Merge pull request #425 from PnX-SI/develop

Develop >> Master

backend/geonature/core/auth/routes.py

@@ -59,7 +59,7 @@ def loginCas():
                 log.error("Error with the inpn authentification service")
                 raise CasAuthentificationError(
                     'Error with the inpn authentification service',
-                     status_code=500
+                    status_code=500
                 )
 
             info_user = response.json()
@@ -80,7 +80,7 @@ def loginCas():
                 )
                 raise CasAuthentificationError(
                     'CAS ERROR: no ID or LOGIN provided',
-                     status_code=500
+                    status_code=500
                 )
             # Reconciliation avec base GeoNature
             if organism_id:
@@ -153,8 +153,7 @@ def loginCas():
             )
             return render_template(
                 'cas_login_error.html',
-                cas_logout=current_app.config['CAS']['CAS_URL_LOGOUT'],
+                cas_logout=current_app.config['CAS_PUBLIC']['CAS_URL_LOGOUT'],
                 url_geonature=current_app.config['URL_APPLICATION']
             )
     return jsonify({'message': 'Authentification error'}, 500)
-

backend/geonature/core/gn_meta/routes.py

@@ -55,7 +55,7 @@ def get_datasets(info_role):
 
     """
     with_mtd_error = False
-    if current_app.config['CAS']['CAS_AUTHENTIFICATION']:
+    if current_app.config['CAS_PUBLIC']['CAS_AUTHENTIFICATION']:
         # synchronise the CA and JDD from the MTD WS
         try:
             mtd_utils.post_jdd_from_user(

backend/geonature/core/gn_synthese/models.py

@@ -109,10 +109,6 @@ class TSources(DB.Model):
     desc_source = DB.Column(DB.Unicode)
     entity_source_pk_field = DB.Column(DB.Unicode)
     url_source = DB.Column(DB.Unicode)
-    target = DB.Column(DB.Unicode)
-    picto_source = DB.Column(DB.Unicode)
-    groupe_source = DB.Column(DB.Unicode)
-    active = DB.Column(DB.Boolean)
     meta_create_date = DB.Column(DB.DateTime)
     meta_update_date = DB.Column(DB.DateTime)
 

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

@@ -1,4 +1,4 @@
-from flask import current_app
+from flask import current_app, request
 from shapely.wkt import loads
 from geoalchemy2.shape import from_shape
 from sqlalchemy import func, or_, and_
@@ -50,7 +50,6 @@ def filter_taxonomy(model, q, filters):
         -Tuple: the SQLAlchemy query and the filter dictionnary
     """
     if 'cd_ref' in filters:
-        from flask import request
         # find all cd_nom where cd_ref = filter['cd_ref']
         sub_query_synonym = DB.session.query(
             Taxref.cd_nom
@@ -74,15 +73,19 @@ def filter_taxonomy(model, q, filters):
         q = q.filter(model.cd_nom.in_(sub_query_lr))
 
     aliased_cor_taxon_attr = {}
+    join_on_taxref = False
     for colname, value in filters.items():
         if colname.startswith('taxhub_attribut'):
+            if not join_on_taxref:
+                q = q.join(Taxref, Taxref.cd_nom == model.cd_nom)
+                join_on_taxref = True
             taxhub_id_attr = colname[16:]
             aliased_cor_taxon_attr[taxhub_id_attr] = aliased(CorTaxonAttribut)
             q = q.join(
                 aliased_cor_taxon_attr[taxhub_id_attr],
                 and_(
                     aliased_cor_taxon_attr[taxhub_id_attr].id_attribut == taxhub_id_attr,
-                    aliased_cor_taxon_attr[taxhub_id_attr].cd_ref == Taxref.cd_ref
+                    aliased_cor_taxon_attr[taxhub_id_attr].cd_ref == func.taxonomie.find_cdref(model.cd_nom)
                 )
             ).filter(
                 aliased_cor_taxon_attr[taxhub_id_attr].valeur_attribut.in_(value)
@@ -144,7 +147,7 @@ def filter_query_all_filters(model, q, filters, user, allowed_datasets):
 
     if 'geoIntersection' in filters:
         # Insersect with the geom send from the map
-        geom_wkt = loads(filters['geoIntersection'][0])
+        geom_wkt = loads(request.args['geoIntersection'])
         # if the geom is a circle
         if 'radius' in filters:
             radius = filters.pop('radius')[0]
@@ -154,8 +157,8 @@ def filter_query_all_filters(model, q, filters, user, allowed_datasets):
         filters.pop('geoIntersection')
 
     if 'period_start' in filters and 'period_end' in filters:
-        period_start = filters.pop('period_min')[0]
-        period_end = filters.pop('period_max')[0]
+        period_start = filters.pop('period_start')[0]
+        period_end = filters.pop('period_end')[0]
         q = q.filter(or_(
             func.gn_commons.is_in_period(
                 func.date(model.date_min),

backend/geonature/utils/config_schema.py

@@ -25,14 +25,17 @@ class CasUserSchemaConf(Schema):
     )
 
 
-class CasSchemaConf(Schema):
+class CasFrontend(Schema):
     CAS_AUTHENTIFICATION = fields.Boolean(missing='false')
     CAS_URL_LOGIN = fields.Url(
         missing='https://preprod-inpn.mnhn.fr/auth/login'
     )
     CAS_URL_LOGOUT = fields.Url(
         missing='https://preprod-inpn.mnhn.fr/auth/logout'
     )
+
+
+class CasSchemaConf(Schema):
     CAS_URL_VALIDATION = fields.String(
         missing='https://preprod-inpn.mnhn.fr/auth/serviceValidate'
     )
@@ -51,6 +54,17 @@ class RightsSchemaConf(Schema):
     ALL_DATA = fields.Integer(missing=3)
 
 
+class MailErrorConf(Schema):
+    MAIL_ON_ERROR = fields.Boolean(missing=False)
+    MAIL_HOST = fields.String(missing="")
+    HOST_PORT = fields.Integer(missing=465)
+    MAIL_FROM = fields.String(missing="")
+    MAIL_USERNAME = fields.String(missing="")
+    MAIL_PASS = fields.String(missing="")
+    MAIL_TO = fields.List(fields.String(), missing=list())
+
+
+# class a utiliser pour les paramètres que l'on ne veut pas passer au frontend
 class GnPySchemaConf(Schema):
     SQLALCHEMY_DATABASE_URI = fields.String(
         required=True,
@@ -73,6 +87,8 @@ class GnPySchemaConf(Schema):
     BASE_DIR = fields.String(
         missing=os.path.dirname(os.path.dirname(os.path.abspath(os.path.dirname(__file__))))
     )
+    MAILERROR = fields.Nested(MailErrorConf, missing=dict())
+    CAS = fields.Nested(CasSchemaConf, missing=dict())
 
 
 class GnFrontEndConf(Schema):
@@ -113,15 +129,7 @@ class Synthese(Schema):
     # Nombre des "dernières observations" affiché à l'arrive sur la synthese
     NB_LAST_OBS = fields.Integer(missing=100)
 
-
-class MailErrorConf(Schema):
-    MAIL_ON_ERROR = fields.Boolean(missing=False)
-    MAIL_HOST = fields.String(missing="")
-    HOST_PORT = fields.Integer(missing=465)
-    MAIL_FROM = fields.String(missing="")
-    MAIL_USERNAME = fields.String(missing="")
-    MAIL_PASS = fields.String(missing="")
-    MAIL_TO = fields.List(fields.String(), missing=list())
+# class a utiliser pour les paramètres que l'on veut passer au frontend
 
 
 class GnGeneralSchemaConf(Schema):
@@ -139,10 +147,9 @@ class GnGeneralSchemaConf(Schema):
     ID_APPLICATION_GEONATURE = fields.Integer(missing=3)
     XML_NAMESPACE = fields.String(missing="{http://inpn.mnhn.fr/mtd}")
     MTD_API_ENDPOINT = fields.Url(missing="https://preprod-inpn.mnhn.fr/mtd")
-    CAS = fields.Nested(CasSchemaConf, missing=dict())
+    CAS_PUBLIC = fields.Nested(CasFrontend, missing=dict())
     RIGHTS = fields.Nested(RightsSchemaConf, missing=dict())
     FRONTEND = fields.Nested(GnFrontEndConf, missing=dict())
-    MAILERROR = fields.Nested(MailErrorConf, missing=dict())
     SYNTHESE = fields.Nested(Synthese, missing=dict())
     # Ajoute la surchouche 'taxonomique' sur l'API nomenclature
     ENABLE_NOMENCLATURE_TAXONOMIC_FILTERS = fields.Boolean(missing=True)

backend/requirements-travis.txt

@@ -10,8 +10,8 @@
 # `Pipfile.lock` and then regenerate `requirements*.txt`.
 ################################################################################
 
-https://github.com/PnX-SI/UsersHub-authentification-module/archive/1.1.1.zip
-https://github.com/PnX-SI/Nomenclature-api-module/archive/develop.zip
+https://github.com/PnX-SI/UsersHub-authentification-module/archive/1.2.0.zip
+https://github.com/PnX-SI/Nomenclature-api-module/archive/1.2.1.zip
 certifi==2017.11.5
 chardet==3.0.4
 click==6.7

backend/requirements.txt

@@ -10,8 +10,8 @@
 # `Pipfile.lock` and then regenerate `requirements*.txt`.
 ################################################################################
 
-https://github.com/PnX-SI/UsersHub-authentification-module/archive/develop.zip
-https://github.com/PnX-SI/Nomenclature-api-module/archive/develop.zip
+https://github.com/PnX-SI/UsersHub-authentification-module/archive/1.2.0.zip
+https://github.com/PnX-SI/Nomenclature-api-module/archive/1.2.1.zip
 certifi==2017.11.5
 chardet==3.0.4
 click==6.7

backend/tests/sample_data.sql

@@ -61,9 +61,6 @@ INSERT INTO gn_meta.cor_dataset_protocol (id_dataset, id_protocol) VALUES
 ;
 SELECT pg_catalog.setval('gn_meta.sinp_datatype_protocols_id_protocol_seq', (SELECT max(id_protocol)+1 FROM gn_meta.cor_dataset_protocol), true);
 
--- INSERT INTO gn_synthese.t_sources (id_source, name_source, desc_source, entity_source_pk_field, url_source, target, picto_source, groupe_source, active) VALUES
--- (1, 'Contact faune flore', 'Données issues du occtax aléatoire', 'pr_occtax.cor_counting_occtax.id_counting_occtax', '/occtax', NULL, NULL, 'CONTACT', true);
-
 
 INSERT INTO pr_occtax.t_releves_occtax (id_releve_occtax,id_dataset,id_digitiser,observers_txt,id_nomenclature_obs_technique,id_nomenclature_grp_typ,date_min,date_max,hour_min,hour_max,altitude_min,altitude_max,meta_device_entry,comment,geom_local,geom_4326,precision) VALUES 
 (1,1,1,'Obervateur test insert',ref_nomenclatures.get_id_nomenclature('TECHNIQUE_OBS', '133'),ref_nomenclatures.get_id_nomenclature('TYP_GRP', 'OBS'),'2017-01-01','2017-01-01','12:05:02','12:05:02',1500,1565,'web','Exemple test','01010000206A0800002E988D737BCC2D41ECFA38A659805841','0101000020E61000000000000000001A40CDCCCCCCCC6C4640',10)

config/default_config.toml.example

@@ -29,15 +29,17 @@ MTD_API_ENDPOINT = "https://preprod-inpn.mnhn.fr/mtd"
 UPLOAD_FOLDER = 'static/medias'
 
 # CAS authentification (Optional, instead of UsersHub local authentification)
-[CAS]
+[CAS_PUBLIC]
     CAS_AUTHENTIFICATION = false
     CAS_URL_LOGIN = 'https://preprod-inpn.mnhn.fr/auth/login'
     CAS_URL_LOGOUT = 'https://preprod-inpn.mnhn.fr/auth/logout'
-    CAS_URL_VALIDATION = 'https://preprod-inpn.mnhn.fr/auth/serviceValidate'
-    [CAS.CAS_USER_WS]
-        URL = 'https://inpn2.mnhn.fr/authentication/information'
-        ID = 'mon_id'
-        PASSWORD = 'mon_pass'
+
+[CAS]
+CAS_URL_VALIDATION = 'https://preprod-inpn.mnhn.fr/auth/serviceValidate'
+[CAS.CAS_USER_WS]
+    URL = 'https://inpn2.mnhn.fr/authentication/information'
+    ID = 'mon_id'
+    PASSWORD = 'mon_pass'
 
 [RIGHTS]
     NOTHING = 0

config/settings.ini.sample

@@ -57,13 +57,13 @@ add_sample_data=true
 # Les trois paramètres ci-dessous visent à indiquer dans quelle version (release, branche ou tag) les scripts doivent être récupés
 
 # Définir dans quelle version de UsersHub (release, branche ou tag) prendre le code SQL permettant la création du schéma utilisateurs de la base de données de GeoNature
-usershub_release=1.3.1
+usershub_release=1.3.2
 
 # Définir dans quelle version de TaxHub (release, branche ou tag) prendre le code SQL permettant la création du schéma taxonomie de la base de données de GeoNature
-taxhub_release=pre-1.3.3
+taxhub_release=1.5.0
 
 # Définir dans quelle version du sous-module des nomenclatures (realease, branche ou tag) prendre le code SQL permettant la création du schéma 'ref_nomenvclature' de la base de données GeoNature
-nomenclature_release=develop
+nomenclature_release=1.2.1
 
 
 #Configuration python