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# Python
__pycache__/
# Files created by this set up:
venv/
build/
dist/
*.egg-info/
.pytest_cache/
.mypy_cache/

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## Directory Structure
Below is the directory and file layout for the `scipaperloader` project:
```plaintext
scipaperloader/
├── app/
│ ├── __init__.py # Initialize Flask app and database
│ ├── models.py # SQLAlchemy database models
│ ├── main.py # Flask routes (main blueprint)
│ ├── templates/ # Jinja2 templates for HTML pages
│ │ ├── base.html # Base layout template with Alpine.js and HTMX
│ │ ├── index.html # Home page template
│ │ ├── upload.html # CSV upload page template
│ │ ├── schedule.html # Schedule configuration page template
│ │ └── logs.html # Logs display page template
│ └── static/ # Static files (CSS, JS, images)
├── scraper.py # Background scraper daemon script
├── tests/
│ └── test_scipaperloader.py # Tests with a Flask test fixture
├── config.py # Configuration settings for different environments
├── pyproject.toml # Project metadata and build configuration
├── setup.cfg # Development tool configurations (linting, testing)
├── Makefile # Convenient commands for development tasks
└── .venv/ # Python virtual environment (not in version control)
```
- The **`app/`** package contains the Flask application code. It includes an `__init__.py` to create the app and set up extensions, a `models.py` defining database models with SQLAlchemy, and a `main.py` defining routes in a Flask Blueprint. The `templates/` directory holds HTML templates (with Jinja2 syntax) and `static/` will contain static assets (e.g., custom CSS or JS files, if any).
- The **`scraper.py`** is a **standalone** Python script acting as a background daemon. It can be run separately to perform background scraping tasks (e.g., periodically fetching new data). This script will use the same database (via SQLAlchemy models or direct database access) to read or write data as needed.
- The **`tests/`** directory includes a test file that uses pytest to ensure the Flask app and its components work as expected. A Flask fixture creates an application instance for testing (with an in-memory database) and verifies routes and database operations (e.g., uploading CSV adds records).
- The **configuration and setup files** at the project root help in development and deployment. `config.py` defines configuration classes (for development, testing, production) so the app can be easily configured. `pyproject.toml` and `setup.cfg` provide project metadata and tool configurations (for packaging, linting, etc.), and a `Makefile` is included to simplify common tasks (running the app, tests, etc.).

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all: run
clean:
rm -rf venv build dist .pytest_cache .mypy_cache *.egg-info
venv:
python3 -m venv venv && \
venv/bin/pip install --upgrade pip setuptools && \
venv/bin/pip install --editable ".[dev]"
run: venv
venv/bin/flask --app scipaperloader --debug run
format: venv
venv/bin/black . && venv/bin/isort .
format-check: venv
venv/bin/black --check . && venv/bin/isort --check .
lint: venv
venv/bin/flake8 .
mypy: venv
venv/bin/mypy
test: venv
venv/bin/pytest
dist: venv format-check lint mypy test
venv/bin/pip wheel --wheel-dir dist --no-deps .

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# SciPaperLoader: Flask Application Initial Structure
## Project Overview
**SciPaperLoader** is a Flask-based web application for managing scientific papers. It provides a web interface (with Jinja2 templates) enhanced by **Alpine.js** for interactive UI components and **HTMX** for partial page updates without full reloads. The application is composed of two main parts: a Flask web app (serving pages for uploading data, configuring schedules, and viewing logs) and a background **scraper daemon** that runs independently to perform long-running tasks (like fetching paper details on a schedule). The project is organized following Flask best practices (using blueprints, separating static files and templates) and is set up for easy development and testing (with configuration files and a pytest test fixture).
## Quick Start
Run the application:
make run
And open it in the browser at [http://localhost:5000/](http://localhost:5000/)
## Prerequisites
Python >=3.8
## Development environment
- `make venv`: creates a virtualenv with dependencies and this application
installed in [development mode](http://setuptools.readthedocs.io/en/latest/setuptools.html#development-mode)
- `make run`: runs a development server in debug mode (changes in source code
are reloaded automatically)
- `make format`: reformats code
- `make lint`: runs flake8
- `make mypy`: runs type checks by mypy
- `make test`: runs tests (see also: [Testing Flask Applications](https://flask.palletsprojects.com/en/3.0.x/testing/))
- `make dist`: creates a wheel distribution (will run tests first)
- `make clean`: removes virtualenv and build artifacts
- add application dependencies in `pyproject.toml` under `project.dependencies`;
add development dependencies under `project.optional-dependencies.*`; run
`make clean && make venv` to reinstall the environment
## Configuration
Default configuration is loaded from `scipaperloader.defaults` and can be
overriden by environment variables with a `FLASK_` prefix. See
[Configuring from Environment Variables](https://flask.palletsprojects.com/en/3.0.x/config/#configuring-from-environment-variables).
Consider using
[dotenv](https://flask.palletsprojects.com/en/3.0.x/cli/#environment-variables-from-dotenv).
## Deployment
See [Deploying to Production](https://flask.palletsprojects.com/en/3.0.x/deploying/).
You may use the distribution (`make dist`) to publish it to a package index,
deliver to your server, or copy in your `Dockerfile`, and insall it with `pip`.
You must set a
[SECRET_KEY](https://flask.palletsprojects.com/en/3.0.x/tutorial/deploy/#configure-the-secret-key)
in production to a secret and stable value.

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[build-system]
requires = ["setuptools"]
build-backend = "setuptools.build_meta"
[project]
name = "scipaperloader"
version = "1.0.0"
requires-python = ">=3.8.1,<4"
dependencies = [
"Flask>=3.0.2,<4",
"SQLAlchemy>=2.0,<3",
"flask_sqlalchemy>=3.0,<4",
]
[project.optional-dependencies]
dev = [
"pytest>=8,<9",
"flake8>=7,<8",
"black>=24.2.0,<25",
"isort>=5.13.1,<6",
"mypy>=1.8.0,<2",
]
[tool.setuptools.package-data]
"*" = ["**/static/**/*", "**/templates/**/*"]
[tool.pytest.ini_options]
testpaths = ["tests"]
[tool.black]
line-length = 88
[tool.isort]
profile = "black"
[tool.mypy]
ignore_missing_imports = true
files = "scipaperloader,tests"

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from flask import Flask
from .config import Config
from .db import db
def create_app(test_config=None):
app = Flask(__name__)
app.config.from_object(Config)
if test_config:
app.config.update(test_config)
db.init_app(app)
with app.app_context():
db.create_all()
from . import views
app.register_blueprint(views.bp)
return app

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import os
class Config:
SECRET_KEY = os.environ.get('SECRET_KEY', 'dev')
SQLALCHEMY_DATABASE_URI = os.environ.get('DATABASE_URL', 'sqlite:///papers.db')
SQLALCHEMY_TRACK_MODIFICATIONS = False

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from flask_sqlalchemy import SQLAlchemy, current_app, g
db = SQLAlchemy()
db_name = 'scipaperloader.db'

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DEBUG = False # make sure DEBUG is off unless enabled explicitly otherwise

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import logging.config
import os
# Since logging is initialized before the application, can't use
# app.debug here, relying on FLASK_DEBUG env var only.
def _is_debug():
flag = os.getenv("FLASK_DEBUG", "").lower()
return flag == "true" or flag == "1"
def init_logging():
msg_fmt = "[%(asctime)s] %(levelname)s in %(module)s: %(message)s"
logging.config.dictConfig(
{
"version": 1,
"formatters": {
"default": {
"format": msg_fmt,
}
},
"handlers": {
"wsgi": {
"class": "logging.StreamHandler",
"stream": "ext://sys.stdout",
"formatter": "default",
}
},
"root": {
"level": "DEBUG" if _is_debug() else "INFO",
"handlers": ["wsgi"],
},
"disable_existing_loggers": False,
}
)

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from .db import db
class Paper(db.Model):
id = db.Column(db.Integer, primary_key=True)
title = db.Column(db.Text)
doi = db.Column(db.String, unique=True, index=True)
alt_id = db.Column(db.String)
issn = db.Column(db.String(32))
type = db.Column(db.String(50))
language = db.Column(db.String(50))
published_date = db.Column(db.Date) # or DateTime/String
status = db.Column(db.String(10)) # 'Pending','Done','Failed'
file_path = db.Column(db.Text)
error_msg = db.Column(db.Text)
# plus maybe timestamps for created/updated
class ScheduleConfig(db.Model):
hour = db.Column(db.Integer, primary_key=True) # 0-23
volume = db.Column(db.Float) # weight or count

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import time
from .db import db
from .models import Paper
def run_scraper():
while True:
with db.app.app_context():
paper = Paper.query.filter_by(status="Pending").first()
if paper:
try:
# Scraping logic (e.g. download PDF)
paper.status = "Done"
paper.file_path = "papers/some_path.pdf"
except Exception as e:
paper.status = "Failed"
paper.error_message = str(e)
db.session.commit()
else:
time.sleep(60)

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.message {
padding: 10px;
font-size: 1.3em;
font-family: Arial, sans-serif;
}

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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>SciPaperLoader</title>
<link href="{{ url_for('static', filename='css/bootstrap.min.css') }}" rel="stylesheet">
<script src="{{ url_for('static', filename='js/bootstrap.bundle.min.js') }}"></script>
<!-- Optional Alpine.js -->
<script src="{{ url_for('static', filename='js/alpine.min.js') }}"></script>
</head>
<body>
<div class="container py-4">
{% block content %}{% endblock %}
</div>
</body>
</html>

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{% extends 'base.html' %}
{% block content %}
<h1>Welcome to SciPaperLoader</h1>
<p>Your paper scraping tool is ready.</p>
<a href="{{ url_for('main.upload') }}" class="btn btn-primary">Upload CSV</a>
{% endblock %}

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scipaperloader/templates/upload.html Normal file
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{% extends 'base.html' %}
{% block content %}
<h1>Welcome to SciPaperLoader</h1>
<p>Your paper scraping tool is ready.</p>
<a href="{{ url_for('main.upload') }}" class="btn btn-primary">Upload CSV</a>
{% endblock %}

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scipaperloader/views.py Normal file
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from flask import Blueprint, render_template, current_app, request
bp = Blueprint('main', __name__)
@bp.route("/")
def index():
return render_template("index.html")
@bp.route("/upload", methods=["GET", "POST"])
def upload():
if request.method == "POST":
# CSV upload logic here
pass
return render_template("upload.html")

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setup.cfg Normal file
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# flake8 doesn't support pyproject.toml yet:
# https://github.com/PyCQA/flake8/issues/234
[flake8]
exclude = setup.py,venv,build,dist
max-line-length = 88

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setup.py Normal file
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# This project uses pyproject.toml for all configuration.
# This file is for compatibility only.
# See https://setuptools.pypa.io/en/latest/userguide/quickstart.html#development-mode
from setuptools import setup
setup()

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tests/test_scipaperloader.py Normal file
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import pytest
from scipaperloader import create_app
@pytest.fixture
def app():
app = create_app({"TESTING": True})
# set up here
yield app
# tear down here
@pytest.fixture
def client(app):
return app.test_client()
def test_index(client):
response = client.get("/")
assert b"It works!" in response.data