formats

scipaperloader/__init__.py

@@ -1,8 +1,10 @@
 from flask import Flask
+
 from .config import Config
 from .db import db
 from .models import init_schedule_config
 
+
 def create_app(test_config=None):
     app = Flask(__name__)
     app.config.from_object(Config)
@@ -18,9 +20,10 @@ def create_app(test_config=None):
 
     @app.context_processor
     def inject_app_title():
-        return {'app_title': app.config['APP_TITLE']}
+        return {"app_title": app.config["APP_TITLE"]}
 
     from . import views
+
     app.register_blueprint(views.bp)
 
     return app

scipaperloader/config.py

@@ -1,7 +1,8 @@
 import os
 
+
 class Config:
-    SECRET_KEY = os.environ.get('SECRET_KEY', 'dev')
+    SECRET_KEY = os.environ.get("SECRET_KEY", "dev")
-    SQLALCHEMY_DATABASE_URI = os.environ.get('DATABASE_URL', 'sqlite:///papers.db')
+    SQLALCHEMY_DATABASE_URI = os.environ.get("DATABASE_URL", "sqlite:///papers.db")
     SQLALCHEMY_TRACK_MODIFICATIONS = False
-    APP_TITLE = os.environ.get('APP_TITLE', 'SciPaperLoader')
+    APP_TITLE = os.environ.get("APP_TITLE", "SciPaperLoader")

scipaperloader/models.py

@@ -1,5 +1,6 @@
 from .db import db
 
+
 class PaperMetadata(db.Model):
     id = db.Column(db.Integer, primary_key=True)
     title = db.Column(db.Text)
@@ -13,17 +14,24 @@ class PaperMetadata(db.Model):
     file_path = db.Column(db.Text)
     error_msg = db.Column(db.Text)
     created_at = db.Column(db.DateTime, default=db.func.current_timestamp())
-    updated_at = db.Column(db.DateTime, default=db.func.current_timestamp(), onupdate=db.func.current_timestamp())
+    updated_at = db.Column(
+        db.DateTime,
+        default=db.func.current_timestamp(),
+        onupdate=db.func.current_timestamp(),
+    )
     # plus maybe timestamps for created/updated
 
+
 class ScheduleConfig(db.Model):
     hour = db.Column(db.Integer, primary_key=True)  # 0-23
     weight = db.Column(db.Float)  # weight
 
+
 class VolumeConfig(db.Model):
     id = db.Column(db.Integer, primary_key=True)
     volume = db.Column(db.Float)  # volume of papers to scrape per day
 
+
 def init_schedule_config():
     """Initialize ScheduleConfig with default values if empty"""
     if ScheduleConfig.query.count() == 0:
@@ -39,7 +47,7 @@ def init_schedule_config():
             # Evening hours (medium volume)
             *[(hour, 0.5) for hour in range(17, 21)],
             # Late evening (high volume)
-            *[(hour, 0.8) for hour in range(21, 24)]
+            *[(hour, 0.8) for hour in range(21, 24)],
         ]
 
         for hour, weight in default_schedule:

scipaperloader/scraper.py

@@ -1,7 +1,9 @@
 import time
+
 from .db import db
 from .models import PaperMetadata
 
+
 def run_scraper():
     while True:
         with db.app.app_context():

scipaperloader/views.py

@@ -1,15 +1,26 @@
-from flask import Blueprint, render_template, current_app, request, flash, redirect, url_for, send_file
-from .models import ScheduleConfig, VolumeConfig, PaperMetadata
-from .db import db
-import pandas as pd
-from io import StringIO
 import codecs
+import csv
 import datetime
 import io
-import csv
+from io import StringIO
+
+import pandas as pd
+from flask import (
+    Blueprint,
+    current_app,
+    flash,
+    redirect,
+    render_template,
+    request,
+    send_file,
+    url_for,
+)
 from sqlalchemy import asc, desc
 
-bp = Blueprint('main', __name__)
+from .db import db
+from .models import PaperMetadata, ScheduleConfig, VolumeConfig
+
+bp = Blueprint("main", __name__)
 
 
 @bp.route("/")
@@ -20,25 +31,27 @@ def index():
 REQUIRED_COLUMNS = {"alternative_id", "journal", "doi", "issn", "title"}
 
 
-@bp.route('/upload', methods=['GET', 'POST'])
+@bp.route("/upload", methods=["GET", "POST"])
 def upload():
-    if request.method == 'POST':
+    if request.method == "POST":
-        file = request.files.get('file')
+        file = request.files.get("file")
-        delimiter = request.form.get('delimiter', ',')
+        delimiter = request.form.get("delimiter", ",")
 
         if not file:
-            return render_template('upload.html', error="No file selected.")
+            return render_template("upload.html", error="No file selected.")
 
         try:
-            stream = codecs.iterdecode(file.stream, 'utf-8')
+            stream = codecs.iterdecode(file.stream, "utf-8")
-            content = ''.join(stream)
+            content = "".join(stream)
             df = pd.read_csv(StringIO(content), delimiter=delimiter)
         except Exception as e:
-            return render_template('upload.html', error=f"Failed to read CSV file: {e}")
+            return render_template("upload.html", error=f"Failed to read CSV file: {e}")
 
         missing = REQUIRED_COLUMNS - set(df.columns)
         if missing:
-            return render_template('upload.html', error=f"Missing required columns: {', '.join(missing)}")
+            return render_template(
+                "upload.html", error=f"Missing required columns: {', '.join(missing)}"
+            )
 
         # Optional: parse 'published_online' to date
         def parse_date(val):
@@ -51,16 +64,16 @@ def upload():
 
         for _, row in df.iterrows():
             metadata = PaperMetadata(
-                title=row['title'],
+                title=row["title"],
-                doi=row['doi'],
+                doi=row["doi"],
-                alt_id=row.get('alternative_id'),
+                alt_id=row.get("alternative_id"),
-                issn=row['issn'],
+                issn=row["issn"],
-                type=row.get('type'),
+                type=row.get("type"),
-                language=row.get('language'),
+                language=row.get("language"),
-                published_online=parse_date(row.get('published_online')),
+                published_online=parse_date(row.get("published_online")),
                 status="New",
                 file_path=None,
-                error_msg=None
+                error_msg=None,
             )
             db.session.add(metadata)
 
@@ -68,26 +81,30 @@ def upload():
             db.session.commit()
         except Exception as e:
             db.session.rollback()
-            return render_template('upload.html', error=f"Failed to save data to database: {e}")
+            return render_template(
+                "upload.html", error=f"Failed to save data to database: {e}"
+            )
 
-        return render_template('upload.html', success="File uploaded and validated successfully!")
+        return render_template(
+            "upload.html", success="File uploaded and validated successfully!"
+        )
 
-    return render_template('upload.html')
+    return render_template("upload.html")
 
 
-@bp.route('/papers')
+@bp.route("/papers")
 def list_papers():
-    page = request.args.get('page', 1, type=int)
+    page = request.args.get("page", 1, type=int)
     per_page = 50
 
     # Filters
-    status = request.args.get('status')
+    status = request.args.get("status")
-    created_from = request.args.get('created_from')
+    created_from = request.args.get("created_from")
-    created_to = request.args.get('created_to')
+    created_to = request.args.get("created_to")
-    updated_from = request.args.get('updated_from')
+    updated_from = request.args.get("updated_from")
-    updated_to = request.args.get('updated_to')
+    updated_to = request.args.get("updated_to")
-    sort_by = request.args.get('sort_by', 'created_at')
+    sort_by = request.args.get("sort_by", "created_at")
-    sort_dir = request.args.get('sort_dir', 'desc')
+    sort_dir = request.args.get("sort_dir", "desc")
 
     query = PaperMetadata.query
 
@@ -97,8 +114,9 @@ def list_papers():
 
     def parse_date(val):
         from datetime import datetime
+
         try:
-            return datetime.strptime(val, '%Y-%m-%d')
+            return datetime.strptime(val, "%Y-%m-%d")
         except (ValueError, TypeError):
             return None
 
@@ -113,7 +131,7 @@ def list_papers():
 
     # Sorting
     sort_col = getattr(PaperMetadata, sort_by, PaperMetadata.created_at)
-    sort_func = desc if sort_dir == 'desc' else asc
+    sort_func = desc if sort_dir == "desc" else asc
     query = query.order_by(sort_func(sort_col))
 
     # Pagination
@@ -129,7 +147,7 @@ def list_papers():
     status_counts = {status: count for status, count in status_counts}
 
     return render_template(
-        'papers.html',
+        "papers.html",
         papers=pagination.items,
         pagination=pagination,
         total_papers=total_papers,
@@ -139,18 +157,18 @@ def list_papers():
     )
 
 
-@bp.route('/papers/export')
+@bp.route("/papers/export")
 def export_papers():
     query = PaperMetadata.query
 
     # Filters
-    status = request.args.get('status')
+    status = request.args.get("status")
-    created_from = request.args.get('created_from')
+    created_from = request.args.get("created_from")
-    created_to = request.args.get('created_to')
+    created_to = request.args.get("created_to")
-    updated_from = request.args.get('updated_from')
+    updated_from = request.args.get("updated_from")
-    updated_to = request.args.get('updated_to')
+    updated_to = request.args.get("updated_to")
-    sort_by = request.args.get('sort_by', 'created_at')
+    sort_by = request.args.get("sort_by", "created_at")
-    sort_dir = request.args.get('sort_dir', 'desc')
+    sort_dir = request.args.get("sort_dir", "desc")
 
     query = PaperMetadata.query
 
@@ -166,35 +184,40 @@ def export_papers():
 
     output = io.StringIO()
     writer = csv.writer(output)
-    writer.writerow(['ID', 'Title', 'Journal', 'DOI', 'ISSN',
+    writer.writerow(
-                    'Status', 'Created At', 'Updated At'])
+        ["ID", "Title", "Journal", "DOI", "ISSN", "Status", "Created At", "Updated At"]
+    )
 
     for paper in query:
-        writer.writerow([
+        writer.writerow(
+            [
                 paper.id,
                 paper.title,
-            getattr(paper, 'journal', ''),
+                getattr(paper, "journal", ""),
                 paper.doi,
                 paper.issn,
                 paper.status,
                 paper.created_at,
-            paper.updated_at
+                paper.updated_at,
-        ])
+            ]
+        )
 
     output.seek(0)
-    return send_file(io.BytesIO(output.read().encode('utf-8')),
+    return send_file(
-                     mimetype='text/csv',
+        io.BytesIO(output.read().encode("utf-8")),
+        mimetype="text/csv",
         as_attachment=True,
-                     download_name='papers.csv')
+        download_name="papers.csv",
+    )
 
     from flask import jsonify, render_template
 
 
-@bp.route('/papers/<int:paper_id>/detail')
+@bp.route("/papers/<int:paper_id>/detail")
 def paper_detail(paper_id):
     paper = PaperMetadata.query.get_or_404(paper_id)
 
-    return render_template('partials/paper_detail_modal.html', paper=paper)
+    return render_template("partials/paper_detail_modal.html", paper=paper)
 
 
 @bp.route("/schedule", methods=["GET", "POST"])
@@ -202,10 +225,10 @@ def schedule():
     if request.method == "POST":
         try:
             # Check if we're updating volume or schedule
-            if 'total_volume' in request.form:
+            if "total_volume" in request.form:
                 # Volume update
                 try:
-                    new_volume = float(request.form.get('total_volume', 0))
+                    new_volume = float(request.form.get("total_volume", 0))
                     if new_volume <= 0 or new_volume > 1000:
                         raise ValueError("Volume must be between 1 and 1000")
 
@@ -234,7 +257,8 @@ def schedule():
                         weight = float(request.form.get(key, 0))
                         if weight < 0 or weight > 5:
                             raise ValueError(
-                                f"Weight for hour {hour} must be between 0 and 5")
+                                f"Weight for hour {hour} must be between 0 and 5"
+                            )
                     except ValueError:
                         raise ValueError(f"Invalid weight value for hour {hour}")
 
@@ -255,10 +279,17 @@ def schedule():
             db.session.rollback()
             flash(f"Error updating schedule: {str(e)}", "error")
 
-    schedule = {sc.hour: sc.weight for sc in ScheduleConfig.query.order_by(
+    schedule = {
-        ScheduleConfig.hour).all()}
+        sc.hour: sc.weight
+        for sc in ScheduleConfig.query.order_by(ScheduleConfig.hour).all()
+    }
     volume = VolumeConfig.query.first()
-    return render_template("schedule.html", schedule=schedule, volume=volume.volume, app_title="PaperScraper")
+    return render_template(
+        "schedule.html",
+        schedule=schedule,
+        volume=volume.volume,
+        app_title="PaperScraper",
+    )
 
 
 @bp.route("/logs")