Intégration de taxhub v2 à GeoNature (#3150)

* TaxHub integration:
- load of blueprint
- add Babel for traductions
- Infer TAXHUB API URL from GN API
- remove taxhub from installation : systemd + apache 
* Taxhub integration (medias + suppression de l'installation standalone de TaxHub
* doc on taxhub
* compat 2.14
* fix multiple heads of migration ebbe0f7ed866
* add endpoint for taxhub media
* Centralisation des parametères relatif à taxhub sous section TAXHUB + API_PREFIX for taxhub api url - retrocompatibily occtax-mobile GeoNature-atlas
* Ajout paramètre taxref_region  
* update requirements
* Correction test_synthese::test_get_observations_for_web
* doc changelog

---------

Co-authored-by: TheoLechemia <[email protected]>
Co-authored-by: jacquesfize <[email protected]>
Co-authored-by: amandine-sahl <[email protected]>

.github/workflows/cypress.yml

@@ -78,6 +78,7 @@ jobs:
           GEONATURE_CONFIG_FILE: config/test_config.toml
           srid_local: 2154
           install_bdc_statuts: true
+          taxref_region: fr
           add_sample_data: true
           install_sig_layers: true
           install_grid_layer_5: true
@@ -100,7 +101,7 @@ jobs:
           cp ./config/settings.ini.sample ./config/settings.ini 
           ./install/05_install_frontend.sh --ci
         env:
-          GEONATURE_CONFIG_FILE: "${{ github.workspace }}/config/test_config.toml"
+          GEONATURE_CONFIG_FILE: '${{ github.workspace }}/config/test_config.toml'
       - name: Install core modules
         run: |
           geonature install-gn-module contrib/occtax OCCTAX --build=false
@@ -115,12 +116,6 @@ jobs:
         run: geonature dev_back &
         env:
           GEONATURE_CONFIG_FILE: config/test_config.toml
-      - name: Run TaxHub backend
-        run: flask run --host=0.0.0.0 &
-        working-directory: ./backend/dependencies/TaxHub/
-        env:
-          TAXHUB_SETTINGS: test_config.py
-          TAXHUB_SQLALCHEMY_DATABASE_URI: "postgresql://geonatadmin:[email protected]:5432/geonature2db"
       - name: Cypress run
         uses: cypress-io/github-action@v5
         with:

.github/workflows/eval.yml

@@ -94,6 +94,7 @@ jobs:
           GEONATURE_CONFIG_FILE: config/test_config.toml
           srid_local: 2154
           install_bdc_statuts: true
+          taxref_region: fr
           add_sample_data: true
           install_sig_layers: true
           install_grid_layer_5: true

.github/workflows/eval_perf.yml

@@ -9,16 +9,16 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        debian-version: ["11", "12"]
+        debian-version: ['11', '12']
         include:
-          - debian-version: "11"
-            python-version: "3.9"
-            postgres-version: "13"
-            postgis-version: "3.2"
-          - debian-version: "12"
-            python-version: "3.11"
-            postgres-version: "15"
-            postgis-version: "3.3"
+          - debian-version: '11'
+            python-version: '3.9'
+            postgres-version: '13'
+            postgis-version: '3.2'
+          - debian-version: '12'
+            python-version: '3.11'
+            postgres-version: '15'
+            postgis-version: '3.3'
 
     name: Debian ${{ matrix.debian-version }}
 
@@ -50,7 +50,7 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: "pip"
+          cache: 'pip'
       - name: Install GDAL
         run: |
           sudo apt update
@@ -94,6 +94,7 @@ jobs:
           GEONATURE_CONFIG_FILE: config/test_config.toml
           srid_local: 2154
           install_bdc_statuts: true
+          taxref_region: fr
           add_sample_data: true
           install_sig_layers: true
           install_grid_layer_5: true

.github/workflows/pytest.yml

@@ -95,6 +95,7 @@ jobs:
           GEONATURE_CONFIG_FILE: config/test_config.toml
           srid_local: 2154
           install_bdc_statuts: true
+          taxref_region: fr
           add_sample_data: true
           install_sig_layers: true
           install_grid_layer_5: true

backend/geonature/app.py

@@ -14,6 +14,7 @@
 from flask import Flask, g, request, current_app, send_from_directory
 from flask.json.provider import DefaultJSONProvider
 from flask_mail import Message
+from flask_babel import Babel
 from flask_cors import CORS
 from flask_login import current_user
 from flask_sqlalchemy.track_modifications import before_models_committed
@@ -82,6 +83,17 @@ def default(o):
         return DefaultJSONProvider.default(o)
 
 
+def get_locale():
+    # if a user is logged in, use the locale from the user settings
+    user = getattr(g, "user", None)
+    if user is not None:
+        return user.locale
+    # otherwise try to guess the language from the user accept
+    # header the browser transmits.  We support de/fr/en in this
+    # example.  The best match wins.
+    return request.accept_languages.best_match(["de", "fr", "en"])
+
+
 def create_app(with_external_mods=True):
     app = Flask(
         __name__.split(".")[0],
@@ -175,12 +187,22 @@ def set_sentry_context():
 
     admin.init_app(app)
 
+    # babel
+    babel = Babel(app, locale_selector=get_locale)
+
     # Enable serving of media files
     app.add_url_rule(
         f"{config['MEDIA_URL']}/<path:filename>",
         view_func=lambda filename: send_from_directory(config["MEDIA_FOLDER"], filename),
         endpoint="media",
     )
+    app.add_url_rule(
+        f"{config['MEDIA_URL']}/taxhub/<path:filename>",
+        view_func=lambda filename: send_from_directory(
+            config["MEDIA_FOLDER"] + "/taxhub", filename
+        ),
+        endpoint="media_taxhub",
+    )
 
     for blueprint_path, url_prefix in [
         ("pypn_habref_api.routes:routes", "/habref"),
@@ -202,6 +224,26 @@ def set_sentry_context():
         app.register_blueprint(blueprint, url_prefix=url_prefix)
 
     with app.app_context():
+        # taxhub api
+        from apptax import taxhub_api_routes
+
+        base_api_prefix = app.config["TAXHUB"].get("API_PREFIX")
+
+        for blueprint_path, url_prefix in taxhub_api_routes:
+            module_name, blueprint_name = blueprint_path.split(":")
+            blueprint = getattr(import_module(module_name), blueprint_name)
+            app.register_blueprint(blueprint, url_prefix="/taxhub" + base_api_prefix + url_prefix)
+
+        # taxhub admin
+        from apptax.admin.admin import adresses
+
+        app.register_blueprint(adresses, url_prefix="/taxhub")
+
+        # register taxhub admin view which need app context
+        from geonature.core.taxonomie.admin import load_admin_views
+
+        load_admin_views(app, admin)
+
         # register errors handlers
         import geonature.core.errors
 

backend/geonature/core/admin/admin.py

@@ -1,3 +1,5 @@
+import os
+
 from flask import g
 from werkzeug.exceptions import Unauthorized
 from flask_admin import Admin, AdminIndexView, expose
@@ -152,4 +154,5 @@ class ProtectedTNomenclaturesAdmin(
     )
 )
 
+
 flask_admin = admin  # for retro-compatibility, usefull for export module for instance

backend/geonature/core/command/main.py

@@ -115,7 +115,6 @@ def default_config():
     required_fields = (
         "URL_APPLICATION",
         "API_ENDPOINT",
-        "API_TAXHUB",
         "SECRET_KEY",
         "SQLALCHEMY_DATABASE_URI",
     )

backend/geonature/core/gn_permissions/admin.py

@@ -9,6 +9,7 @@
 from markupsafe import Markup
 from sqlalchemy.orm import contains_eager, joinedload
 from sqlalchemy import select
+from markupsafe import Markup
 
 from geonature.utils.env import db
 from geonature.utils.config import config

backend/geonature/core/taxonomie/admin.py

@@ -0,0 +1,92 @@
+import os
+from apptax.admin.admin_view import (
+    BibListesView,
+    TaxrefView,
+    TMediasView,
+    BibAttributsView,
+    BibThemesView,
+)
+from geonature.utils.env import db
+
+from apptax.admin.admin import adresses
+from apptax.taxonomie.models import Taxref, BibListes, TMedias, BibAttributs, BibThemes
+from geonature.core.admin.utils import CruvedProtectedMixin
+
+
+class CruvedProtectedBibListesView(CruvedProtectedMixin, BibListesView):
+    module_code = "TAXHUB"
+    object_code = "LISTE"
+    extra_actions_perm = {".import_cd_nom_view": "C"}
+
+
+class CruvedProtectedTaxrefView(CruvedProtectedMixin, TaxrefView):
+    module_code = "TAXHUB"
+    object_code = "TAXON"
+
+
+class CruvedProtectedTMediasView(CruvedProtectedMixin, TMediasView):
+    module_code = "TAXHUB"
+    object_code = "TAXON"
+
+
+class CruvedProtectedBibAttributsView(CruvedProtectedMixin, BibAttributsView):
+    module_code = "TAXHUB"
+    object_code = "ATTRIBUT"
+
+
+class CruvedProtectedBibThemes(CruvedProtectedMixin, BibThemesView):
+    module_code = "TAXHUB"
+    object_code = "THEME"
+
+
+def load_admin_views(app, admin):
+    static_folder = os.path.join(adresses.root_path, "static")
+
+    admin.add_view(
+        CruvedProtectedTaxrefView(
+            Taxref,
+            db.session,
+            name="Taxref",
+            endpoint="taxons",
+            category="TaxHub",
+            static_folder=static_folder,
+        )
+    )
+    admin.add_view(
+        CruvedProtectedBibListesView(
+            BibListes,
+            db.session,
+            name="Listes",
+            category="TaxHub",
+            static_folder=static_folder,
+        )
+    )
+
+    admin.add_view(
+        CruvedProtectedBibAttributsView(
+            BibAttributs,
+            db.session,
+            name="Attributs",
+            category="TaxHub",
+            static_folder=static_folder,
+        )
+    )
+    admin.add_view(
+        CruvedProtectedBibThemes(
+            BibThemes,
+            db.session,
+            name="Thèmes",
+            category="TaxHub",
+            static_folder=static_folder,
+        )
+    )
+
+    admin.add_view(
+        CruvedProtectedTMediasView(
+            TMedias,
+            db.session,
+            name="Médias",
+            category="TaxHub",
+            static_folder=static_folder,
+        )
+    )