update app: use custom requirements and other docker-compose adaptations

Dockerfile-back

@@ -21,8 +21,9 @@ RUN echo "appuser ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
 COPY vendor/GeoNature-citizen/ /home/appuser/citizen/
 
 # patches
-#COPY patches/back/requirements.txt /home/appuser/citizen/backend/requirements.txt #use the requirements from the GnC repo
-COPY patches/back/default_config.toml /home/appuser/citizen/config/default_config.toml
+#NB: use custom requirements.txt for avoiding fiona installation (GDAL issue)
+COPY patches/back/requirements.txt /home/appuser/citizen/backend/requirements.txt
+COPY patches/back/default_config.toml /home/appuser/citizen/config/config.toml
 COPY patches/settings.ini /home/appuser/citizen/config/settings.ini
 COPY patches/back/wsgi.py /home/appuser/citizen/backend/wsgi.py
 COPY patches/back/server.py /home/appuser/citizen/backend/server.py

docker-compose.override.yml

@@ -41,13 +41,14 @@ services:
       - ./vendor/GeoNature-citizen/backend/var/log/:/home/appuser/citizen/backend/var/log/
       - ./patches/settings.ini:/home/appuser/citizen/config/settings.ini
       - ./patches/settings.ini:/home/appuser/citizen/backend/config/settings.ini
-      - ./patches/back/default_config.toml:/home/appuser/citizen/config/default_config.toml
+      - ./patches/back/default_config.toml:/home/appuser/citizen/config/config.toml
       - ./patches/back/start_gunicorn.sh:/home/appuser/citizen/backend/start_gunicorn.sh
       - ./patches/back/wsgi.py:/home/appuser/citizen/backend/wsgi.py
       - ./patches/back/server.py:/home/appuser/citizen/backend/server.py
     ports:
       - "5002:5002"
-    command: bash start_gunicorn.sh
+    #command: bash start_gunicorn.sh
+    command: python wsgi.py
   taxhub:
     build:
       dockerfile: ./Dockerfile-taxhub

patches/back/requirements.txt

@@ -1,35 +1,53 @@
-certifi==2019.6.16
-chardet==3.0.4
-Click==7.0
-colorlog==4.0.2
-flasgger==0.9.3
-Flask==1.1.1
-Flask-Admin==1.5.3
-Flask-CKEditor==0.4.3
-Flask-Cors==3.0.8
-Flask-JWT-Extended==3.21.0
-Flask-SQLAlchemy==2.4.0
-GeoAlchemy2==0.6.3
+attrs==21.4.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
+certifi==2021.10.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
+charset-normalizer==2.0.11; python_full_version >= "3.6.0" and python_version >= "3"
+click-plugins==1.1.1
+click==7.1.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6" and python_version < "4"
+cligj==0.7.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version < "4"
+coloredlogs==15.0.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+# fiona==1.8.21
+flasgger==0.9.5
+flask-admin==1.6.0; python_version >= "3.6"
+flask-caching==1.10.1; python_version >= "3.5"
+flask-ckeditor==0.4.6
+flask-cors==3.0.10
+flask-jwt-extended==4.3.1; python_version >= "3.6" and python_version < "4"
+flask-sqlalchemy==2.5.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+flask==1.1.4; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+geoalchemy2==0.8.5
+geog==0.0.2
 geojson==2.5.0
-gunicorn==20.0.4
-idna==2.8
-itsdangerous==1.1.0
-Jinja2==2.10.1
-jsonschema==2.6.0
-MarkupSafe==1.1.1
-mistune==0.8.4
-passlib==1.7.1
-psycopg2-binary==2.8.3
-PyJWT==1.7.1
-PyYAML==5.1.2
-requests==2.22.0
-Shapely==1.7.1
-six==1.12.0
-SQLAlchemy==1.3.7
-toml==0.10.0
-urllib3==1.25.3
-Werkzeug==0.15.5
-WTForms==2.2.1
-gunicorn==20.0.4
-httplib2==0.19.0
+greenlet==1.1.2; python_version >= "3" and python_full_version < "3.0.0" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0") or python_version >= "3" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0") and python_full_version >= "3.5.0"
+gunicorn==20.1.0; python_version >= "3.5"
+humanfriendly==10.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
+idna==3.3; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.5"
+importlib-metadata==4.8.3; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.6.0" and python_version < "3.8" and python_version >= "3.6"
+itsdangerous==1.1.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+jinja2==2.11.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+jsonschema==4.0.0
+markupsafe==2.0.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+marshmallow==3.14.1; python_version >= "3.6"
+mistune==2.0.2
+munch==2.5.0
+numpy==1.19.5; python_version >= "3.6"
+passlib==1.7.4
+psycopg2-binary==2.9.3; python_version >= "3.6"
+pyjwt==2.3.0; python_version >= "3.6" and python_version < "4"
+pyreadline3==3.4.1; sys_platform == "win32" and python_version >= "3.8" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0")
+pyreadline==2.1; sys_platform == "win32" and python_version < "3.8" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0")
+pyrsistent==0.18.0; python_version >= "3.6"
+python-dateutil==2.8.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
+pyyaml==6.0; python_version >= "3.6"
+requests==2.27.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0")
+shapely==1.8.0; python_version >= "3.6"
+six==1.16.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
+sqlalchemy==1.4.31; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0")
+toml==0.10.2; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
+typing-extensions==4.0.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.6.0" and python_version < "3.8" and python_version >= "3.6"
+urllib3==1.26.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4"
+# utils-flask-sqlalchemy-geo==0.2.8
+utils-flask-sqlalchemy==0.2.6
+werkzeug==1.0.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0"
+wtforms==3.0.0; python_version >= "3.6"
 xlwt==1.3.0
+zipp==3.6.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.6.0" and python_version < "3.8" and python_version >= "3.6"

patches/back/server.py

@@ -96,7 +96,7 @@ def get_app(config, _app=None, with_external_mods=True, url_prefix="/api"):
         from gncitizen.core.users.routes import users_api
         from gncitizen.core.commons.routes import commons_api
         from gncitizen.core.observations.routes import obstax_api
-        from gncitizen.core.ref_geo.routes import geo_api
+        #from gncitizen.core.ref_geo.routes import geo_api
         from gncitizen.core.badges.routes import badges_api
         from gncitizen.core.taxonomy.routes import taxo_api
         from gncitizen.core.sites.routes import sites_api
@@ -104,7 +104,7 @@ def get_app(config, _app=None, with_external_mods=True, url_prefix="/api"):
         app.register_blueprint(users_api, url_prefix=url_prefix)
         app.register_blueprint(commons_api, url_prefix=url_prefix)
         app.register_blueprint(obstax_api, url_prefix=url_prefix)
-        app.register_blueprint(geo_api, url_prefix=url_prefix)
+        #app.register_blueprint(geo_api, url_prefix=url_prefix)
         app.register_blueprint(badges_api, url_prefix=url_prefix)
         app.register_blueprint(taxo_api, url_prefix=url_prefix)
         app.register_blueprint(sites_api, url_prefix=url_prefix + "/sites")