Merge pull request #1661 from PnX-SI/hotfixes

release 2.9.1

.github/workflows/pytest.yml

@@ -4,12 +4,12 @@ on:
   push:
     branches:
       - master
-      - freeze
+      - hotfixes
       - develop
   pull_request:
     branches:
       - master
-      - freeze
+      - hotfixes
       - develop
 
 jobs:

VERSION

@@ -1 +1 @@
-2.9.0
+2.9.1

backend/geonature/app.py

@@ -127,7 +127,7 @@ def load_current_user():
     # Pass the ID_APP to the submodule to avoid token conflict between app on the same server
     with app.app_context():
         try:
-            gn_app = Application.query.filter_by(code_application='GN').one()
+            gn_app = Application.query.filter_by(code_application=config['CODE_APPLICATION']).one()
         except (ProgrammingError, NoResultFound):
             logging.warning("Warning: unable to find GeoNature application, database not yet initialized?")
         else:

backend/geonature/core/auth/routes.py

@@ -79,7 +79,7 @@ def loginCas():
             cookie_exp = datetime.datetime.utcnow()
             expiration = current_app.config["COOKIE_EXPIRATION"]
             cookie_exp += datetime.timedelta(seconds=expiration)
-            # generation d'un token
+            user["id_application"] = current_app.config["ID_APP"]
             s = Serializer(current_app.config["SECRET_KEY"], expiration)
             token = s.dumps(user)
             response.set_cookie("token", token, expires=cookie_exp)
@@ -180,4 +180,4 @@ def insert_user_and_org(info_user):
         raise CasAuthentificationError(
             "Error insering user in GeoNature", status_code=500
         )
-    return user
+    return user

backend/geonature/core/gn_meta/models.py

@@ -648,7 +648,7 @@ class TAcquisitionFramework(CruvedMixin, FilterMixin, db.Model):
     unique_acquisition_framework_id = DB.Column(
         UUIDType(as_uuid=True), default=select([func.uuid_generate_v4()])
     )
-    acquisition_framework_name = DB.Column(DB.Unicode)
+    acquisition_framework_name = DB.Column(DB.Unicode(255))
     acquisition_framework_desc = DB.Column(DB.Unicode)
     id_nomenclature_territorial_level = DB.Column(
         DB.Integer,

backend/geonature/core/gn_meta/mtd/__init__.py

@@ -30,7 +30,7 @@ def _get_xml(self, path):
         url = urljoin(self.api_endpoint, path)
         url = url.format(ID_INSTANCE=self.instance_id)
         response = requests.get(url)
-        assert(response.status_code == 200)
+        response.raise_for_status()
         return response.content
 
     def _get_af_xml(self):
@@ -77,38 +77,49 @@ def add_unexisting_digitizer(id_digitizer):
         insert_user_and_org(user)
 
 
+def add_or_update_organism(uuid, nom, email):
+    statement = (
+        pg_insert(Organisme)
+        .values(
+            uuid_organisme=uuid,
+            nom_organisme=nom,
+            email_organisme=email,
+        )
+        .on_conflict_do_update(
+            index_elements=['uuid_organisme'],
+            set_=dict(
+                nom_organisme=nom,
+                email_organisme=email,
+            ),
+        )
+        .returning(Organisme.id_organisme)
+    )
+    return db.session.execute(statement).scalar()
+
+
 def associate_actors(actors, CorActor, pk_name, pk_value):
     for actor in actors:
         if not actor['uuid_organism']:
             continue
-        statement = pg_insert(Organisme) \
-            .values(
-                uuid_organisme=actor['uuid_organism'],
-                nom_organisme=actor['organism'],
-                email_organisme=actor['email'],
-            ).on_conflict_do_update(
-                index_elements=['uuid_organisme'],
-                set_=dict(
-                    nom_organisme=actor['organism'],
-                    email_organisme=actor['email'],
-                ),
+        with db.session.begin_nested():
+            id_organism = add_or_update_organism(
+                uuid=actor['uuid_organism'],
+                nom=actor['organism'] or '',
+                email=actor['email'],
             )
-        db.session.execute(statement)
-        # retrieve organism id
-        org = Organisme.query \
-                .filter_by(uuid_organisme=actor['uuid_organism']) \
-                .first()
-        statement = pg_insert(CorActor) \
+        statement = (
+            pg_insert(CorActor)
             .values(
-                #id_acquisition_framework=af.id_acquisition_framework,
-                id_organism=org.id_organisme,
+                id_organism=id_organism,
                 id_nomenclature_actor_role=func.ref_nomenclatures.get_id_nomenclature(
                     "ROLE_ACTEUR", actor["actor_role"]
                 ),
                 **{pk_name: pk_value},
-            ).on_conflict_do_nothing(
+            )
+            .on_conflict_do_nothing(
                 index_elements=[pk_name, 'id_organism', 'id_nomenclature_actor_role'],
             )
+        )
         db.session.execute(statement)
 
 
@@ -120,24 +131,28 @@ def sync_af_and_ds():
 
     af_list = mtd_api.get_af_list()
     for af in af_list:
-        add_unexisting_digitizer(af['id_digitizer'])
+        with db.session.begin_nested():
+            add_unexisting_digitizer(af['id_digitizer'])
         actors = af.pop('actors')
-        statement = pg_insert(TAcquisitionFramework) \
-            .values(**af) \
+        statement = (
+            pg_insert(TAcquisitionFramework)
+            .values(**af)
             .on_conflict_do_update(
                 index_elements=['unique_acquisition_framework_id'],
                 set_=af)
-        db.session.execute(statement)
-        af = TAcquisitionFramework.query \
-                .filter_by(unique_acquisition_framework_id=af['unique_acquisition_framework_id']) \
-                .first()
+            .returning(TAcquisitionFramework.id_acquisition_framework)
+        )
+        af_id = db.session.execute(statement).scalar()
+        af = TAcquisitionFramework.query.get(af_id)
         associate_actors(actors, CorAcquisitionFrameworkActor,
                          'id_acquisition_framework', af.id_acquisition_framework)
+        # TODO: remove actors removed from MTD
     db.session.commit()
 
     ds_list = mtd_api.get_ds_list()
     for ds in ds_list:
-        add_unexisting_digitizer(ds['id_digitizer'])
+        with db.session.begin_nested():
+            add_unexisting_digitizer(ds['id_digitizer'])
         actors = ds.pop('actors')
         af_uuid = ds.pop('uuid_acquisition_framework')
         af = TAcquisitionFramework.query.filter_by(unique_acquisition_framework_id=af_uuid).first()

backend/geonature/core/gn_meta/mtd/xml_parser.py

@@ -5,6 +5,8 @@
 from lxml import etree as ET
 
 from geonature.utils.config import config
+from geonature.core.gn_meta.models import TAcquisitionFramework
+
 
 namespace = config["XML_NAMESPACE"]
 
@@ -74,7 +76,8 @@ def parse_acquisition_framework(ca):
 
     # We extract all the required informations from the different tags of the XML file
     ca_uuid = get_tag_content(ca, "identifiantCadre")
-    ca_name = get_tag_content(ca, "libelle")
+    ca_name_max_length = TAcquisitionFramework.acquisition_framework_name.property.columns[0].type.length
+    ca_name = get_tag_content(ca, "libelle")[:ca_name_max_length-1]
     ca_desc = get_tag_content(ca, "description", default_value="")
     date_info = ca.find(namespace + "ReferenceTemporelle")
     ca_create_date = get_tag_content(ca, "dateCreationMtd", default_value=datetime.datetime.now())

backend/geonature/core/gn_permissions/decorators.py

@@ -66,18 +66,18 @@ def __check_cruved_scope(*args, **kwargs):
             if user_with_highter_perm:
                 user_with_highter_perm = user_with_highter_perm[0]
 
-            # if get_role = True : set info_role as kwargs
-            if get_role:
-                kwargs["info_role"] = user_with_highter_perm
-            if get_scope:
-                kwargs["scope"] = int(user_with_highter_perm.value_filter)
             # if no perm or perm = 0 -> raise 403
             if user_with_highter_perm is None or user_with_highter_perm.value_filter == "0":
                 if object_code:
                     message = f"""User {user["id_role"]} cannot "{action}" in {module_code} on {object_code}"""
                 else:
                     message = f"""User {user["id_role"]} cannot "{action}" in {module_code}"""
                 raise Forbidden(description=message)
+            # if get_role = True : set info_role as kwargs
+            if get_role:
+                kwargs["info_role"] = user_with_highter_perm
+            if get_scope:
+                kwargs["scope"] = int(user_with_highter_perm.value_filter)
             g.user = user_with_highter_perm
             return fn(*args, **kwargs)
 

backend/geonature/core/gn_synthese/models.py

@@ -24,7 +24,6 @@
 
 from geonature.core.gn_meta.models import TDatasets, TAcquisitionFramework
 from geonature.core.ref_geo.models import LAreas
-from geonature.core.ref_geo.models import LiMunicipalities
 from geonature.core.gn_commons.models import THistoryActions, TValidations, last_validation, \
                                              TMedias, TModules
 from geonature.utils.env import DB, db
@@ -282,10 +281,7 @@ def has_instance_permission(self, scope):
                 return True
             if g.current_user in self.cor_observers:
                 return True
-            if scope == 2:
-                if g.current_user.organisme in self.dataset.organism_actors:
-                    return True
-            return False
+            return self.dataset.has_instance_permission(scope)
         elif scope == 3:
             return True
 
@@ -467,8 +463,8 @@ def serialize_geofn(self, geoCol, idCol):
 class VColorAreaTaxon(DB.Model):
     __tablename__ = "v_color_taxon_area"
     __table_args__ = {"schema": "gn_synthese"}
-    cd_nom = DB.Column(DB.Integer(), ForeignKey("taxonomie.taxref.cd_nom"), primary_key=True)
-    id_area = DB.Column(DB.Integer(), ForeignKey("ref_geo.l_area.id_area"), primary_key=True)
+    cd_nom = DB.Column(DB.Integer(), ForeignKey(Taxref.cd_nom), primary_key=True)
+    id_area = DB.Column(DB.Integer(), ForeignKey(LAreas.id_area), primary_key=True)
     nb_obs = DB.Column(DB.Integer())
     last_date = DB.Column(DB.DateTime())
     color = DB.Column(DB.Unicode())

backend/geonature/core/gn_synthese/routes.py

@@ -4,6 +4,7 @@
 import time
 
 from collections import OrderedDict
+from warnings import warn
 
 from flask import Blueprint, request, current_app, send_from_directory, render_template, jsonify
 from werkzeug.exceptions import Forbidden, NotFound
@@ -765,7 +766,11 @@ def get_color_taxon():
     """
     params = request.args
     limit = int(params.get("limit", 100))
-    offset = int(params.get("offset", 0))
+    page = params.get("page", 1, int)
+
+    if "offset" in request.args:
+        warn("offset is deprecated, please use page for pagination (start at 1)", DeprecationWarning)
+        page = (int(request.args["offset"]) / limit) + 1
     id_areas_type = params.getlist("code_area_type")
     cd_noms = params.getlist("cd_nom")
     id_areas = params.getlist("id_area")
@@ -780,11 +785,13 @@ def get_color_taxon():
         if not LAreas in [mapper.class_ for mapper in q._join_entities]:
             q = q.join(LAreas, LAreas.id_area == VColorAreaTaxon.id_area)
         q = q.filter(LAreas.id_area.in_(tuple(id_areas)))
+    q = q.order_by(VColorAreaTaxon.cd_nom).order_by(VColorAreaTaxon.id_area)
     if len(cd_noms) > 0:
         q = q.filter(VColorAreaTaxon.cd_nom.in_(tuple(cd_noms)))
-    data = q.limit(limit).offset(offset).all()
+    results = q.paginate(page=page, per_page=limit, error_out=False)
+
 
-    return jsonify([d.as_dict() for d in data])
+    return jsonify([d.as_dict() for d in results.items])
 
 
 @routes.route("/taxa_count", methods=["GET"])

backend/geonature/core/users/register_post_actions.py

@@ -161,7 +161,7 @@ def send_email_for_recovery(data):
     """
     user = data["role"]
     recipients = current_app.config["MAIL_CONFIG"]["MAIL_USERNAME"]
-    url_password = current_app.config["URL_APPLICATION"] + "#/new-password?token=" + data["token"]
+    url_password = current_app.config["URL_APPLICATION"] + "/#/new-password?token=" + data["token"]
 
     msg_html = render_template(
         "email_login_and_new_pass.html",

backend/geonature/utils/config_schema.py

@@ -342,6 +342,7 @@ class GnGeneralSchemaConf(Schema):
     API_ENDPOINT = fields.Url(required=True)
     API_TAXHUB = fields.Url(required=True)
     LOCAL_SRID = fields.Integer(load_default=2154)
+    CODE_APPLICATION = fields.String(load_default='GN')
     XML_NAMESPACE = fields.String(load_default="{http://inpn.mnhn.fr/mtd}")
     MTD_API_ENDPOINT = fields.Url(load_default="https://preprod-inpn.mnhn.fr/mtd")
     CAS_PUBLIC = fields.Nested(CasFrontend, load_default=CasFrontend().load({}))

backend/requirements.txt

@@ -5,4 +5,4 @@ pypnnomenclature@https://github.com/PnX-SI/Nomenclature-api-module/archive/1.5.1
 pypn_habref_api@https://github.com/PnX-SI/Habref-api-module/archive/0.3.0.tar.gz
 utils-flask-sqlalchemy-geo@https://github.com/PnX-SI/Utils-Flask-SQLAlchemy-Geo/archive/0.2.2.zip
 utils-flask-sqlalchemy@https://github.com/PnX-SI/Utils-Flask-SQLAlchemy/archive/0.2.6.zip
-taxhub@https://github.com/PnX-SI/TaxHub/archive/1.9.3.zip
+taxhub@https://github.com/PnX-SI/TaxHub/archive/1.9.4.zip

config/settings.ini.sample

@@ -85,7 +85,7 @@ install_usershub_schema=true
 usershub_release=2.2.1
 
 # 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=1.9.0
+taxhub_release=1.9.4
 
 # Proxy - si le serveur sur lequel se trouve GeoNature se trouve derrière un proxy
 # laisser vide si vous n'avez pas de proxy

docs/CHANGELOG.rst

@@ -2,6 +2,27 @@
 CHANGELOG
 =========
 
+2.9.1 (2022-01-27)
+------------------
+
+**🚀 Nouveautés**
+
+* Utilisation du paramètre ``page`` de Flask à la place du paramètre maison ``offset`` pour la pagination des routes (rétro-compatible)
+* Installation de TaxHub en version 1.9.4 (version corrective) par défaut
+* Ajout du paramètre de configuration ``CODE_APPLICATION`` (par défaut ``GN``) (#1635)
+
+**🐛 Corrections**
+
+* Correction de l'URL de réinitialisation de mot passe envoyée par email (#1620)
+* Correction d’un problème d’authentification avec le CAS
+* Occtax : Correction des listes déroulantes masquées dans le bloc dénombrement, en rajoutant un scroll
+* Correction de l'URL de l'API de TaxHub (slash final manquant) pour l'affichage des photos sur la fiche d'un profil de taxon
+* Correction de la synchronisation des métadonnées depuis MTD
+* Correction de la génération du token quand on utilise le CAS de l'INPN pour se connecter à GeoNature
+* Correction des permissions trop restrictives d’accès aux données de la synthèse
+* Correction de la pagination de la route ``/color_taxon`` en rajoutant un ordonnancement par ``cd_nom`` et ``id_area`` (utilisé par Occtax-mobile)
+* Contournement d'un problème de redirection incorrecte par l’API de TaxHub lorsque celui-ci est mal configuré (#1438, #1616)
+
 2.9.0 - Actias luna (2022-01-13)
 --------------------------------
 
@@ -35,7 +56,7 @@ CHANGELOG
 * Association automatique et paramétrable des jeux de données personnels auto-générés à des modules (Occtax par défaut) (#1555)
 * Utilisation du C du CRUVED de l'utilisateur pour lister les jeux de données dans lesquels il peut ajouter des données dans les différents modules (et non plus le R du CRUVED sur GeoNature) (#659)
 
-**Corrections**
+**🐛 Corrections**
 
 * [OCCTAX] Correction de l'enregistrement des dénombrements lors de l'enchainement des relevés (#1479 par @jbrieuclp)
 * [OCCTAX] Correction du filtre du champs "Habitat" par typologie d'habitat

docs/versions-compatibility.rst

@@ -3,6 +3,27 @@ COMPATIBILITE
 
 Versions fournies et testées des dépendances
 
+GeoNature 2.9.1
+---------------
+
++----------------------------+---------+
+| Application / Module       | Version |
++============================+=========+
+| TaxHub                     | 1.9.4   |
++----------------------------+---------+
+| UsersHub                   | 2.2.2   |
++----------------------------+---------+
+| Nomenclature-Api           | 1.5.1   |
++----------------------------+---------+
+| Authentification-Api       | 1.5.9   |
++----------------------------+---------+
+| Habref-Api                 | 0.3.0   |
++----------------------------+---------+
+| Utils-Flask-SQLAlchemy     | 0.2.6   |
++----------------------------+---------+
+| Utils-Flask-SQLAlchemy-Geo | 0.2.2   |
++----------------------------+---------+
+
 GeoNature 2.9.0
 ---------------
 

frontend/src/app/GN2CommonModule/form/data-form.service.ts

@@ -162,7 +162,7 @@ export class DataFormService {
 
   getTaxaBibList() {
     return Observable.of([])
-    return this._http.get<any>(`${AppConfig.API_TAXHUB}/biblistes`).map(d => d.data);
+    return this._http.get<any>(`${AppConfig.API_TAXHUB}/biblistes/`).map(d => d.data);
   }
 
   async getTaxonInfoSynchrone(cd_nom: number): Promise<any> {

frontend/src/app/GN2CommonModule/form/nomenclature/nomenclature.component.html

@@ -8,6 +8,7 @@
 	[placeholder]="placeholder||label"
 	[virtualScroll]="true"
 	[formControl]="parentFormControl"
+  appendTo="body"
 >
 	<ng-template 
     ng-option-tmp