF id_habitat attribute
-    :qparam str taxonomy_lr: Filter by TAXREF cd_ref attribute
-    :qparam str taxhub_attribut*: Generig TAXREF filter, given attribute & value
+    :qparam str taxhub_attribut*: filtre générique TAXREF en fonction de l'attribut et de la valeur.
+    :qparam str *_red_lists: filtre générique de listes rouges. Filtre sur les valeurs. Voir config.
+    :qparam str *_status: filtre générique de statuts (BdC Statuts). Filtre sur les types. Voir config.
     :qparam str observers: Filter on observer
     :qparam str id_organism: Filter on organism
     :qparam str date_min: Start date
@@ -290,6 +292,7 @@ def get_one_synthese(scope, id_synthese):
 
     if not synthese.has_instance_permission(scope=scope):
         raise Forbidden()
+
     geofeature = synthese.as_geofeature(fields=Synthese.nomenclature_fields + fields)
     return jsonify(geofeature)
 
@@ -440,6 +443,7 @@ def export_observations_web(info_role):
     cruved = cruved_scope_for_user_in_module(info_role.id_role, module_code="SYNTHESE")[0]
     if cruved["R"] > cruved["E"]:
         synthese_query_class.filter_query_with_cruved(info_role)
+
     results = DB.session.execute(
         synthese_query_class.query.limit(current_app.config["SYNTHESE"]["NB_MAX_OBS_EXPORT"])
     )

backend/geonature/core/gn_synthese/utils/query_select_sqla.py

@@ -8,6 +8,8 @@
 import datetime
 import uuid
 
+from flask import current_app
+
 from sqlalchemy import func, or_, and_, select
 from sqlalchemy.sql import text
 from sqlalchemy.orm import aliased
@@ -16,7 +18,7 @@
 from geoalchemy2.shape import from_shape
 
 from geonature.utils.env import DB
-from geonature.core.taxonomie.models import Taxref, CorTaxonAttribut, TaxrefLR
+from geonature.core.taxonomie.models import TaxrefLR
 from geonature.core.gn_synthese.models import (
     CorObserverSynthese,
     CorAreaSynthese,
@@ -28,6 +30,15 @@
     TDatasets,
 )
 from geonature.utils.errors import GeonatureApiError
+from apptax.taxonomie.models import (
+    Taxref,
+    CorTaxonAttribut,
+    TaxrefBdcStatutTaxon,
+    bdc_statut_cor_text_area,
+    TaxrefBdcStatutCorTextValues,
+    TaxrefBdcStatutText,
+    TaxrefBdcStatutValues,
+)
 
 
 class SyntheseQuery:
@@ -339,6 +350,95 @@ def filter_other_filters(self):
             if colname.startswith("area"):
                 self.add_join(CorAreaSynthese, CorAreaSynthese.id_synthese, self.model.id_synthese)
                 self.query = self.query.where(CorAreaSynthese.id_area.in_(value))
+            elif colname.endswith("_red_lists"):
+                red_list_id = colname.replace("_red_lists", "")
+                all_red_lists_cfg = current_app.config["SYNTHESE"]["RED_LISTS_FILTERS"]
+                red_list_cfg = next(
+                    (item for item in all_red_lists_cfg if item["id"] == red_list_id), None
+                )
+                red_list_cte = (
+                    select([TaxrefBdcStatutTaxon.cd_ref, bdc_statut_cor_text_area.c.id_area])
+                    .select_from(
+                        TaxrefBdcStatutTaxon.__table__.join(
+                            TaxrefBdcStatutCorTextValues,
+                            TaxrefBdcStatutCorTextValues.id_value_text
+                            == TaxrefBdcStatutTaxon.id_value_text,
+                        )
+                        .join(
+                            TaxrefBdcStatutText,
+                            TaxrefBdcStatutText.id_text == TaxrefBdcStatutCorTextValues.id_text,
+                        )
+                        .join(
+                            TaxrefBdcStatutValues,
+                            TaxrefBdcStatutValues.id_value
+                            == TaxrefBdcStatutCorTextValues.id_value,
+                        )
+                        .join(
+                            bdc_statut_cor_text_area,
+                            bdc_statut_cor_text_area.c.id_text == TaxrefBdcStatutText.id_text,
+                        )
+                    )
+                    .where(TaxrefBdcStatutValues.code_statut.in_(value))
+                    .where(TaxrefBdcStatutText.cd_type_statut == red_list_cfg["status_type"])
+                    .where(TaxrefBdcStatutText.enable == True)
+                    .cte(name=f"{red_list_id}_red_list")
+                )
+                cas_red_list = aliased(CorAreaSynthese)
+                self.add_join(cas_red_list, cas_red_list.id_synthese, self.model.id_synthese)
+                self.add_join(Taxref, Taxref.cd_nom, self.model.cd_nom)
+                self.add_join_multiple_cond(
+                    red_list_cte,
+                    [
+                        red_list_cte.c.cd_ref == Taxref.cd_ref,
+                        red_list_cte.c.id_area == cas_red_list.id_area,
+                    ],
+                )
+
+            elif colname.endswith("_status"):
+                status_id = colname.replace("_status", "")
+                all_status_cfg = current_app.config["SYNTHESE"]["STATUS_FILTERS"]
+                status_cfg = next(
+                    (item for item in all_status_cfg if item["id"] == status_id), None
+                )
+                # Check if a checkbox was used.
+                if (
+                    isinstance(value, list)
+                    and value[0] == True
+                    and len(status_cfg["status_types"]) == 1
+                ):
+                    value = status_cfg["status_types"]
+                status_cte = (
+                    select([TaxrefBdcStatutTaxon.cd_ref, bdc_statut_cor_text_area.c.id_area])
+                    .select_from(
+                        TaxrefBdcStatutTaxon.__table__.join(
+                            TaxrefBdcStatutCorTextValues,
+                            TaxrefBdcStatutCorTextValues.id_value_text
+                            == TaxrefBdcStatutTaxon.id_value_text,
+                        )
+                        .join(
+                            TaxrefBdcStatutText,
+                            TaxrefBdcStatutText.id_text == TaxrefBdcStatutCorTextValues.id_text,
+                        )
+                        .join(
+                            bdc_statut_cor_text_area,
+                            bdc_statut_cor_text_area.c.id_text == TaxrefBdcStatutText.id_text,
+                        )
+                    )
+                    .where(TaxrefBdcStatutText.cd_type_statut.in_(value))
+                    .where(TaxrefBdcStatutText.enable == True)
+                    .distinct()
+                    .cte(name=f"{status_id}_status")
+                )
+                cas_status = aliased(CorAreaSynthese)
+                self.add_join(cas_status, cas_status.id_synthese, self.model.id_synthese)
+                self.add_join(Taxref, Taxref.cd_nom, self.model.cd_nom)
+                self.add_join_multiple_cond(
+                    status_cte,
+                    [
+                        status_cte.c.cd_ref == Taxref.cd_ref,
+                        status_cte.c.id_area == cas_status.id_area,
+                    ],
+                )
             elif colname.startswith("id_"):
                 col = getattr(self.model.__table__.columns, colname)
                 self.query = self.query.where(col.in_(value))

backend/geonature/tests/test_synthese.py

@@ -188,6 +188,32 @@ def test_get_observations_for_web(self, users, synthese_data, taxon_attribut):
         validate_json(instance=r.json, schema=schema)
         assert len(r.json["features"]) >= 2
 
+        # test status lr
+        query_string = {"regulations_status": ["REGLLUTTE"]}
+        r = self.client.get(url, query_string=query_string)
+        assert r.status_code == 200
+        # test status znieff
+        query_string = {"znief_status": True}
+        r = self.client.get(url, query_string=query_string)
+        assert r.status_code == 200
+        # test status protection
+        query_string = {"protections_status": ["PN"]}
+        r = self.client.get(url, query_string=query_string)
+        assert r.status_code == 200
+        # test LR
+        query_string = {"worldwide_red_lists": ["LC"]}
+        r = self.client.get(url, query_string=query_string)
+        assert r.status_code == 200
+        query_string = {"european_red_lists": ["LC"]}
+        r = self.client.get(url, query_string=query_string)
+        assert r.status_code == 200
+        query_string = {"national_red_lists": ["LC"]}
+        r = self.client.get(url, query_string=query_string)
+        assert r.status_code == 200
+        query_string = {"regional_red_lists": ["LC"]}
+        r = self.client.get(url, query_string=query_string)
+        assert r.status_code == 200
+
     def test_get_synthese_data_cruved(self, app, users, synthese_data, datasets):
         set_logged_user_cookie(self.client, users["self_user"])
 

backend/geonature/utils/config_schema.py

@@ -255,9 +255,76 @@ class GnFrontEndConf(Schema):
 
 
 class Synthese(Schema):
+    # --------------------------------------------------------------------
+    # SYNTHESE - SEARCH FORM
     AREA_FILTERS = fields.List(
         fields.Dict, load_default=[{"label": "Communes", "type_code": "COM"}]
     )
+    # Nombre de résultat à afficher pour la rechercher autocompleté de taxon
+    TAXON_RESULT_NUMBER = fields.Integer(load_default=20)
+    # Afficher ou non l'arbre taxonomique
+    DISPLAY_TAXON_TREE = fields.Boolean(load_default=True)
+    # Switch the observer form input in free text input (true) or in select input (false)
+    SEARCH_OBSERVER_WITH_LIST = fields.Boolean(load_default=False)
+    # Id of the observer list -- utilisateurs.t_menus
+    ID_SEARCH_OBSERVER_LIST = fields.Integer(load_default=1)
+    # Regulatory or not status list of fields
+    STATUS_FILTERS = fields.List(
+        fields.Dict,
+        missing=[
+            {
+                "id": "protections",
+                "show": True,
+                "display_name": "Taxons protégés",
+                "status_types": ["PN", "PR", "PD"],
+            },
+            {
+                "id": "regulations",
+                "show": True,
+                "display_name": "Taxons réglementés",
+                "status_types": ["REGLII", "REGLLUTTE", "REGL", "REGLSO"],
+            },
+            {
+                "id": "znief",
+                "show": True,
+                "display_name": "Espèces déterminantes ZNIEFF",
+                "status_types": ["ZDET"],
+            },
+        ],
+    )
+    # Red lists list of fields
+    RED_LISTS_FILTERS = fields.List(
+        fields.Dict,
+        missing=[
+            {
+                "id": "worldwide",
+                "show": True,
+                "display_name": "Liste rouge mondiale",
+                "status_type": "LRM",
+            },
+            {
+                "id": "european",
+                "show": True,
+                "display_name": "Liste rouge européenne",
+                "status_type": "LRE",
+            },
+            {
+                "id": "national",
+                "show": True,
+                "display_name": "Liste rouge nationale",
+                "status_type": "LRN",
+            },
+            {
+                "id": "regional",
+                "show": True,
+                "display_name": "Liste rouge régionale",
+                "status_type": "LRR",
+            },
+        ],
+    )
+
+    # --------------------------------------------------------------------
+    # SYNTHESE - OBSERVATIONS LIST
     # Listes des champs renvoyés par l'API synthese '/synthese'
     # Si on veut afficher des champs personnalisés dans le frontend (paramètre LIST_COLUMNS_FRONTEND) il faut
     # d'abbord s'assurer que ces champs sont bien renvoyé par l'API !
@@ -267,6 +334,9 @@ class Synthese(Schema):
     )
     # Colonnes affichées sur la liste des résultats de la sytnthese
     LIST_COLUMNS_FRONTEND = fields.List(fields.Dict, load_default=DEFAULT_LIST_COLUMN)
+
+    # --------------------------------------------------------------------
+    # SYNTHESE - DOWNLOADS (AKA EXPORTS)
     EXPORT_COLUMNS = fields.List(fields.String(), load_default=DEFAULT_EXPORT_COLUMNS)
     # Certaines colonnes sont obligatoires pour effectuer les filtres CRUVED
     EXPORT_ID_SYNTHESE_COL = fields.String(load_default="id_synthese")
@@ -279,28 +349,28 @@ class Synthese(Schema):
     EXPORT_METADATA_ACTOR_COL = fields.String(load_default="acteurs")
     # Formats d'export disponibles ["csv", "geojson", "shapefile", "gpkg"]
     EXPORT_FORMAT = fields.List(fields.String(), load_default=["csv", "geojson", "shapefile"])
-    # Nombre de résultat à afficher pour la rechercher autocompleté de taxon
-    TAXON_RESULT_NUMBER = fields.Integer(load_default=20)
+    # Nombre max d'observation dans les exports
+    NB_MAX_OBS_EXPORT = fields.Integer(load_default=50000)
+
+    # --------------------------------------------------------------------
+    # SYNTHESE - OBSERVATION DETAILS
     # Liste des id attributs Taxhub à afficher sur la fiche détaile de la synthese
     # et sur les filtres taxonomiques avancés
     ID_ATTRIBUT_TAXHUB = fields.List(fields.Integer(), load_default=[102, 103])
-    # nom des colonnes de la table gn_synthese.synthese que l'on veux retirer des filres dynamiques
-    # et de la modale d'information détaillée d'une observation
-    # example = "[non_digital_proof]"
+    # Display email on synthese and validation info obs modal
+    DISPLAY_EMAIL = fields.Boolean(load_default=True)
+
+    # --------------------------------------------------------------------
+    # SYNTHESE - SHARED PARAMETERS
+    # Nom des colonnes de la table gn_synthese.synthese que l'on veux retirer des filtres dynamiques
+    # et de la modale d'information détaillée d'une observation example = "[non_digital_proof]"
     EXCLUDED_COLUMNS = fields.List(fields.String(), load_default=[])
-    # Afficher ou non l'arbre taxonomique
-    DISPLAY_TAXON_TREE = fields.Boolean(load_default=True)
-    # Switch the observer form input in free text input (true) or in select input (false)
-    SEARCH_OBSERVER_WITH_LIST = fields.Boolean(load_default=False)
-    # id of the observer list -- utilisateurs.t_menus
-    ID_SEARCH_OBSERVER_LIST = fields.Integer(load_default=1)
+
     # Nombre max d'observation à afficher sur la carte
     NB_MAX_OBS_MAP = fields.Integer(load_default=50000)
-    # clusteriser les layers sur la carte
+    # Clusteriser les layers sur la carte
     ENABLE_LEAFLET_CLUSTER = fields.Boolean(load_default=True)
-    # Nombre max d'observation dans les exports
-    NB_MAX_OBS_EXPORT = fields.Integer(load_default=50000)
-    # Nombre des "dernières observations" affiché à l'arrive sur la synthese
+    # Nombre des "dernières observations" affichées à l'arrivée sur la synthese
     NB_LAST_OBS = fields.Integer(load_default=100)
 
     # Display email on synthese and validation info obs modal

config/default_config.toml.example

@@ -199,9 +199,9 @@ MAIL_ON_ERROR = false
     ZOOM_ON_CLICK = 16
 
     # Restreindre la recherche OpenStreetMap (sur la carte dans l'encart "Rechercher un lieu")
-    # à certains pays. Les pays doivent être au format ISO_3166-1 : 
+    # à certains pays. Les pays doivent être au format ISO_3166-1 :
     # https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2 et séparés par une virgule.
-    # Exemple : OSM_RESTRICT_COUNTRY_CODES = "fr,es,be,ch" (Restreint à France, Espagne, Belgique 
+    # Exemple : OSM_RESTRICT_COUNTRY_CODES = "fr,es,be,ch" (Restreint à France, Espagne, Belgique
     # et Suisse)
     # Laisser à null pour n'avoir aucune restriction
     OSM_RESTRICT_COUNTRY_CODES = null
@@ -405,6 +405,18 @@ MAIL_ON_ERROR = false
     DISCUSSION_MAX_LENGTH = 1500
     ALERT_MODULES = ["SYNTHESE","VALIDATION"]
     PIN_MODULES = ["SYNTHESE","VALIDATION"]
+    RED_LISTS_FILTERS = [
+        { "id" = "worldwide", "show" = true, "display_name" = "Liste rouge mondiale", "status_type" = "LRM" },
+        { "id" = "european", "show" = true, "display_name" = "Liste rouge européenne", "status_type" = "LRE" },
+        { "id" = "national", "show" = true, "display_name" = "Liste rouge nationale", "status_type" = "LRN" },
+        { "id" = "regional", "show" = true, "display_name" = "Liste rouge régionale", "status_type" = "LRR" },
+    ]
+    STATUS_FILTERS = [
+        { "id" = "protections", "show" = true, "display_name" = "Taxons protégés", "status_types" = ["PN", "PR", "PD"] },
+        { "id" = "regulations", "show" = true, "display_name" = "Taxons réglementés", "status_types" = ["REGLII", "REGL", "REGLSO"] },
+        { "id" = "invasive", "show" = true, "display_name" = "Espèces envahissantes", "status_types" = ["REGLLUTTE"] },
+        { "id" = "znief", "show" = true, "display_name" = "Espèces déterminantes ZNIEFF", "status_types" = ["ZDET"] },
+    ]
 
 # Configuration de l'accès sans authentication
 [PUBLIC_ACCESS]