black formatting

README.md

@@ -3,6 +3,11 @@
 
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) 
 [![CI-CD](https://github.com/openCONTRABASS/CONTRABASS-webservice/actions/workflows/main.yml/badge.svg)](https://github.com/openCONTRABASS/CONTRABASS-webservice/actions/workflows/main.yml)
+[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=openCONTRABASS_CONTRABASS-webservice&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=openCONTRABASS_CONTRABASS-webservice)
+[![codecov](https://codecov.io/gh/openCONTRABASS/CONTRABASS-webservice/branch/main/graph/badge.svg?token=T1S7E99XJJ)](https://codecov.io/gh/openCONTRABASS/CONTRABASS-webservice)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) 
+
+```CONTRABASS RESTful API``` is a python-based asynchronous-tasks RESTful API intended for the computation and analysis of vulnerabilities in genome-scale metabolic models. These webservices are just a backed for [CONTRABASS python tool](https://github.com/openCONTRABASS/CONTRABASS). 
 
 ## Table of Contents
 - [License](#license)

src/restapi/app.py

@@ -16,6 +16,7 @@
     along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """
 import eventlet
+
 eventlet.monkey_patch()
 
 import os
@@ -45,21 +46,21 @@
 from .exception_handler import init_exception_handler
 
 basedir = os.path.abspath(os.path.dirname(__file__))
-load_dotenv(os.path.join(basedir, '../../.env'))
+load_dotenv(os.path.join(basedir, "../../.env"))
 
 
 LOGGER = logging.getLogger(__name__)
 
 app = Flask(__name__)
-app.config.from_object(os.environ['APP_SETTINGS'])
+app.config.from_object(os.environ["APP_SETTINGS"])
 
 # Logger config
 logging.config.dictConfig(app.config["DICT_LOGGER"])
 
 # Database config
 
 # MONGODB
-'''
+"""
 from .database import db
 
 app.config['MONGODB_SETTINGS'] = {
@@ -69,25 +70,22 @@
     'alias': ''
 }
 db.init_app(app)
-'''
+"""
 # MYSQL
 db.init_app(app)
 
 LOGGER.info("Successfully init db connection")
 
 # Swagger config
-app.config['SWAGGER'] = {
-    'title': 'CONTRABASS API',
-    'uiversion': 3
-}
-Swagger(app, template_file='swagger.yml')
+app.config["SWAGGER"] = {"title": "CONTRABASS API", "uiversion": 3}
+Swagger(app, template_file="swagger.yml")
 LOGGER.info("Successfully init Swagger")
 
 # Register blueprints
-app.register_blueprint(submit_bp, url_prefix='/')
-app.register_blueprint(models_bp, url_prefix='/')
-app.register_blueprint(results_bp, url_prefix='/')
-app.register_blueprint(websockets_bp, url_prefix='/')
+app.register_blueprint(submit_bp, url_prefix="/")
+app.register_blueprint(models_bp, url_prefix="/")
+app.register_blueprint(results_bp, url_prefix="/")
+app.register_blueprint(websockets_bp, url_prefix="/")
 LOGGER.info("Successfully init blueprints")
 
 # Register exception handlers
@@ -98,32 +96,38 @@
 CORS(app)
 
 # Init websockets
-socketio = SocketIO(app, \
-                    cors_allowed_origins='*', \
-                    logger=True, \
-                    engineio_logger=True, \
-                    message_queue=app.config['REDIS_BROKER_URL'])
+socketio = SocketIO(
+    app,
+    cors_allowed_origins="*",
+    logger=True,
+    engineio_logger=True,
+    message_queue=app.config["REDIS_BROKER_URL"],
+)
 
 
 @app.errorhandler(404)
 def page_not_found(e):
-    #return render_template('404.html'), 404
-    response = jsonify({'message': "Not found"})
+    # return render_template('404.html'), 404
+    response = jsonify({"message": "Not found"})
     response.status_code = 404
     return response
 
-@app.route('/hola/<name>')
+
+@app.route("/hola/<name>")
 def hello_name(name):
     return "Hello {}!".format(name)
 
-@socketio.on('connect')
+
+@socketio.on("connect")
 def test_connect():
     LOGGER.info("Client connected via websocket")
 
-@socketio.on('join')
+
+@socketio.on("join")
 def on_join(room_name):
     LOGGER.info(f"socket.io/join {room_name}")
     join_room(room_name)
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     socketio.run(app)

src/restapi/beans/Chokepoint.py

@@ -1,7 +1,4 @@
-
-
 class Chokepoint:
-
     def __init__(self, reaction, metabolite):
         self.__reaction = reaction
         self.__metabolite = metabolite

src/restapi/beans/ConfigChokepoints.py

@@ -1,6 +1,4 @@
-
 class ConfigReactionsSets:
-
     def __init__(self):
         self.__objective = None
         self.__fraction_of_optimum = None

src/restapi/beans/ConfigReactionsSets.py

@@ -1,8 +1,8 @@
 from .OptimizationEnum import *
 from .MediumEnum import *
 
-class ConfigReactionsSets:
 
+class ConfigReactionsSets:
     def __init__(self):
         self.__objective = None
         self.__fraction_of_optimum = None

src/restapi/beans/MediumEnum.py

@@ -1,5 +1,6 @@
 from enum import Enum
 
+
 class MediumEnum(Enum):
     DEFAULT = 1
-    COMPLETE = 2
+    COMPLETE = 2

src/restapi/beans/ModelId.py

@@ -1,6 +1,4 @@
-
 class ModelId:
-
     def __init__(self, model, metabolites, reactions, genes):
         self.model_uuid = model
         self.metabolites = metabolites

src/restapi/beans/OptimizationEnum.py

@@ -1,5 +1,6 @@
 from enum import Enum
 
+
 class OptimizationEnum(Enum):
     FBA = 1
-    pFBA = 2
+    pFBA = 2

src/restapi/beans/ResponseChannel.py

@@ -2,7 +2,6 @@
 
 
 class ResponseChannel:
-
     def __init__(self, channel=None):
         self.channel = channel
 
@@ -14,6 +13,7 @@ def channel_attr(self):
     def channel_attr(self, channel):
         self.channel = channel
 
+
 class ResponseChannelEncoder(JSONEncoder):
     def default(self, o):
-        return o.__dict__
+        return o.__dict__

src/restapi/beans/ResponseChokepoints.py

@@ -2,7 +2,6 @@
 
 
 class ResponseChokepoints:
-
     def __init__(self, status=None, finished=None, result=None, pending_length=None):
         self.__status = status
         self.__finished = finished
@@ -41,6 +40,7 @@ def pending_length(self):
     def pending_length(self, pending_length):
         self.__pending_length = pending_length
 
+
 class ResponseChokepointsEncoder(JSONEncoder):
     def default(self, o):
-        return o.__dict__
+        return o.__dict__

src/restapi/beans/ResponseEndpoint.py

@@ -2,7 +2,6 @@
 
 
 class ResponseEndpoint:
-
     def __init__(self, endpoint=None):
         self.endpoint = endpoint
 
@@ -14,6 +13,7 @@ def endpoint_attr(self):
     def endpoint_attr(self, endpoint):
         self.endpoint = endpoint
 
+
 class ResponseEndpointEncoder(JSONEncoder):
     def default(self, o):
-        return o.__dict__
+        return o.__dict__

src/restapi/beans/ResponseReport.py

@@ -2,8 +2,14 @@
 
 
 class ResponseReport:
-
-    def __init__(self, status=None, finished=None, file_spreadsheet=None, file_html=None, pending_length=None):
+    def __init__(
+        self,
+        status=None,
+        finished=None,
+        file_spreadsheet=None,
+        file_html=None,
+        pending_length=None,
+    ):
         self.status = status
         self.finished = finished
         self.file_spreadsheet = file_spreadsheet
@@ -49,4 +55,3 @@ def pending_length_attr(self):
     @pending_length_attr.setter
     def pending_length_attr(self, pending_length):
         self.pending_length = pending_length
-

src/restapi/beans/TaskFormCriticalReactions.py

@@ -1,8 +1,18 @@
 from wtforms import Form, StringField, DecimalField, validators
 
+
 class TaskFormCriticalReactions(Form):
-    objective = StringField('objective',
-                            [validators.optional(), validators.Length(min=1, max=256)])
-    fraction_of_optimum = DecimalField('fraction_of_optimum',
-                                       [validators.optional(),
-                                        validators.NumberRange(min=0.0, max=1.0, message='Fraction of optimum must be in the range [0, 1]')])
+    objective = StringField(
+        "objective", [validators.optional(), validators.Length(min=1, max=256)]
+    )
+    fraction_of_optimum = DecimalField(
+        "fraction_of_optimum",
+        [
+            validators.optional(),
+            validators.NumberRange(
+                min=0.0,
+                max=1.0,
+                message="Fraction of optimum must be in the range [0, 1]",
+            ),
+        ],
+    )

src/restapi/beans/TaskFormReactionsSets.py

@@ -1,19 +1,40 @@
-from wtforms import Form, StringField, DecimalField, SelectField, BooleanField, validators
+from wtforms import (
+    Form,
+    StringField,
+    DecimalField,
+    SelectField,
+    BooleanField,
+    validators,
+)
 from .OptimizationEnum import *
 from .MediumEnum import *
 
+
 class TaskFormReactionsSets(Form):
-    objective = StringField('objective',
-                            [validators.optional(), validators.Length(min=1, max=256)])
-    fraction_of_optimum = DecimalField('fraction_of_optimum',
-                                       [validators.optional(),
-                                        validators.NumberRange(min=0.0, max=1.0, message='Fraction of optimum must be in the range [0, 1]')])
-    medium = SelectField(u'Growth medium',
-                         [validators.optional()],
-                         choices=[name for name, member in MediumEnum.__members__.items()])
-    optimization = SelectField(u'Growth Optimization',
-                               [validators.optional()],
-                               choices=[name for name, member in OptimizationEnum.__members__.items()])
-    skip_knockout = BooleanField(u'Skip knock-out computation',
-                                 [validators.optional()],
-                                 default=True)
+    objective = StringField(
+        "objective", [validators.optional(), validators.Length(min=1, max=256)]
+    )
+    fraction_of_optimum = DecimalField(
+        "fraction_of_optimum",
+        [
+            validators.optional(),
+            validators.NumberRange(
+                min=0.0,
+                max=1.0,
+                message="Fraction of optimum must be in the range [0, 1]",
+            ),
+        ],
+    )
+    medium = SelectField(
+        u"Growth medium",
+        [validators.optional()],
+        choices=[name for name, member in MediumEnum.__members__.items()],
+    )
+    optimization = SelectField(
+        u"Growth Optimization",
+        [validators.optional()],
+        choices=[name for name, member in OptimizationEnum.__members__.items()],
+    )
+    skip_knockout = BooleanField(
+        u"Skip knock-out computation", [validators.optional()], default=True
+    )

src/restapi/beans/TaskInit.py

@@ -1,7 +1,4 @@
-
-
 class TaskInit:
-
     def __init__(self, task_id, pending_length=None):
         self.task_id = task_id
         self.pending_length = pending_length
@@ -20,4 +17,4 @@ def pending_length_attr(self):
 
     @pending_length_attr.setter
     def pending_length_attr(self, pending_length):
-        self.pending_length = pending_length
+        self.pending_length = pending_length

src/restapi/beans/WebsocketEvent.py

@@ -1,7 +1,7 @@
 from json import JSONEncoder
 
-class WebsocketEvent:
 
+class WebsocketEvent:
     def __init__(self, event, message):
         self.event = event
         self.message = message
@@ -22,6 +22,7 @@ def message_attr(self):
     def message_attr(self, message):
         self.message = message
 
+
 class ResponseWebsocketEventEncoder(JSONEncoder):
     def default(self, o):
-        return o.__dict__
+        return o.__dict__