Split into docker containers

This commit is contained in:
Marc Ducobu
2021-05-31 15:42:58 +02:00
parent eac9028900
commit 53ae96e0a9
21 changed files with 1557 additions and 8 deletions

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# Database
SQLALCHEMY_DATABASE_URI = "postgresql+psycopg2://postgres:postgres@db:5432/referentielsdb"
SQLALCHEMY_TRACK_MODIFICATIONS = false
# JWT Auth
JWT_SECRET_KEY = 'jwt-secret-string'
JWT_BLACKLIST_ENABLED = true
JWT_BLACKLIST_TOKEN_CHECKS = ['access', 'refresh']
# Application
appName = 'GeoNature-citizen' # Application name in the home page
DEFAULT_LANGUAGE = 'fr'
# Debug
DEBUG = false
SQLALCHEMY_DEBUG_LEVEL = 'WARNING'
# URL_APPLICATION = "http://mydomain.org" # Replace mydomain.org by your domain
URL_APPLICATION = "http://taxhub:5000"
API_TAXHUB = "http://taxhub:5000/api/"
# API_TAXHUB = "http://mytaxhub.org/api/" # Replace mytaxhub.org by your TaxHub url
SECRET_KEY = 'MyS3cr3tK3y'
CONFIRM_MAIL_SALT = 'your-secret-salt' # secret salt for corfirm mail token
MEDIA_FOLDER = 'media'
[RESET_PASSWD]
SUBJECT = "Link"
FROM = 'contact@geonature-citizen.fr'
TEXT_TEMPLATE = '''
Bonjour,\r\nVoici votre nouveau mot de passe :\r\n{passwd}\r\n"{app_url}
'''
HTML_TEMPLATE = '''
Bonjour,<br /><br />Voici votre nouveau mot de passe :<br />
{passwd}
<br /><br />"
<a href="{app_url}">Connexion</a>'
'''
[CONFIRM_EMAIL]
SUBJECT = "Activez votre compte"
FROM = 'contact@geonature-citizen.fr'
HTML_TEMPLATE = '''<p> Bonjour,</p><br /><p>Nous vous confirmons que votre compte a bien été créé.</p>
<p> Afin d'activer votre compte veuillez <a href="{activate_url}">cliquer ici.</a>
<p>Nous vous souhaitons la bienvenue sur notre site.</p><br />
<p>Bien à vous.</p>
'''
[MAIL]
MAIL_USE_SSL = false
MAIL_STARTTLS = true
MAIL_HOST = 'smtpd host'
MAIL_PORT = 493 # mandatory SSL port
MAIL_AUTH_LOGIN = 'smtpd/relay host username'
MAIL_AUTH_PASSWD = 'smtpd/relay host password'
# API flasgger main config

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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
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
xlwt==1.3.0

160
patches/back/server.py Normal file
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import sys
import os
import logging
from flask import Flask, current_app
from flask_cors import CORS
from gncitizen.utils.env import (
db,
list_and_import_gnc_modules,
jwt,
swagger,
admin,
ckeditor,
)
from gncitizen.utils.init_data import create_schemas, populate_modules
from gncitizen import __version__
basedir = os.path.abspath(os.path.dirname(__file__))
class ReverseProxied(object):
def __init__(self, app, script_name=None, scheme=None, server=None):
self.app = app
self.script_name = script_name
self.scheme = scheme
self.server = server
def __call__(self, environ, start_response):
script_name = environ.get("HTTP_X_SCRIPT_NAME", "") or self.script_name
if script_name:
environ["SCRIPT_NAME"] = script_name
path_info = environ["PATH_INFO"]
if path_info.startswith(script_name):
environ["PATH_INFO"] = path_info[len(script_name) :]
scheme = environ.get("HTTP_X_SCHEME", "") or self.scheme
if scheme:
environ["wsgi.url_scheme"] = scheme
server = environ.get("HTTP_X_FORWARDED_SERVER", "") or self.server
if server:
environ["HTTP_HOST"] = server
return self.app(environ, start_response)
def get_app(config, _app=None, with_external_mods=True, url_prefix="/api"):
# Make sure app is a singleton
if _app is not None:
return _app
app = Flask(__name__)
app.config.update(config)
if app.config["DEBUG"]:
from flask.logging import default_handler
import colorlog
handler = colorlog.StreamHandler()
handler.setFormatter(
colorlog.ColoredFormatter(
"""%(log_color)s%(asctime)s %(levelname)s:%(name)s:%(message)s [in %(pathname)s:%(lineno)d]"""
)
)
logger = logging.getLogger("werkzeug")
logger.addHandler(handler)
app.logger.removeHandler(default_handler)
for l in logging.Logger.manager.loggerDict.values():
if hasattr(l, "handlers"):
l.handlers = [handler]
# else:
# # TODO: sourced from app.config['LOGGING']
# logging.basicConfig()
# logger = logging.getLogger()
# logger.setLevel(logging.INFO)
logging.getLogger("sqlalchemy.engine").setLevel(
getattr(sys.modules["logging"], app.config["SQLALCHEMY_DEBUG_LEVEL"])
)
CORS(app, supports_credentials=True)
# app.config['PROPAGATE_EXCEPTIONS'] = False
# ... brings back those cors headers on error response in debug mode
# to trace client-side error handling
# but drops the embedded debugger ¯\_(ツ)_/¯
# https://github.com/corydolphin/flask-cors/issues/67
# https://stackoverflow.com/questions/29825235/getting-cors-headers-in-a-flask-500-error
# Bind app to DB
db.init_app(app)
# JWT Auth
jwt.init_app(app)
swagger.init_app(app)
admin.init_app(app)
ckeditor.init_app(app)
with app.app_context():
from gncitizen.core.users.routes import routes
app.register_blueprint(routes, url_prefix=url_prefix)
from gncitizen.core.commons.routes import routes
app.register_blueprint(routes, url_prefix=url_prefix)
from gncitizen.core.observations.routes import routes
app.register_blueprint(routes, url_prefix=url_prefix)
from gncitizen.core.ref_geo.routes import routes
app.register_blueprint(routes, url_prefix=url_prefix)
from gncitizen.core.badges.routes import routes
app.register_blueprint(routes, url_prefix=url_prefix)
from gncitizen.core.taxonomy.routes import routes
app.register_blueprint(routes, url_prefix=url_prefix)
from gncitizen.core.sites.routes import routes
app.register_blueprint(routes, url_prefix=url_prefix + "/sites")
CORS(app, supports_credentials=True)
# Chargement des mosdules tiers
if with_external_mods:
for conf, manifest, module in list_and_import_gnc_modules(app):
try:
prefix = url_prefix + conf["api_url"]
except Exception as e:
current_app.logger.debug(e)
prefix = url_prefix
app.register_blueprint(
module.backend.blueprint.blueprint, url_prefix=prefix
)
try:
module.backend.models.create_schema(db)
except Exception as e:
current_app.logger.debug(e)
# chargement de la configuration
# du module dans le blueprint.config
module.backend.blueprint.blueprint.config = conf
app.config[manifest["module_name"]] = conf
_app = app
create_schemas(db)
db.create_all()
populate_modules(db)
return app

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patches/back/wsgi.py Normal file
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"""
Give a unique entry point for gunicorn
"""
from gncitizen.utils.env import load_config
from server import get_app
# get the app config file
config = load_config()
# give the app context from server.py in a app object
app = get_app(config)
port = app.config["API_PORT"] if app.config.get("API_PORT", False) else 5002
if __name__ == "__main__":
app.debug = True
app.run(host="0.0.0.0", port=port)

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export const AppConfig = {
appName: "GeoNature-citizen",
API_ENDPOINT:"http://localhost:8080/citizen/api",
API_TAXHUB:"http://localhost:5000/api/",
FRONTEND:{
PROD_MOD:true,
MULTILINGUAL:false,
DISPLAY_FOOTER: true,
DISPLAY_TOPBAR: true,
DISPLAY_SIDEBAR: true,
DISPLAY_STATS: true,
DISPLAY_BADGES: true,
NEW_OBS_FORM_MODAL_VERSION: true
},
META: {
keywords: 'biodiversite enquetes participatif observations',
},
about: true,
URL_APPLICATION:"http://localhost:4000/",
REWARDS: true,
termsOfUse: {
fr: "assets/cgu.pdf",
en: "assets/termsOfUse.pdf"
},
signup:true,
email_contact:false,
platform_intro: {
fr: "Bienvenue<br /> sur GeoNature Citizen",
en: "Welcome<br /> on GeoNature Citizen"
},
platform_teaser: {
fr: "Hae duae provinciae bello quondam piratico catervis mixtae praedonum a Servilio pro consule missae sub iugum factae sunt vectigales. et hae quidem regiones velut in prominenti terrarum lingua positae ob orbe eoo monte Amano disparantur.",
en: "Hae duae provinciae bello quondam piratico catervis mixtae praedonum a Servilio pro consule missae sub iugum factae sunt vectigales. et hae quidem regiones velut in prominenti terrarum lingua positae ob orbe eoo monte Amano disparantur."
},
platform_participate: {
fr: "PARTICIPER AU PROGRAMME",
en: "PARTICIPATE"
},
programs_label: {
fr: "Programmes",
en: "Surveys"
},
program_label: {
fr: "Le programme",
en: "Survey"
},
program_share_an_observation: {
fr: "PARTAGER UNE OBSERVATION",
en: "SHARE AN OBSERVATION"
},
program_add_an_observation: {
fr: "AJOUTER UNE OBSERVATION",
en: "CONTRIBUTE AN OBSERVATION"
},
program_allow_email_contact: {
fr: "J'accepte que mon adresse e-mail puisse être utilisée pour recontacter à propos de mon observation",
en : "I agree that my e-mail address can be used to recontact about my observation"
},
taxonSelectInputThreshold: 7,
taxonAutocompleteInputThreshold: 12,
taxonAutocompleteFields: [
"nom_complet",
"nom_vern",
"nom_vern_eng",
"cd_nom"
],
taxonDisplaySciName: true,
program_list_observers_names: true,
program_list_sort: "-timestamp_create",
details_espece_url: "<url_inpn_or_atlas>/cd_nom/", // !! gardez bien le cd_nom/ dans l'url
registration_message : "Vous inscrire vous permet de gérer vos observations"
}

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@@ -7,9 +7,9 @@ my_local=fr_FR.UTF-8
my_url=http://localhost:8080/
url_application=http://localhost:8080/ # Url For the frontend
api_endpoint=http://localhost:8080/api # Url for the geonature api don't forget /api
api_endpoint=http://localhost:8080/citizen/api # Url for the geonature api don't forget /api
api_port=5002
api_taxhub=http://localhost/taxhub/api/ # Url for the taxhub api
api_taxhub=http://localhost:8080/taxhub/api/ # Url for the taxhub api
install_taxhub=1
taxhub_version=1.7.3
@@ -27,15 +27,15 @@ admin_password=MotDePasseAChanger
# Localisation du server PostgreSQL.
# Les scripts d'installation automatique ne fonctionnent que si votre BDD est sur le même serveur (localhost)
pg_host=localhost
pg_host=db
# Port sur lequel PostgreSQL ecoute
pg_port=5432
#Base de donnée Geonature
pg_dbname=dbname
pg_dbname=postgres
# Nom de l'utilisateur propriétaire des bases UsersHub, GeoNature, TaxHub
user_pg=dbuser
user_pg=postgres
# Pass de l'utilisateur propriétaire des bases UsersHub, GeoNature, TaxHub
user_pg_pass=dbpwd
user_pg_pass=postgres
#########################
### Gunicorn settings ###

29
patches/taxhub/config.py Normal file
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'''
TaxHub global settings file
'''
# Database settings
SQLALCHEMY_DATABASE_URI = "postgresql://postgres:postgres@db/referentielsdb"
SQLALCHEMY_TRACK_MODIFICATIONS = False
DEBUG=True
SESSION_TYPE = 'filesystem'
SECRET_KEY = 'super secret key'
COOKIE_EXPIRATION = 3600
COOKIE_AUTORENEW = True
# File
import os
BASE_DIR = os.path.abspath(os.path.dirname(__file__))
UPLOAD_FOLDER = 'static/medias'
# Authentification crypting method (hash or md5)
PASS_METHOD='hash'
# ID APPLICATION TaxHub
# User in the authentification submodule to avoid token conflict between app on the same server
ID_APP = 2

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#!/bin/bash
# Make sure only root can run our script
if [ "$(id -u)" == 0 ]; then
echo "This script must not be run as root" 1>&2
exit 1
fi
#Création des répertoires systèmes
. create_sys_dir.sh
create_sys_dir
if [ ! -f settings.ini ]; then
cp settings.ini.sample settings.ini
fi
# nano settings.ini
#include user config = settings.ini
. settings.ini
#get app path
DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
LOG_DIR=$DIR/var/log
function database_exists () {
# /!\ Will return false if psql can't list database. Edit your pg_hba.conf
# as appropriate.
if [ -z $1 ]
then
# Argument is null
return 0
else
# Grep db name in the list of database
sudo -u postgres -s -- psql -tAl | grep -q "^$1|"
return $?
fi
}
if database_exists $db_name
then
if $drop_apps_db
then
echo "Suppression de la base..."
sudo -u postgres -s dropdb $db_name
else
echo "La base de données existe et le fichier de settings indique de ne pas la supprimer."
fi
fi
if ! database_exists $db_name
then
echo "Création de la base..."
sudo -u postgres -s createdb -O $user_pg $db_name
sudo -n -u postgres -s psql -d $db_name -c "CREATE EXTENSION IF NOT EXISTS pg_trgm;" &> $LOG_DIR/installdb/install_db.log
sudo -n -u postgres -s psql -d $db_name -c 'CREATE EXTENSION IF NOT EXISTS "uuid-ossp";' &>> $LOG_DIR/installdb/install_db.log
sudo -n -u postgres -s psql -d $db_name -c 'CREATE EXTENSION IF NOT EXISTS "pg_trgm";' &>> $LOG_DIR/installdb/install_db.log
# Mise en place de la structure de la base et des données permettant son fonctionnement avec l'application
echo "Création de la structure de la base..."
export PGPASSWORD=$user_pg_pass;psql -h $db_host -U $user_pg -d $db_name -f data/taxhubdb.sql &> $LOG_DIR/installdb/install_db.log
export PGPASSWORD=$user_pg_pass;psql -h $db_host -U $user_pg -d $db_name -f data/generic_drop_and_restore_deps_views.sql &> $LOG_DIR/installdb/install_db.log
echo "Décompression des fichiers du taxref..."
array=( TAXREF_INPN_v13.zip ESPECES_REGLEMENTEES_v11.zip LR_FRANCE_20160000.zip BDC_STATUTS_13.zip)
for i in "${array[@]}"
do
if [ ! -f '/tmp/taxhub/'$i ]
then
wget http://geonature.fr/data/inpn/taxonomie/$i -P /tmp/taxhub
unzip /tmp/taxhub/$i -d /tmp/taxhub
else
echo $i exists
fi
done
echo "Insertion des données taxonomiques de l'inpn... (cette opération peut être longue)"
cd $DIR
sudo -u postgres -s psql -d $db_name -f data/inpn/data_inpn_taxhub.sql &>> $LOG_DIR/installdb/install_db.log
echo "Création de la vue représentant la hierarchie taxonomique..."
export PGPASSWORD=$user_pg_pass;psql -h $db_host -U $user_pg -d $db_name -f data/materialized_views.sql &>> $LOG_DIR/installdb/install_db.log
echo "Insertion de données de base"
export PGPASSWORD=$user_pg_pass;psql -h $db_host -U $user_pg -d $db_name -f data/taxhubdata.sql &>> $LOG_DIR/installdb/install_db.log
echo "Insertion de fonctions génériques de détection de vues dépendantes"
export PGPASSWORD=$user_pg_pass;psql -h $db_host -U $user_pg -d $db_name -f data/generic_drop_and_restore_deps_views.sql &>> $LOG_DIR/installdb/install_db.log
if $insert_geonatureatlas_data
then
echo "Insertion de données nécessaires à GeoNature-atlas"
export PGPASSWORD=$user_pg_pass;psql -h $db_host -U $user_pg -d $db_name -f data/taxhubdata_atlas.sql &>> $LOG_DIR/installdb/install_db.log
fi
if $insert_attribut_example
then
echo "Insertion d'un exemple d'attribut"
export PGPASSWORD=$user_pg_pass;psql -h $db_host -U $user_pg -d $db_name -f data/taxhubdata_example.sql &>> $LOG_DIR/installdb/install_db.log
fi
if $insert_taxons_example
then
echo "Insertion de 8 taxons exemple"
export PGPASSWORD=$user_pg_pass;psql -h $db_host -U $user_pg -d $db_name -f data/taxhubdata_taxons_example.sql &>> $LOG_DIR/installdb/install_db.log
fi
if [ $users_schema = "local" ]
then
echo "Création du schéma Utilisateur..."
wget https://raw.githubusercontent.com/PnX-SI/UsersHub/$usershub_release/data/usershub.sql -P /tmp
wget https://raw.githubusercontent.com/PnX-SI/UsersHub/$usershub_release/data/usershub-data.sql -P /tmp
wget https://raw.githubusercontent.com/PnX-SI/UsersHub/$usershub_release/data/usershub-dataset.sql -P /tmp
export PGPASSWORD=$user_pg_pass;psql -h $db_host -U $user_pg -d $db_name -f /tmp/usershub.sql &>> $LOG_DIR/installdb/install_db.log
export PGPASSWORD=$user_pg_pass;psql -h $db_host -U $user_pg -d $db_name -f /tmp/usershub-data.sql &>> $LOG_DIR/installdb/install_db.log
export PGPASSWORD=$user_pg_pass;psql -h $db_host -U $user_pg -d $db_name -f /tmp/usershub-dataset.sql &>> $LOG_DIR/installdb/install_db.log
export PGPASSWORD=$user_pg_pass;psql -h $db_host -U $user_pg -d $db_name -f data/adds_for_usershub.sql &>> $LOG_DIR/installdb/install_db.log
else
echo "Connexion à la base Utilisateur..."
cp data/create_fdw_utilisateurs.sql /tmp/taxhub/create_fdw_utilisateurs.sql
cp data/grant.sql /tmp/taxhub/grant.sql
sed -i "s#\$user_pg#$user_pg#g" /tmp/taxhub/create_fdw_utilisateurs.sql
sed -i "s#\$usershub_host#$usershub_host#g" /tmp/taxhub/create_fdw_utilisateurs.sql
sed -i "s#\$usershub_db#$usershub_db#g" /tmp/taxhub/create_fdw_utilisateurs.sql
sed -i "s#\$usershub_port#$usershub_port#g" /tmp/taxhub/create_fdw_utilisateurs.sql
sed -i "s#\$usershub_user#$usershub_user#g" /tmp/taxhub/create_fdw_utilisateurs.sql
sed -i "s#\$usershub_pass#$usershub_pass#g" /tmp/taxhub/create_fdw_utilisateurs.sql
sed -i "s#\$usershub_user#$usershub_user#g" /tmp/taxhub/grant.sql
sudo -u postgres -s psql -d $db_name -f /tmp/taxhub/create_fdw_utilisateurs.sql &>> $LOG_DIR/installdb/install_db.log
sudo -u postgres -s psql -d $db_name -f /tmp/taxhub/grant.sql &>> $LOG_DIR/installdb/install_db.log
fi
# Vaccum database
echo "Vaccum database ... (cette opération peut être longue)"
export PGPASSWORD=$user_pg_pass;psql -h $db_host -U $user_pg -d $db_name -c "VACUUM FULL VERBOSE;" &>> $LOG_DIR/installdb/install_db.log
fi

65
patches/taxhub/server.py Normal file
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# coding: utf8
from flask import Flask
from flask_cors import CORS
from apptax.database import db
db = db
app_globals = {}
def init_app():
if app_globals.get('app', False):
app = app_globals['app']
else:
app = Flask(__name__)
with app.app_context():
app.config.from_pyfile('config.py')
db.init_app(app)
db.app = app
app.config['DB'] = db
@app.teardown_request
def _manage_transaction(exception):
if exception:
db.session.rollback()
else:
db.session.commit()
db.session.remove()
from pypnusershub import routes
app.register_blueprint(routes.routes, url_prefix='/api/auth')
from apptax.index import routes
app.register_blueprint(routes, url_prefix='/')
from apptax.taxonomie.routesbibnoms import adresses
app.register_blueprint(adresses, url_prefix='/api/bibnoms')
from apptax.taxonomie.routestaxref import adresses
app.register_blueprint(adresses, url_prefix='/api/taxref')
from apptax.taxonomie.routesbibattributs import adresses
app.register_blueprint(adresses, url_prefix='/api/bibattributs')
from apptax.taxonomie.routesbiblistes import adresses
app.register_blueprint(adresses, url_prefix='/api/biblistes')
from apptax.taxonomie.routestmedias import adresses
app.register_blueprint(adresses, url_prefix='/api/tmedias')
from apptax.taxonomie.routesbibtypesmedia import adresses
app.register_blueprint(adresses, url_prefix='/api/bibtypesmedia')
from apptax.utils.routesconfig import adresses
app.register_blueprint(adresses, url_prefix='/api/config')
return app
app = init_app()
CORS(app, supports_credentials=True)
if __name__ == '__main__':
app.run(host="0.0.0.0", debug=True)

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##########################################
###### TAXHUB installation settings ######
##########################################
app_name=taxhub
#######################
### Python settings ###
#######################
venv_dir=venv
python_path=/usr/bin/python3
###########################
### PostgreSQL settings ###
###########################
# Drop eventual existing database during installation
drop_apps_db=false
# DB host
db_host=db
# PostgreSQL port
db_port=5432
# Database name
db_name=referentielsdb
# Database owner username
user_pg=postgres
# Database owner password
user_pg_pass=postgres
### Users schema localisation
# Possible values : 'local' or 'foreign'
# 'local' means that the 'utilisateurs' schema has to be installed in TaxHub database.
# 'foreign' means that the 'utilisateurs' schema is in another database. An FDW schema will be created on it.
# Nota : foreign requires UsersHub to be already installed
usershub_release=2.1.1
users_schema=local
### UsersHub relation settings - Required if users_schema=foreign
usershub_host=db
usershub_db=referentielsdb
usershub_port=5432
usershub_user=postgres
usershub_pass=postgres
###############
### Options ###
###############
# Insert GeoNature-atlas data (theme & attributs)
insert_geonatureatlas_data=true
# Insert an example of attribute (Migrateur)
insert_attribut_example=false
# Insert 8 examples of taxons and add it to the Occtax list
insert_taxons_example=true
#########################
### Gunicorn settings ###
#########################
gun_num_workers=4
gun_host=0.0.0.0
gun_port=5000