Merge remote-tracking branch upstream/dev into origin/dev

Author: hypsug0

.pre-commit-config.yaml

@@ -39,8 +39,19 @@ repos:
             "--config=setup.cfg",
             "--select=E9,F63,F7,F82,QGS101,QGS102,QGS103,QGS104,QGS106",
           ]
+  - repo: local
+    hooks:
+      - id: generate-requirements
+        name: Generate Python Requirements
+        entry: |
+          bash -c "cd backend && \
+            poetry export -f requirements.txt -o requirements.txt --without-hashes && \
+            poetry export -f requirements.txt --only=dev -o requirements-dev.txt --without-hashes && \
+            poetry export -f requirements.txt --only=docs -o requirements-docs.txt --without-hashes"
+        language: system
+        types: [python]
 
 ci:
-    autoupdate_schedule: quarterly
-    skip: []
-    submodules: false
+  autoupdate_schedule: quarterly
+  skip: []
+  submodules: false

CHANGELOG.md

@@ -1,6 +1,29 @@
 # CHANGELOG
 
-## 1.3.0 - Unreleased
+## 1.3.2 - 2025-12-01
+
+> [!WARNING]
+> **Version 1.3.x will be the latest release compatible with python 3.9**
+
+### :bug: Fixes
+
+* Refix servor error when creating or updating programs (missing requirements up to date, temporary patch to fix #477).
+
+### :technologist: Development
+
+* New Makefile to facilitate certain maintenance operations
+* Requirements are now generated automatically during commit validation using pre-commit.
+
+## 1.3.1 - 2025-11-30
+
+> [!WARNING]
+> **Version 1.3.x will be the latest release compatible with python 3.9**
+
+### :bug: Fixes
+
+* Fix servor error when creating or updating programs (temporary patch to fix #477).
+
+## 1.3.0 - 2025-11-26
 
 > [!WARNING]  
 > **Require TaxHub 2.x (i.e. GeoNature >= 2.15.x)**
@@ -22,7 +45,7 @@
 ### :technologist: Development
 
 * Add calls to two TaxHub API routes in order to get media types and bibattribut.
-* Add component taxonomy-research which calls `allnamebylist` TaxHub API route in Form Observation Program 
+* Add component taxonomy-research which calls `allnamebylist` TaxHub API route in Form Observation Program
 * Remove TaxHub list from cache backend
 
 ### :speech_balloon: Release note

Makefile

@@ -0,0 +1,47 @@
+# Define variables
+APP_NAME := gncitizen
+BACKEND_DIR := backend
+FRONTEND_DIR := frontend
+DOCKER_COMPOSE_FILE := docker-compose.yml
+
+include .env
+
+DOCKER_IMAGE_BACKEND := $(APP_NAME)-backend
+DOCKER_IMAGE_FRONTEND := $(APP_NAME)-frontend
+
+# Phony targets
+.PHONY: all install-dependencies generate-requirements build docker-start clean
+
+# Default target
+all: install-dependencies generate-requirements build docker-start
+
+# Install dependencies for frontend and backend
+install-dependencies:
+	cd $(BACKEND_DIR) && \
+		if [ -f poetry.lock ]; then \
+			poetry install; \
+		elif [ -f requirements.txt ]; then \
+			pip install -r requirements.txt; \
+		fi
+	cd $(FRONTEND_DIR) && npm install
+
+# Generate Python requirements files
+generate-requirements:
+	cd $(BACKEND_DIR) && \
+		poetry export -f requirements.txt -o requirements.txt --without-hashes && \
+		poetry export -f requirements.txt --only=dev -o requirements-dev.txt --without-hashes && \
+		poetry export -f requirements.txt --only=docs -o requirements-docs.txt --without-hashes
+
+# Build Docker images for backend and frontend
+build:
+	docker build -t $(DOCKER_IMAGE_BACKEND) -f $(BACKEND_DIR)/Dockerfile $(BACKEND_DIR)
+	docker build -t $(DOCKER_IMAGE_FRONTEND) -f $(FRONTEND_DIR)/Dockerfile $(FRONTEND_DIR)
+
+# Start project using docker-compose
+docker-start:
+	docker-compose -f $(DOCKER_COMPOSE_FILE) up -d
+
+# Clean up Docker containers and images
+clean:
+	docker-compose -f $(DOCKER_COMPOSE_FILE) down
+	docker rmi $(DOCKER_IMAGE_BACKEND) $(DOCKER_IMAGE_FRONTEND)

README.md

@@ -35,6 +35,9 @@ Documentation : https://geonature-citizen.readthedocs.io
 - https://observation.lehavre.fr
 - https://enquetes.cbiodiv.org
 - https://jobservemonparc.fr
+- https://obs.parc-livradois-forez.org
+- https://citizen.parc-naturel-pilat.fr
+- https://observatoire-biodiversite.parcdesbauges.com
 
 ## Solutions logicielles
 

VERSION

@@ -1 +1 @@
-1.3.0
+1.3.2

backend/gncitizen/core/observations/models.py

@@ -27,7 +27,7 @@
     "comment",
     "timestamp_create",
     "json_data",
-    "name"
+    "name",
 )
 
 TAXREF_KEYS = ["nom_vern", "cd_nom", "cd_ref", "lb_nom"]
@@ -155,9 +155,7 @@ def get_feature(self):
         """get obs data as geojson feature"""
 
         result_dict = self.as_dict(True)
-        result_dict["observer"] = (
-            self.observer.as_simple_dict() if self.observer else None
-        )
+        result_dict["observer"] = self.observer.as_simple_dict() if self.observer else None
         result_dict["validator"] = (
             self.validator_ref.as_simple_dict() if self.validator_ref else None
         )
@@ -171,9 +169,7 @@ def get_feature(self):
         for k in result_dict:
             if k in OBS_KEYS:
                 feature["properties"][k] = (
-                    result_dict[k].name
-                    if isinstance(result_dict[k], Enum)
-                    else result_dict[k]
+                    result_dict[k].name if isinstance(result_dict[k], Enum) else result_dict[k]
                 )
         feature["properties"]["photos"] = [
             {

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, shape
-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
@@ -27,6 +23,9 @@
     taxhub_rest_get_taxon_list,
 )
 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 (
@@ -247,9 +246,8 @@ 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))
+
             newobs = (
                 db.session.query(ObservationModel)
                 .options(db.joinedload(ObservationModel.medias))
@@ -265,13 +263,9 @@ def post_observation():
             else:
                 taxon_list_data = None
 
-            features_with_taxhub_info = set_taxa_info_from_taxhub(
-                taxon_list_data, [features]
-            )
+            features_with_taxhub_info = set_taxa_info_from_taxhub(taxon_list_data, [features])
         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 (
             {
@@ -324,7 +318,7 @@ def get_all_observations() -> Union[FeatureCollection, Tuple[Dict, int]]:
                 ProgramsModel.id_program == ObservationModel.id_program,
                 isouter=True,
             )
-            .order_by(desc(ObservationModel.timestamp_create))
+            .order_by(desc(ObservationModel.date))
             .filter(*filters)
         )
 
@@ -347,9 +341,7 @@ def get_all_observations() -> Union[FeatureCollection, Tuple[Dict, int]]:
 
         if id_taxonomy_list or cd_nom_list:
             taxon_list_data = taxhub_rest_get_taxon_list(params_to_update=params)
-            features_with_taxhub_info = set_taxa_info_from_taxhub(
-                taxon_list_data, features
-            )
+            features_with_taxhub_info = set_taxa_info_from_taxhub(taxon_list_data, features)
         else:
             features_with_taxhub_info = features
 
@@ -408,10 +400,7 @@ 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:
@@ -434,9 +423,7 @@ def update_observation():
                 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(
-                        shape_geometry
-                    )
+                    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)
@@ -457,8 +444,7 @@ 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))
@@ -475,14 +461,10 @@ 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
@@ -499,9 +481,7 @@ 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"]]
 
@@ -525,9 +505,7 @@ def update_observation():
                 try:
                     observer = obs_to_update_obj.observer
                     send_user_email(
-                        subject=current_app.config["VALIDATION_EMAIL"][
-                            "SUBJECT"
-                        ].format(
+                        subject=current_app.config["VALIDATION_EMAIL"]["SUBJECT"].format(
                             program=f"{obs_to_update_obj.program_ref.title}",
                             observation=f"{obs_to_update_obj.name} (#{obs_to_update_obj.id_observation})",
                         ),
@@ -541,12 +519,8 @@ 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/routes.py

@@ -226,7 +226,14 @@ def get_program_sites(id):
         description: List of all sites
     """
     try:
-        sites = SiteModel.query.filter_by(id_program=id).all()
+        sites = (
+            db.session.query(SiteModel)
+            .join(VisitModel, SiteModel.id_site == VisitModel.id_site)
+            .filter(SiteModel.id_program == id)
+            .order_by(VisitModel.date.desc())
+            .order_by(SiteModel.timestamp_create.desc())
+            .all()
+        )
         return prepare_sites(sites)
     except Exception as e:
         return {"error_message": str(e)}, 400

backend/gncitizen/core/taxonomy/routes.py

@@ -1,8 +1,6 @@
 from typing import Any, Dict, List, Union
 
 from flask import Blueprint, current_app, request
-from utils_flask_sqla.response import json_resp
-
 from gncitizen.utils.taxonomy import (
     get_all_attributes,
     get_all_medias_types,
@@ -12,6 +10,7 @@
     taxhub_rest_get_all_lists,
     taxhub_rest_get_taxon_list,
 )
+from utils_flask_sqla.response import json_resp
 
 taxo_api = Blueprint("taxonomy", __name__)
 

backend/gncitizen/utils/taxonomy.py

@@ -74,9 +74,7 @@ def taxhub_rest_get_all_lists() -> Optional[Dict]:
     if res.status_code == 200:
         try:
             taxa_lists = res.json()["data"]
-            taxa_lists = [
-                taxa for taxa in taxa_lists if not taxa["id_liste"] in excluded_list_ids
-            ]
+            taxa_lists = [taxa for taxa in taxa_lists if not taxa["id_liste"] in excluded_list_ids]
             for taxa_list in taxa_lists:
                 taxonomy_lists.append(
                     (
@@ -255,9 +253,7 @@ def set_taxa_info_from_taxhub(taxhub_data, features):
             if feature["properties"]["cd_nom"] == taxon["cd_nom"]:
                 excluded_keys = {"medias", "attributs"}
                 filtered_data = {
-                    key: value
-                    for key, value in taxon.items()
-                    if key not in excluded_keys
+                    key: value for key, value in taxon.items() if key not in excluded_keys
                 }
 
                 if (