Merge pull request #2 from diverso-lab/refactoring

Refactoring

Dockerfile.dev

@@ -1,24 +1,29 @@
 # Use an official Python runtime as a parent image
 FROM python:3.11-alpine
 
-# Set the working directory in the container to /app
+# Instala el cliente de MySQL para poder usarlo en el script de espera
+RUN apk add --no-cache mysql-client
+
+# Establece el directorio de trabajo en el contenedor en /app
 WORKDIR /app
 
-# Copy the contents of the local app/ directory to the /app directory in the container
+# Copia el contenido del directorio local app/ al directorio /app en el contenedor
 COPY app/ ./app
 
-# Copy requirements.txt at the /app working directory
+# Copia requirements.txt en el directorio de trabajo /app
 COPY requirements.txt .
 
-# Install any needed packages specified in requirements.txt
+# Copia el script wait-for-db.sh y establece los permisos de ejecución
+COPY --chmod=+x scripts/wait-for-db.sh ./scripts/
+
+# Instala los paquetes necesarios especificados en requirements.txt
 RUN pip install --no-cache-dir -r requirements.txt
 
-# Update pip
+# Actualiza pip
 RUN pip install --no-cache-dir --upgrade pip
 
-# Expose port 5000
+# Expone el puerto 5000
 EXPOSE 5000
 
-# Run the application
-CMD flask db upgrade && flask run --host=0.0.0.0 --port=5000 --reload --debug
-
+# Ajusta el comando CMD para ejecutar correctamente el script wait-for-db.sh
+CMD sh ./scripts/wait-for-db.sh && flask db upgrade && flask run --host=0.0.0.0 --port=5000 --reload --debug

README.md

@@ -25,11 +25,12 @@ Create an `.env` file in the root of the project with this information. It is im
 
 ```
 FLASK_APP_NAME=UVLHUB.IO
-MYSQL_HOSTNAME=db
-MYSQL_DATABASE=uvlhubdb
-MYSQL_USER=uvlhubuser
-MYSQL_PASSWORD=uvlhubpass
-MYSQL_ROOT_PASSWORD=uvlhubrootpass
+MARIADB_HOSTNAME=db
+MARIADB_PORT=3306
+MARIADB_DATABASE=uvlhubdb
+MARIADB_USER=uvlhubuser
+MARIADB_PASSWORD=uvlhubpass
+MARIADB_ROOT_PASSWORD=uvlhubrootpass
 ZENODO_ACCESS_TOKEN=<GET_ACCESS_TOKEN_IN_ZENODO>
 ```
 

app/__init__.py

@@ -1,13 +1,13 @@
 import os
 import secrets
 import logging
+import importlib.util
 
-from flask import Flask, render_template
+from flask import Flask, render_template, Blueprint, flash, redirect, url_for
 from flask_login import current_user
 from flask_sqlalchemy import SQLAlchemy
 from dotenv import load_dotenv
 from flask_migrate import Migrate
-from flask_wtf import CSRFProtect
 
 # Load environment variables
 load_dotenv()
@@ -23,8 +23,11 @@ def create_app(config_name=None):
 
     # Database configuration
     app.config['SQLALCHEMY_DATABASE_URI'] = (
-        f"mysql+pymysql://{os.getenv('MYSQL_USER', 'default_user')}:{os.getenv('MYSQL_PASSWORD', 'default_password')}"
-        f"@{os.getenv('MYSQL_HOSTNAME', 'localhost')}:3306/{os.getenv('MYSQL_DATABASE', 'default_db')}"
+        f"mysql+pymysql://{os.getenv('MARIADB_USER', 'default_user')}:"
+        f"{os.getenv('MARIADB_PASSWORD', 'default_password')}@"
+        f"{os.getenv('MARIADB_HOSTNAME', 'localhost')}:"
+        f"{os.getenv('MARIADB_PORT', '3306')}/"
+        f"{os.getenv('MARIADB_DATABASE', 'default_db')}"
     )
 
     # Timezone
@@ -40,23 +43,9 @@ def create_app(config_name=None):
     db.init_app(app)
     migrate.init_app(app, db)
 
-    # Import blueprints
-    from app.tests.routes import test_routes
-    from .auth import auth_bp
-    from .dataset import dataset_bp
-    from .explore import explore_bp
-    from .profile import profile_bp
-    from .team import team_bp
-    from .public import public_bp
-
     # Register blueprints
-    app.register_blueprint(test_routes)
-    app.register_blueprint(auth_bp)
-    app.register_blueprint(dataset_bp)
-    app.register_blueprint(explore_bp)
-    app.register_blueprint(profile_bp)
-    app.register_blueprint(team_bp)
-    app.register_blueprint(public_bp)
+    register_blueprints(app)
+    print_registered_blueprints(app)
 
     from flask_login import LoginManager
     login_manager = LoginManager()
@@ -65,7 +54,7 @@ def create_app(config_name=None):
 
     @login_manager.user_loader
     def load_user(user_id):
-        from app.auth.models import User
+        from app.blueprints.auth.models import User
         return User.query.get(int(user_id))
 
     # Logging
@@ -119,7 +108,7 @@ def upload_folder_name():
 
 def get_user_by_token(token):
     # TODO
-    from app.auth.models import User
+    from app.blueprints.auth.models import User
     return User.query.first()
 
 
@@ -129,16 +118,46 @@ def get_authenticated_user_profile():
     return None
 
 
+def get_authenticated_user():
+    if current_user.is_authenticated:
+        return current_user
+    return None
+
+
 def datasets_counter() -> int:
-    from app.dataset.models import DataSet
+    from app.blueprints.dataset.models import DataSet
     count = DataSet.query.count()
     return count
 
 
 def feature_models_counter() -> int:
-    from app.dataset.models import FeatureModel
+    from app.blueprints.dataset.models import FeatureModel
     count = FeatureModel.query.count()
     return count
 
 
+def register_blueprints(app):
+    app.blueprint_url_prefixes = {}
+    base_dir = os.path.abspath(os.path.dirname(__file__))
+    blueprints_dir = os.path.join(base_dir, 'blueprints')
+    for blueprint_name in os.listdir(blueprints_dir):
+        blueprint_path = os.path.join(blueprints_dir, blueprint_name)
+        if os.path.isdir(blueprint_path) and not blueprint_name.startswith('__'):
+            try:
+                routes_module = importlib.import_module(f'app.blueprints.{blueprint_name}.routes')
+                for item in dir(routes_module):
+                    if isinstance(getattr(routes_module, item), Blueprint):
+                        blueprint = getattr(routes_module, item)
+                        app.register_blueprint(blueprint)
+            except ModuleNotFoundError as e:
+                print(f"Could not load the module for Blueprint '{blueprint_name}': {e}")
+
+
+def print_registered_blueprints(app):
+    print("Registered blueprints")
+    for name, blueprint in app.blueprints.items():
+        url_prefix = app.blueprint_url_prefixes.get(name, 'No URL prefix set')
+        print(f"Name: {name}, URL prefix: {url_prefix}")
+
+
 app = create_app()

app/auth/__init__.py → app/blueprints/auth/__init__.py

@@ -2,4 +2,3 @@
 
 auth_bp = Blueprint('auth', __name__, template_folder='templates')
 
-from . import routes

app/auth/models.py → app/blueprints/auth/models.py

@@ -10,7 +10,7 @@ class User(db.Model, UserMixin):
     id = db.Column(db.Integer, primary_key=True)
 
     email = db.Column(db.String(256), unique=True, nullable=False)
-    password = db.Column(db.String(128), nullable=False)
+    password = db.Column(db.String(256), nullable=False)
     created_at = db.Column(db.DateTime, nullable=False, default=datetime.utcnow)
 
     data_sets = db.relationship('DataSet', backref='user', lazy=True)

app/auth/routes.py → app/blueprints/auth/routes.py

@@ -1,11 +1,10 @@
-from flask import (render_template, redirect, url_for,
-                   request, current_app)
+from flask import (render_template, redirect, url_for)
 from flask_login import current_user, login_user, logout_user
 
-from . import auth_bp
-from .forms import SignupForm, LoginForm
-from .models import User
-from ..profile.models import UserProfile
+from app.blueprints.auth import auth_bp
+from app.blueprints.auth.forms import SignupForm, LoginForm
+
+from app.blueprints.profile.models import UserProfile
 
 
 @auth_bp.route("/signup/", methods=["GET", "POST"])
@@ -20,6 +19,7 @@ def show_signup_form():
         email = form.email.data
         password = form.password.data
 
+        from app.blueprints.auth.models import User
         user = User.get_by_email(email)
         if user is not None:
             error = f'Email {email} in use'
@@ -46,6 +46,7 @@ def login():
         return redirect(url_for('public.index'))
     form = LoginForm()
     if form.validate_on_submit():
+        from app.blueprints.auth.models import User
         user = User.get_by_email(form.email.data)
 
         if user is not None and user.check_password(form.password.data):

app/dataset/__init__.py → app/blueprints/dataset/__init__.py

@@ -1,5 +1,3 @@
 from flask import Blueprint
 
 dataset_bp = Blueprint('dataset', __name__, template_folder='templates')
-
-from . import routes

app/dataset/forms.py → app/blueprints/dataset/forms.py

@@ -1,9 +1,8 @@
 from flask_wtf import FlaskForm
 from wtforms import StringField, SelectField, FieldList, FormField, SubmitField, TextAreaField
 from wtforms.validators import DataRequired, URL, Optional
-from enum import Enum
 
-from .models import PublicationType
+from app.blueprints.dataset.models import PublicationType
 
 
 class AuthorForm(FlaskForm):

app/dataset/models.py → app/blueprints/dataset/models.py

@@ -218,7 +218,6 @@ def __repr__(self):
         return f'<FileDownload id={self.id} file_id={self.file_id} date={self.download_date} cookie={self.download_cookie}>'
 
 
-
 def get_human_readable_size(size):
     if size < 1024:
         return f'{size} bytes'

app/dataset/routes.py → app/blueprints/dataset/routes.py

@@ -1,4 +1,3 @@
-import io
 import logging
 import os
 import json
@@ -11,19 +10,16 @@
 from typing import List
 from zipfile import ZipFile
 
-from flask import flash, redirect, render_template, url_for, request, jsonify, send_file, send_from_directory, abort, \
-    current_app, make_response
+from flask import render_template, request, jsonify, send_from_directory, current_app, make_response
 from flask_login import login_required, current_user
-from werkzeug.utils import secure_filename
 
 import app
-from .forms import DataSetForm
-from .models import DataSet, DSMetrics, FeatureModel, File, FMMetaData, FMMetrics, DSMetaData, Author, PublicationType, \
-    DSDownloadRecord, DSViewRecord, FileDownloadRecord
-from . import dataset_bp
-from ..auth.models import User
-from ..flama import flamapy_valid_model
-from ..zenodo import zenodo_create_new_deposition, test_zenodo_connection, zenodo_upload_file, \
+from app.blueprints.dataset.forms import DataSetForm
+from app.blueprints.dataset.models import DataSet, FeatureModel, File, FMMetaData, DSMetaData, Author, \
+    PublicationType, DSDownloadRecord, DSViewRecord, FileDownloadRecord
+from app.blueprints.dataset import dataset_bp
+from app.blueprints.auth.models import User
+from app.zenodo import zenodo_create_new_deposition, zenodo_upload_file, \
     zenodo_publish_deposition, zenodo_get_doi, test_full_zenodo_connection
 
 
@@ -542,7 +538,6 @@ def api_create_dataset():
             # iterate for each feature model (one feature model = one request to Zenodo
             try:
                 for feature_model in feature_models:
-
                     zenodo_upload_file(deposition_id, feature_model, user=user)
 
                     # Wait for 0.6 seconds before the next API call to ensure we do not exceed

app/explore/__init__.py → app/blueprints/explore/__init__.py

@@ -1,5 +1,3 @@
 from flask import Blueprint
 
 explore_bp = Blueprint('explore', __name__, template_folder='templates')
-
-from . import routes

app/explore/routes.py → app/blueprints/explore/routes.py

@@ -2,12 +2,12 @@
 
 import unidecode
 
-from flask import render_template, request, abort, jsonify
-from sqlalchemy import or_, desc, asc, any_
+from flask import render_template, request, jsonify
+from sqlalchemy import or_, any_
 
-from . import explore_bp
-from .forms import ExploreForm
-from ..dataset.models import DataSet, DSMetaData, Author, FeatureModel, FMMetaData, PublicationType
+from app.blueprints.explore import explore_bp
+from app.blueprints.explore.forms import ExploreForm
+from app.blueprints.dataset.models import DataSet, DSMetaData, Author, FeatureModel, FMMetaData, PublicationType
 
 
 @explore_bp.route('/explore', methods=['GET', 'POST'])

app/profile/__init__.py → app/blueprints/profile/__init__.py

@@ -1,5 +1,3 @@
 from flask import Blueprint
 
 profile_bp = Blueprint('profile', __name__, template_folder='templates')
-
-from . import routes

app/profile/models.py → app/blueprints/profile/models.py

@@ -13,4 +13,4 @@ class UserProfile(db.Model):
     def save(self):
         if not self.id:
             db.session.add(self)
-        db.session.commit()
+        db.session.commit()

app/blueprints/profile/repositories.py

@@ -0,0 +1,7 @@
+from app.blueprints.profile.models import UserProfile
+from app.repositories.BaseRepository import BaseRepository
+
+
+class UserProfileRepository(BaseRepository):
+    def __init__(self):
+        super().__init__(UserProfile)

app/blueprints/profile/routes.py

@@ -0,0 +1,22 @@
+from flask import request, render_template, flash, redirect, url_for, current_app
+from flask_login import login_required
+
+from app.blueprints.profile import profile_bp
+from app.blueprints.profile.forms import UserProfileForm
+
+from app import get_authenticated_user_profile
+from app.blueprints.profile.services import UserProfileService
+
+
+@profile_bp.route('/profile/edit', methods=['GET', 'POST'])
+@login_required
+def edit_profile():
+    form = UserProfileForm()
+    if request.method == 'POST':
+
+        service = UserProfileService()
+        result, errors = service.update_profile(get_authenticated_user_profile().id, form)
+        return service.handle_service_response(result, errors, 'profile.edit_profile', 'Profile updated successfully',
+                                               'profile/edit.html', form)
+
+    return render_template('profile/edit.html', form=form)

app/blueprints/profile/services.py

@@ -0,0 +1,16 @@
+from app.blueprints.profile.repositories import UserProfileRepository
+from app.services.BaseService import BaseService
+
+from flask import current_app
+
+
+class UserProfileService(BaseService):
+    def __init__(self):
+        super().__init__(UserProfileRepository())
+
+    def update_profile(self, user_profile_id, form):
+        if form.validate():
+            updated_instance = self.update(user_profile_id, **form.data)
+            return updated_instance, None
+        else:
+            return None, form.errors