Prepare V1.2.0

.github/workflows/documentation.yml

@@ -25,7 +25,7 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  PYTHON_VERSION: 3.11
+  PYTHON_VERSION: 3.12
 
 # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
 permissions:
@@ -49,7 +49,7 @@ jobs:
       - name: Install dependencies
         run: |
           cd backend
-          poetry install --only=docs
+          poetry install --only=docs --no-root
 
       - name: Build doc using Sphinx
         run: |

.github/workflows/linter.yml

@@ -16,7 +16,7 @@ on:
 env:
   BACKEND_FOLDER: "backend"
   FRONTEND_FOLDER: "frontend"
-  PYTHON_VERSION: 3.9
+  PYTHON_VERSION: 3.12
 
 jobs:
   lint-py:

.github/workflows/test_install.yml

@@ -28,7 +28,7 @@ jobs:
       matrix:
         os: ["ubuntu-latest"]
         node-version: ["14.21.3"]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     # The type of runner that the job will run on
     runs-on: ${{ matrix.os }}
 

README.md

@@ -30,7 +30,7 @@ Documentation : https://geonature-citizen.readthedocs.io
 - https://enquetes.lashf.org
 - https://observatoire-biodiversite.parc-du-vercors.fr
 - https://enquetes-biodivrennes.fr
-- https://enquetes.clicnat.fr
+- https://citizen.clicnat.fr
 - https://obs-citoyenne.pyrenees-parcnational.fr
 - https://observation.lehavre.fr
 - https://enquetes.cbiodiv.org

VERSION

@@ -1 +1 @@
-1.1.0
+1.2.0

backend/gncitizen/core/commons/routes.py

@@ -115,10 +115,11 @@ def get_modules():
 def get_stat():
     try:
         stats = {}
-        stats["nb_obs"] = ObservationModel.query.count()
-        stats["nb_user"] = UserModel.query.count()
-        stats["nb_program"] = ProgramsModel.query.filter(ProgramsModel.is_active).count()
-        stats["nb_espece"] = ObservationModel.query.distinct(ObservationModel.cd_nom).count()
+        stats["count_obs"] = ObservationModel.query.count()
+        stats["count_users"] = UserModel.query.count()
+        stats["count_programs"] = ProgramsModel.query.filter(ProgramsModel.is_active).count()
+        stats["count_taxa"] = ObservationModel.query.distinct(ObservationModel.cd_nom).count()
+        stats["count_sites"] = SiteModel.query.count()
         return (stats, 200)
     except Exception as e:
         current_app.logger.critical("[get_observations] Error: %s", str(e))

backend/gncitizen/core/observations/admin.py

@@ -1,8 +1,7 @@
 from flask_admin.actions import action
-from wtforms import SelectField
-
 from gncitizen.utils.admin import CustomJSONField, CustomTileView, json_formatter
 from server import db
+from wtforms import SelectField
 
 from .models import ObservationModel, ValidationStatus
 
@@ -15,6 +14,7 @@ def enum_formatter(view, context, model, name):
 class ObservationView(CustomTileView):
     can_export = True
     # column_exclude_list = ["geom"]
+    column_display_pk = True
     form_overrides = {"json_schema": CustomJSONField, "validation_status": SelectField}
     form_args = {
         "validation_status": {
@@ -27,6 +27,7 @@ class ObservationView(CustomTileView):
         "validation_status": enum_formatter,
     }
     column_filters = (
+        "id_observation",
         "email",
         "cd_nom",
         "date",
@@ -45,6 +46,7 @@ class ObservationView(CustomTileView):
         "municipality",
         "obs_txt",
         "email",
+        "uuid_sinp",
     )
     can_create = False
 

backend/gncitizen/core/observations/routes.py

@@ -9,10 +9,6 @@
 from flask_jwt_extended import jwt_required
 from geoalchemy2.shape import from_shape
 from geojson import FeatureCollection
-from shapely.geometry import Point, asShape
-from sqlalchemy import desc
-from utils_flask_sqla.response import json_resp
-
 from gncitizen.core.commons.models import MediaModel, ProgramsModel
 from gncitizen.utils.env import admin
 from gncitizen.utils.errors import GeonatureApiError
@@ -23,6 +19,9 @@
 from gncitizen.utils.media import save_upload_files
 from gncitizen.utils.taxonomy import get_specie_from_cd_nom
 from server import db
+from shapely.geometry import Point, shape
+from sqlalchemy import desc
+from utils_flask_sqla.response import json_resp
 
 from .admin import ObservationView
 from .models import (
@@ -187,11 +186,12 @@ def post_observation():
             raise GeonatureApiError(e)
 
         try:
-            _coordinates = json.loads(request_datas["geometry"])
-            _point = Point(_coordinates["x"], _coordinates["y"])
-            _shape = asShape(_point)
-            newobs.geom = from_shape(Point(_shape), srid=4326)
+            geometry = json.loads(request_datas["geometry"])
+            shape_geometry = shape(geometry)
+            newobs.geom = from_shape(shape_geometry, srid=4326)
             current_app.logger.debug("[post_observation] newobs geom ", newobs.geom)
+            if not newobs.municipality:
+                newobs.municipality = get_municipality_id_from_wkb(shape_geometry)
         except Exception as e:
             current_app.logger.warning("[post_observation] coords ", e)
             raise GeonatureApiError(e) from e
@@ -217,8 +217,6 @@ def post_observation():
                 newobs.obs_txt = "Anonyme"
 
         # If municipality is not provided: call API_CITY
-        if not newobs.municipality:
-            newobs.municipality = get_municipality_id_from_wkb(_coordinates)
 
         # If taxon name is not provided: call taxhub
         if not newobs.name:
@@ -243,15 +241,11 @@ def post_observation():
                 newobs.id_observation,
                 ObservationMediaModel,
             )
-            current_app.logger.debug(
-                "[post_observation] ObsTax UPLOAD FILE {}".format(file)
-            )
+            current_app.logger.debug("[post_observation] ObsTax UPLOAD FILE {}".format(file))
             features["properties"]["images"] = file
 
         except Exception as e:
-            current_app.logger.warning(
-                "[post_observation] ObsTax ERROR ON FILE SAVING", str(e)
-            )
+            current_app.logger.warning("[post_observation] ObsTax ERROR ON FILE SAVING", str(e))
             # raise GeonatureApiError(e)
 
         return (
@@ -371,10 +365,7 @@ def update_observation():
     observation_to_update = ObservationModel.query.filter_by(
         id_observation=request.form.get("id_observation")
     )
-    if (
-        observation_to_update.one().id_role != current_user.id_user
-        and not current_user.validator
-    ):
+    if observation_to_update.one().id_role != current_user.id_user and not current_user.validator:
         abort(403, "unauthorized")
 
     try:
@@ -393,14 +384,11 @@ def update_observation():
                 update_obs[prop] = update_data[prop]
         if "geometry" in update_data:
             try:
-                _coordinates = json.loads(update_data["geometry"])
-                _point = Point(_coordinates["x"], _coordinates["y"])
-                _shape = asShape(_point)
-                update_obs["geom"] = from_shape(Point(_shape), srid=4326)
+                geometry = json.loads(update_data["geometry"])
+                shape_geometry = shape(geometry)
+                update_obs["geom"] = from_shape(shape_geometry, srid=4326)
                 if not update_obs["municipality"]:
-                    update_obs["municipality"] = get_municipality_id_from_wkb(
-                        _coordinates
-                    )
+                    update_obs["municipality"] = get_municipality_id_from_wkb(shape_geometry)
             except Exception as e:
                 current_app.logger.warning("[post_observation] coords ", e)
                 raise GeonatureApiError(e)
@@ -421,8 +409,7 @@ def update_observation():
             if len(id_media_to_delete):
                 db.session.query(ObservationMediaModel).filter(
                     ObservationMediaModel.id_media.in_(tuple(id_media_to_delete)),
-                    ObservationMediaModel.id_data_source
-                    == update_data.get("id_observation"),
+                    ObservationMediaModel.id_data_source == update_data.get("id_observation"),
                 ).delete(synchronize_session="fetch")
                 db.session.query(MediaModel).filter(
                     MediaModel.id_media.in_(tuple(id_media_to_delete))
@@ -439,14 +426,10 @@ def update_observation():
                 update_data.get("id_observation"),
                 ObservationMediaModel,
             )
-            current_app.logger.debug(
-                "[post_observation] ObsTax UPLOAD FILE {}".format(file)
-            )
+            current_app.logger.debug("[post_observation] ObsTax UPLOAD FILE {}".format(file))
 
         except Exception as e:
-            current_app.logger.warning(
-                "[post_observation] ObsTax ERROR ON FILE SAVING", str(e)
-            )
+            current_app.logger.warning("[post_observation] ObsTax ERROR ON FILE SAVING", str(e))
             # raise GeonatureApiError(e)
         obs_validation = (
             "non_validatable_status" in update_data
@@ -463,9 +446,7 @@ def update_observation():
             new_validation_status = ValidationStatus.VALIDATED
             if non_validatable_status:
                 status = [
-                    s
-                    for s in INVALIDATION_STATUSES
-                    if s["value"] == non_validatable_status
+                    s for s in INVALIDATION_STATUSES if s["value"] == non_validatable_status
                 ][0]
                 new_validation_status = ValidationStatus[status["link"]]
 
@@ -500,12 +481,8 @@ def update_observation():
                         ),
                     )
                 except Exception as e:
-                    current_app.logger.warning(
-                        "send validation_email failed. %s", str(e)
-                    )
-                    return {
-                        "message": f"""send validation_email failed: "{str(e)}" """
-                    }, 400
+                    current_app.logger.warning("send validation_email failed. %s", str(e))
+                    return {"message": f"""send validation_email failed: "{str(e)}" """}, 400
 
         return ("observation updated successfully"), 200
     except Exception as e:

backend/gncitizen/core/sites/admin.py

@@ -1,9 +1,8 @@
 """Flask-Admin views for site module"""
 
 from flask_admin.contrib.sqla.view import ModelView
-from markupsafe import Markup
-
 from gncitizen.utils.admin import CustomJSONField, CustomTileView, json_formatter
+from markupsafe import Markup
 
 from .models import VisitModel
 
@@ -20,9 +19,9 @@ class SiteView(CustomTileView):
         VisitModel,
     ]
     column_formatters = {"visits": _visits_list_formatter}
-    # column_exclude_list = ["geom"]
     column_list = [
         "id_site",
+        "uuid_sinp",
         "name",
         "visits",
         "site_type.type",

backend/gncitizen/core/sites/routes.py

@@ -7,18 +7,17 @@
 from flask_jwt_extended import jwt_required
 from geoalchemy2.shape import from_shape
 from geojson import FeatureCollection
-from shapely.geometry import Point, asShape
-from sqlalchemy import or_
-from utils_flask_sqla.response import json_resp
-from utils_flask_sqla_geo.generic import get_geojson_feature
-
 from gncitizen.core.commons.models import MediaModel, ProgramsModel
 from gncitizen.core.users.models import UserModel
 from gncitizen.utils.env import admin
 from gncitizen.utils.errors import GeonatureApiError
 from gncitizen.utils.jwt import get_id_role_if_exists, get_user_if_exists
 from gncitizen.utils.media import save_upload_files
 from server import db
+from shapely.geometry import Point, shape
+from sqlalchemy import or_
+from utils_flask_sqla.response import json_resp
+from utils_flask_sqla_geo.generic import get_geojson_feature
 
 from .admin import SiteView, VisitView
 from .models import MediaOnVisitModel, SiteModel, SiteTypeModel, VisitModel
@@ -53,7 +52,7 @@ def get_types():
 @json_resp
 def get_site(pk):
     """Get a site by id
-    ---
+    ---asShape
     tags:
       - Sites (External module)
     parameters:
@@ -319,8 +318,8 @@ def post_site():
             raise GeonatureApiError(e)
 
         try:
-            shape = asShape(request_data["geometry"])
-            newsite.geom = from_shape(Point(shape), srid=4326)
+            shape_geometry = shape(request_data["geometry"])
+            newsite.geom = from_shape(shape_geometry, srid=4326)
         except Exception as e:
             current_app.logger.debug(e)
             raise GeonatureApiError(e)
@@ -365,8 +364,8 @@ def update_site():
         for prop in ["name", "id_type"]:
             update_site[prop] = update_data[prop]
         try:
-            shape = asShape(update_data["geometry"])
-            update_site["geom"] = from_shape(Point(shape), srid=4326)
+            shape_geometry = shape(update_data["geometry"])
+            update_site["geom"] = from_shape(shape_geometry, srid=4326)
         except Exception as e:
             current_app.logger.warning("[update_site] coords ", e)
             raise GeonatureApiError(e)
@@ -588,9 +587,7 @@ def export_sites_xls(user_id):
         xls_file = io.BytesIO()
         wb.save(xls_file)
         output = make_response(xls_file.getvalue())
-        output.headers["Content-Disposition"] = (
-            "attachment; filename=" + "export_sites.xls"
-        )
+        output.headers["Content-Disposition"] = "attachment; filename=" + "export_sites.xls"
         output.headers["Content-type"] = "application/xls"
         return output
     except Exception as e:

backend/gncitizen/core/users/models.py

@@ -1,14 +1,13 @@
 #!/usr/bin/env python3
 
 from flask import current_app
+from gncitizen.core.commons.models import ProgramsModel, TimestampMixinModel, TModules
 from passlib.hash import pbkdf2_sha256 as sha256
+from server import db
 from sqlalchemy import event
 from sqlalchemy.ext.declarative import declared_attr
 from utils_flask_sqla_geo.serializers import serializable
 
-from gncitizen.core.commons.models import ProgramsModel, TimestampMixinModel, TModules
-from server import db
-
 logger = current_app.logger
 
 
@@ -116,24 +115,13 @@ def to_json(x):
     def __repr__(self):
         return f"{self.username} <{self.id_user}>"
 
-    # @classmethod
-    # def delete_all(cls):
-    #     try:
-    #         num_rows_deleted = db.session.query(cls).delete()
-    #         db.session.commit()
-    #         return {'message': '{} row(s) deleted'.format(num_rows_deleted)}
-    #     except:
-    #         return {'message': 'Something went wrong'}
-
 
 @event.listens_for(UserModel.password, "set", retval=True)
 def hash_user_password(_target, value, oldvalue, _initiator):
     """Evenement qui hash le mot de passe systèmatiquement"""
-    logger.debug(f"<hash_user_password> OLD PWD {oldvalue} / NEW PWD {value != ''}")
     if value != "" and not sha256.identify(value):
-        logger.debug("<hash_user_password> Update new password")
         return UserModel.generate_hash(value)
-    return value
+    return oldvalue
 
 
 class GroupsModel(db.Model):