Merge pull request #2706 from PnX-SI/develop

Develop > Master / 2.13.1

.github/ISSUE_TEMPLATE/rapport-de-bug.md

@@ -13,8 +13,8 @@ Version de GeoNature affectée par le bug.
 **Description du bug**
 Description du problème rencontré (message d’erreur, code HTTP de retour inattendu, …).
 
-**Comportement attendue**
-Description du comportement attendue en lieu et place du problème rencontré.
+**Comportement attendu**
+Description du comportement attendu en lieu et place du problème rencontré.
 
 **Comment reproduire**
 Étapes à suivre pour reproduire le problème (sur quelle page se rendre, sur quel bouton cliquer, avec quelles données présentes, …).

VERSION

@@ -1 +1 @@
-2.13.0
+2.13.1

backend/Dockerfile

@@ -6,7 +6,6 @@ ENV PIP_ROOT_USER_ACTION=ignore
 RUN --mount=type=cache,target=/root/.cache \
     pip install --upgrade pip setuptools wheel
 
-
 FROM build AS build-habref
 WORKDIR /build/
 COPY /backend/dependencies/Habref-api-module .
@@ -114,12 +113,12 @@ RUN --mount=type=cache,target=/root/.cache \
     pip install --upgrade pip setuptools wheel
 
 WORKDIR /dist
-ENV GEONATURE_STATIC_PATH=/dist/static/
+ENV GEONATURE_STATIC_FOLDER=/dist/static/
 COPY /backend/static/ ./static/
 COPY --from=node /dist/node_modules/ ./static/node_modules/
-ENV GEONATURE_CUSTOM_STATIC_PATH=/dist/custom/
+ENV GEONATURE_CUSTOM_STATIC_FOLDER=/dist/custom/
 RUN mkdir custom
-ENV GEONATURE_MEDIA_PATH=/dist/media/
+ENV GEONATURE_MEDIA_FOLDER=/dist/media/
 RUN mkdir -p media/attachments
 
 WORKDIR /dist/geonature
@@ -140,13 +139,20 @@ COPY --from=build-utils-geo /build/dist/*.whl .
 COPY --from=build-geonature /build/dist/*.whl .
 
 COPY --chmod=755 /install/03b_populate_db.sh /populate_db.sh
-COPY --chmod=755 /install/assets/docker_startup.sh /startup.sh
+COPY --chmod=755 /install/assets/docker_entrypoint.sh /entrypoint.sh
 
 ENV GEONATURE_CONFIG_FILE ""
 
 EXPOSE 8000
 
-CMD ["/startup.sh"]
+ENTRYPOINT ["/entrypoint.sh"]
+CMD [ "gunicorn", "geonature:create_app()", \
+    "--name=geonature", \
+    "--workers=2", \
+    "--threads=2", \
+    "--access-logfile=-", \
+    "--bind=0.0.0.0:8000" \
+]
 
 
 FROM wheels-light AS wheels

backend/geonature/core/gn_commons/routes.py

@@ -59,14 +59,14 @@ def list_modules():
     """
     params = request.args
     q = TModules.query.options(joinedload(TModules.objects))
+    exclude = current_app.config["DISABLED_MODULES"]
     if "exclude" in params:
-        q = q.filter(TModules.module_code.notin_(params.getlist("exclude")))
+        exclude.extend(params.getlist("exclude"))
+    q = q.filter(TModules.module_code.notin_(exclude))
     q = q.order_by(TModules.module_order.asc()).order_by(TModules.module_label.asc())
     modules = q.all()
     allowed_modules = []
     for module in modules:
-        if module.module_code in current_app.config["DISABLED_MODULES"]:
-            continue
         module_allowed = False
         # HACK : on a besoin d'avoir le module GeoNature en front pour l'URL de la doc
         if module.module_code == "GEONATURE":

backend/geonature/core/gn_synthese/routes.py

@@ -796,15 +796,18 @@ def get_autocomplete_taxons_synthese():
         .join(Synthese, Synthese.cd_nom == VMTaxrefListForautocomplete.cd_nom)
     )
     search_name = search_name.replace(" ", "%")
-    q = q.filter(VMTaxrefListForautocomplete.unaccent_search_name.ilike("%" + search_name + "%"))
+    q = q.filter(
+        VMTaxrefListForautocomplete.unaccent_search_name.ilike(
+            func.unaccent("%" + search_name + "%")
+        )
+    )
     regne = request.args.get("regne")
     if regne:
         q = q.filter(VMTaxrefListForautocomplete.regne == regne)
 
     group2_inpn = request.args.get("group2_inpn")
     if group2_inpn:
         q = q.filter(VMTaxrefListForautocomplete.group2_inpn == group2_inpn)
-
     q = q.order_by(desc(VMTaxrefListForautocomplete.cd_nom == VMTaxrefListForautocomplete.cd_ref))
     limit = request.args.get("limit", 20)
     data = q.order_by(desc("idx_trgm")).limit(20).all()
@@ -1106,11 +1109,21 @@ def create_report(permissions):
         TReport.id_synthese == id_synthese,
         TReport.report_type.has(BibReportsTypes.type == type_name),
     )
+
+    user_pin = TReport.query.filter(
+        TReport.id_synthese == id_synthese,
+        TReport.report_type.has(BibReportsTypes.type == "pin"),
+        TReport.id_role == g.current_user.id_role,
+    )
     # only allow one alert by id_synthese
-    if type_name in ["alert", "pin"]:
+    if type_name in ["alert"]:
         alert_exists = report_query.one_or_none()
         if alert_exists is not None:
             raise Conflict("This type already exists for this id")
+    if type_name in ["pin"]:
+        pin_exist = user_pin.one_or_none()
+        if pin_exist is not None:
+            raise Conflict("This type already exists for this id")
     new_entry = TReport(
         id_synthese=id_synthese,
         id_role=g.current_user.id_role,

backend/requirements-dependencies.in

@@ -1,7 +1,7 @@
-pypnusershub>=1.6.9,<2
+pypnusershub>=1.6.10,<2
 pypnnomenclature>=1.5.4,<2
 pypn_habref_api>=0.3.2,<1
 utils-flask-sqlalchemy-geo>=0.2.8,<1
-utils-flask-sqlalchemy>=0.3.5,<1
-taxhub>=1.12.0,<2
-pypn-ref-geo>=1.3.0,<2
+utils-flask-sqlalchemy>=0.3.6,<1
+taxhub>=1.12.1,<2
+pypn-ref-geo>=1.4.0,<2

backend/requirements-dev.txt

@@ -37,14 +37,14 @@
     # via
     #   -r requirements-submodules.in
     #   pypn-ref-geo
-alembic==1.11.1
+alembic==1.12.0
     # via
     #   flask-migrate
     #   pypn-ref-geo
     #   pypnusershub
 amqp==5.1.1
     # via kombu
-async-timeout==4.0.2
+async-timeout==4.0.3
     # via redis
 attrs==23.1.0
     # via fiona
@@ -56,23 +56,23 @@ billiard==3.6.4.0
     # via celery
 blinker==1.6.2
     # via flask-mail
-boto3==1.28.2
+boto3==1.28.47
     # via taxhub
-botocore==1.31.2
+botocore==1.31.47
     # via
     #   boto3
     #   s3transfer
 cached-property==1.5.2
     # via kombu
-cairocffi==1.6.0
+cairocffi==1.6.1
     # via
     #   cairosvg
     #   weasyprint
-cairosvg==2.7.0
+cairosvg==2.7.1
     # via weasyprint
 celery[redis]==5.2.7
     # via -r requirements-common.in
-certifi==2023.5.7
+certifi==2023.7.22
     # via
     #   fiona
     #   requests
@@ -83,7 +83,7 @@ cffi==1.15.1
     #   weasyprint
 charset-normalizer==3.2.0
     # via requests
-click==8.1.4
+click==8.1.7
     # via
     #   -r requirements-common.in
     #   celery
@@ -104,7 +104,7 @@ click-repl==0.3.0
     # via celery
 cligj==0.7.2
     # via fiona
-cryptography==41.0.2
+cryptography==41.0.3
     # via authlib
 cssselect2==0.7.0
     # via
@@ -156,7 +156,7 @@ flask-marshmallow==0.14.0
     #   pypn-habref-api
     #   pypnnomenclature
     #   pypnusershub
-flask-migrate==4.0.4
+flask-migrate==4.0.5
     # via
     #   -r requirements-common.in
     #   pypn-habref-api
@@ -187,7 +187,7 @@ geojson==3.0.1
     # via
     #   -r requirements-common.in
     #   utils-flask-sqlalchemy-geo
-gunicorn==20.1.0
+gunicorn==21.2.0
     # via
     #   -r requirements-common.in
     #   taxhub
@@ -206,6 +206,7 @@ importlib-metadata==4.13.0 ; python_version < "3.10"
     #   celery
     #   click
     #   flask
+    #   gunicorn
     #   kombu
     #   mako
     #   munch
@@ -264,6 +265,7 @@ packaging==23.1
     # via
     #   -r requirements-common.in
     #   geoalchemy2
+    #   gunicorn
     #   marshmallow
     #   marshmallow-sqlalchemy
 pillow==9.5.0
@@ -274,7 +276,7 @@ pillow==9.5.0
     #   weasyprint
 prompt-toolkit==3.0.39
     # via click-repl
-psycopg2==2.9.6
+psycopg2==2.9.7
     # via
     #   -r requirements-common.in
     #   pypn-habref-api
@@ -300,15 +302,15 @@ python-dotenv==0.21.1
     #   pypnnomenclature
     #   taxhub
     #   usershub
-pytz==2023.3
+pytz==2023.3.post1
     # via celery
-redis==4.6.0
+redis==5.0.0
     # via celery
 requests==2.31.0
     # via
     #   pypn-habref-api
     #   pypnusershub
-s3transfer==0.6.1
+s3transfer==0.6.2
     # via boto3
 shapely==1.8.5.post1
     # via

backend/requirements.txt

@@ -4,14 +4,14 @@
 #
 #    pip-compile --resolver=backtracking requirements.in
 #
-alembic==1.11.2
+alembic==1.12.0
     # via
     #   flask-migrate
     #   pypn-ref-geo
     #   pypnusershub
 amqp==5.1.1
     # via kombu
-async-timeout==4.0.2
+async-timeout==4.0.3
     # via redis
 attrs==23.1.0
     # via fiona
@@ -23,9 +23,9 @@ billiard==3.6.4.0
     # via celery
 blinker==1.6.2
     # via flask-mail
-boto3==1.28.21
+boto3==1.28.47
     # via taxhub
-botocore==1.31.21
+botocore==1.31.47
     # via
     #   boto3
     #   s3transfer
@@ -50,7 +50,7 @@ cffi==1.15.1
     #   weasyprint
 charset-normalizer==3.2.0
     # via requests
-click==8.1.6
+click==8.1.7
     # via
     #   -r requirements-common.in
     #   celery
@@ -116,7 +116,7 @@ flask-marshmallow==0.14.0
     #   pypn-habref-api
     #   pypnnomenclature
     #   pypnusershub
-flask-migrate==4.0.4
+flask-migrate==4.0.5
     # via
     #   -r requirements-common.in
     #   pypn-habref-api
@@ -237,13 +237,13 @@ pyphen==0.14.0
     # via weasyprint
 pypn-habref-api==0.3.2
     # via -r requirements-dependencies.in
-pypn-ref-geo==1.3.0
+pypn-ref-geo==1.4.0
     # via
     #   -r requirements-dependencies.in
     #   taxhub
 pypnnomenclature==1.5.4
     # via -r requirements-dependencies.in
-pypnusershub==1.6.9
+pypnusershub==1.6.10
     # via
     #   -r requirements-dependencies.in
     #   pypnnomenclature
@@ -259,15 +259,15 @@ python-dotenv==0.21.1
     #   pypn-ref-geo
     #   pypnnomenclature
     #   taxhub
-pytz==2023.3
+pytz==2023.3.post1
     # via celery
-redis==4.6.0
+redis==5.0.0
     # via celery
 requests==2.31.0
     # via
     #   pypn-habref-api
     #   pypnusershub
-s3transfer==0.6.1
+s3transfer==0.6.2
     # via boto3
 shapely==1.8.5.post1
     # via
@@ -295,7 +295,7 @@ sqlalchemy==1.3.24
     #   utils-flask-sqlalchemy
     #   utils-flask-sqlalchemy-geo
     #   wtforms-sqlalchemy
-taxhub==1.12.0
+taxhub==1.12.1
     # via
     #   -r requirements-dependencies.in
     #   pypnnomenclature
@@ -317,7 +317,7 @@ urllib3==1.26.16
     #   botocore
     #   requests
     #   taxhub
-utils-flask-sqlalchemy==0.3.5
+utils-flask-sqlalchemy==0.3.6
     # via
     #   -r requirements-dependencies.in
     #   pypn-habref-api