Merge d4bb629 into 123ee7c

.bumpversion.cfg

@@ -1,17 +1,17 @@
 [bumpversion]
-current_version = 0.2.2
+current_version = 0.3.0.dev0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<release>[a-z]+)(?P<build>\d+))?
-serialize = 
+serialize =
 	{major}.{minor}.{patch}.{release}{build}
 	{major}.{minor}.{patch}
 message = :bookmark: Bump version: {current_version} → {new_version}
 
 [bumpversion:part:release]
 optional_value = prod
 first_value = dev
-values = 
+values =
 	dev
 	prod
 
@@ -27,4 +27,8 @@ replace = {new_version}
 search = {current_version}
 replace = {new_version}
 
+[bumpversion:file:pyproject.toml]
+search = {current_version}
+replace = {new_version}
+
 [bumpversion:part:build]

.readthedocs.yml → .readthedocs.yaml

@@ -8,18 +8,18 @@ version: 2
 build:
   os: "ubuntu-22.04"
   tools:
-    python: "3.10"
+    python: "3.11"
   jobs:
     post_create_environment:
       # Install poetry
       # https://python-poetry.org/docs/#installing-manually
       - pip install poetry
-      # Tell poetry to not use a virtual environment
-      - poetry config virtualenvs.create false
     post_install:
       # Install dependencies with 'docs' dependency group
       # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
-      - poetry install
+      # VIRTUAL_ENV needs to be set manually for now.
+      # See https://github.com/readthedocs/readthedocs.org/pull/11152/
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --no-root
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

.vscode/settings.json

@@ -1,3 +1,17 @@
 {
-    "esbonio.sphinx.confDir": "${workspaceFolder}/flask-data/smarter/docs/source"
+    "esbonio.sphinx.confDir": "${workspaceFolder}/flask-data/smarter/docs/source",
+    "cSpell.words": [
+        "affymetrix",
+        "exitfirst",
+        "iname",
+        "INITDB",
+        "jsonify",
+        "mongodump",
+        "mongorestore",
+        "pytest",
+        "reqparse",
+        "showlocals",
+        "uwsgi",
+        "uwsgitop"
+    ]
 }

README.md

@@ -18,24 +18,12 @@ MONGODB_ROOT_USER=<root user>
 MONGODB_ROOT_PASS=<root pass>
 MONGODB_SMARTER_USER=<smarter user>
 MONGODB_SMARTER_PASS=<smarter pass>
-JWT_SECRET_KEY=<secret key>
 ```
 
 > *TODO*: manage sensitive data using secret in docker-compose, as described
 [here](https://docs.docker.com/engine/swarm/secrets/#use-secrets-in-compose) and
 [here](https://docs.docker.com/compose/compose-file/#secrets)
 
-### Genereate the JWT secret key
-
-[Here](https://stackoverflow.com/a/23728630/4385116) you can find hints on
-how to define a secret key with python:
-
-```python
-import string
-import secrets
-print(''.join(secrets.choice(string.ascii_letters + string.digits) for _ in range(50)))
-```
-
 ## Setting the proper permissions
 
 Set `mongodb-home` folder permissions with:
@@ -53,12 +41,11 @@ cd flask-data/
 find . -type f -iname "*.py" -exec chmod g-w {} \;
 ```
 
-## Add a smarter user
-
-Add a smarter user by calling a *flask script*:
+## Build and run the application
 
 ```bash
-docker-compose run --rm uwsgi flask users create smarter
+docker-compose build
+docker-compose up
 ```
 
 ## Connect to mongodb

docker-compose.yml

@@ -1,7 +1,5 @@
 
 # User/password credentials are stored in .env file
-version: '3.8'
-
 services:
 
   mongo:

flask-data/smarter/__init__.py

@@ -13,7 +13,7 @@
 __copyright__ = "Copyright 2021, IBBA-CNR"
 __credits__ = ["Paolo Cozzi, ..."]
 __license__ = "GNU General Public License v3"
-__version__ = "0.2.2"
+__version__ = "0.3.0.dev0"
 __maintainer__ = "Paolo Cozzi"
 __email__ = 'paolo.cozzi@ibba.cnr.it'
 __status__ = "Development"

flask-data/smarter/app.py

@@ -6,25 +6,24 @@
 @author: Paolo Cozzi <paolo.cozzi@ibba.cnr.it>
 """
 
-import os
-
 from bson import ObjectId
+import logging
 from logging.config import dictConfig
+from logging.handlers import SMTPHandler
 
-from flask import Flask, redirect, url_for
+from decouple import config
+from flask import Flask, redirect, url_for, has_request_context, request
+from flask.logging import default_handler
 from flask_restful import Api
-from flask_bcrypt import Bcrypt
-from flask_jwt_extended import JWTManager
 from flask.json import JSONEncoder
 from flask_cors import CORS
 from flasgger import Swagger
 
 from database.db import initialize_db, DB_ALIAS
 from resources.errors import errors
 from resources.routes import initialize_routes
-from commands import usersbp
 
-__version__ = "0.2.2"
+__version__ = "0.3.0.dev0"
 
 # https://flask.palletsprojects.com/en/2.0.x/logging/#basic-configuration
 dictConfig({
@@ -43,6 +42,43 @@
     }
 })
 
+mail_handler = SMTPHandler(
+    mailhost=(
+        config('EMAIL_HOST', default='localhost'),
+        config('EMAIL_PORT', cast=int, default=1025)
+    ),
+    fromaddr=config('DEFAULT_FROM_EMAIL', default="server-error@example.com"),
+    toaddrs=[email.strip() for email in config(
+        'ADMINS', default="admin@example.com").split(',')],
+    subject='SMARTER-backend Application Error',
+    credentials=(
+        config('EMAIL_HOST_USER', default=None),
+        config('EMAIL_HOST_PASSWORD', default=None)
+    ),
+    secure=()
+)
+mail_handler.setLevel(logging.ERROR)
+
+
+class RequestFormatter(logging.Formatter):
+    def format(self, record):
+        if has_request_context():
+            record.url = request.url
+            record.remote_addr = request.remote_addr
+        else:
+            record.url = None
+            record.remote_addr = None
+
+        return super().format(record)
+
+
+formatter = RequestFormatter(
+    '[%(asctime)s] %(remote_addr)s requested %(url)s\n'
+    '%(levelname)s in %(module)s: %(message)s'
+)
+mail_handler.setFormatter(formatter)
+default_handler.setFormatter(formatter)
+
 
 class CustomJSONEncoder(JSONEncoder):
     def default(self, obj):
@@ -54,33 +90,30 @@ def default(self, obj):
 
 
 # https://stackoverflow.com/a/56474420/4385116
-def create_app(config={}):
+def create_app():
     """This function create Flask app. Is required by wsgi because it need to
     be called after service is started and forked, not when importing the
     module during initialization. To start the flask app, first import
     the module and then create all the stuff by invoking this function
-    You need call the run method on the returned values to start acception
+    You need call the run method on the returned values to start accepting
     requests
 
-    Args:
-        config (dict): pass parameters to this app (not yet defined)
-
     Returns:
         Flask: a flask initialized application
     """
 
     app = Flask(__name__)
     CORS(app)
     api = Api(app, errors=errors)
-    Bcrypt(app)
-    JWTManager(app)
+
+    # check debug mode
+    if config('DEBUG', cast=bool, default=True):
+        # in debug mode, the default logging will be set to DEBUG level
+        app.debug = True
 
     # deal with ObjectId in json responses
     app.json_encoder = CustomJSONEncoder
 
-    # workaround to make flasgger deal with jwt-token headers
-    app.config["JWT_AUTH_URL_RULE"] = True
-
     # Swagger stuff
     swagger_template = {
         "swagger": "2.0",
@@ -115,38 +148,33 @@ def create_app(config={}):
 
     # http://docs.mongoengine.org/projects/flask-mongoengine/en/latest/#configuration
     app.config['MONGODB_SETTINGS'] = {
-        'host': 'mongodb://mongo/smarter',
-        'username': os.getenv("MONGODB_SMARTER_USER"),
-        'password': os.getenv("MONGODB_SMARTER_PASS"),
+        'host': config(
+            'MONGODB_SMARTER_DB',
+            default='mongodb://mongo/smarter'
+        ),
+        'username': config('MONGODB_SMARTER_USER'),
+        'password': config("MONGODB_SMARTER_PASS"),
         'authentication_source': 'admin',
         'alias': DB_ALIAS,
         # NOTE: This fixes "UserWarning: MongoClient opened before fork."
         # I'm not aware of side effects yet. Default value is/was "True"
         'connect': False
     }
 
-    # override configuration with custom values
-    if 'host' in config:
-        app.logger.error(f"Setting custom host: {config['host']}")
-        app.config['MONGODB_SETTINGS']['host'] = config['host']
-
-    # https://flask-jwt-extended.readthedocs.io/en/stable/basic_usage/
-    app.config["JWT_SECRET_KEY"] = os.getenv('JWT_SECRET_KEY')
-
     # connect to database
     initialize_db(app)
 
     app.logger.debug("Database initialized")
     app.logger.debug(f"Got encoder {app.json_encoder}")
 
-    # you MUST register the blueprint
-    app.register_blueprint(usersbp)
-
     # add resources
     initialize_routes(api)
 
     app.logger.debug("Routes initialized")
 
+    if not app.debug:
+        app.logger.addHandler(mail_handler)
+
     # add a redirect for the index page
     @app.route('/smarter-api/')
     def index():

flask-data/smarter/database/models.py

@@ -10,8 +10,6 @@
 
 from enum import Enum
 
-from flask_bcrypt import check_password_hash
-
 from .db import db, DB_ALIAS
 
 # Get an instance of a logger
@@ -39,19 +37,6 @@ class SmarterDBException(Exception):
     pass
 
 
-class User(db.Document):
-    username = db.StringField(required=True, unique=True)
-    password = db.StringField(required=True, min_length=6)
-
-    def check_password(self, password):
-        return check_password_hash(self.password, password)
-
-    meta = {
-        'db_alias': DB_ALIAS,
-        'collection': 'user'
-    }
-
-
 class SmarterInfo(db.Document):
     """A class to track database status informations"""
 
@@ -96,7 +81,7 @@ def __str__(self):
 class SupportedChip(db.Document):
     name = db.StringField(required=True, unique=True)
     species = db.StringField(required=True)
-    manifacturer = db.StringField()
+    manufacturer = db.StringField()
     n_of_snps = db.IntField(default=0)
 
     meta = {