Rename & fix of all html templates to imrove linting. Added .db and .R files to gitignore.

.gitignore

@@ -9,3 +9,7 @@ dist/
 *.egg-info/
 .pytest_cache/
 .mypy_cache/
+
+*.db
+
+*.R

scipaperloader/blueprints/main.py

@@ -6,14 +6,14 @@ bp = Blueprint("main", __name__)
 
 @bp.route("/")
 def index():
-    return render_template("index.html")
+    return render_template("index.html.jina")
 
 
 @bp.route("/logs")
 def logs():
-    return render_template("logs.html", app_title="PaperScraper")
+    return render_template("logs.html.jina", app_title="PaperScraper")
 
 
 @bp.route("/about")
 def about():
-    return render_template("about.html", app_title="PaperScraper")
+    return render_template("about.html.jina", app_title="PaperScraper")

scipaperloader/blueprints/papers.py

@@ -72,7 +72,7 @@ def list_papers():
     status_counts = {status: count for status, count in status_counts}
 
     return render_template(
-        "papers.html",
+        "papers.html.jina",
         papers=pagination.items,
         pagination=pagination,
         total_papers=total_papers,
@@ -137,4 +137,4 @@ def export_papers():
 @bp.route("/<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.jina", paper=paper)

scipaperloader/blueprints/schedule.py

@@ -72,7 +72,7 @@ def schedule():
     }
     volume = VolumeConfig.query.first()
     return render_template(
-        "schedule.html",
+        "schedule.html.jina",
         schedule=schedule,
         volume=volume.volume if volume else 0,
         app_title="PaperScraper",

scipaperloader/blueprints/upload.py

@@ -32,19 +32,19 @@ def upload():
         duplicate_strategy = request.form.get("duplicate_strategy", "skip")
 
         if not file:
-            return render_template("upload.html", error="No file selected.")
+            return render_template("upload.html.jina", error="No file selected.")
 
         try:
             stream = codecs.iterdecode(file.stream, "utf-8")
             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.jina", 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)}"
+                "upload.html.jina", error=f"Missing required columns: {', '.join(missing)}"
             )
 
         # Optional: parse 'published_online' to date
@@ -126,7 +126,7 @@ def upload():
         except Exception as e:
             db.session.rollback()
             return render_template(
-                "upload.html", error=f"Failed to save data to database: {e}"
+                "upload.html.jina", error=f"Failed to save data to database: {e}"
             )
 
         # Prepare error samples for display
@@ -145,13 +145,13 @@ def upload():
             session["error_data"] = error_csv.getvalue()
 
         return render_template(
-            "upload.html", 
+            "upload.html.jina", 
             success=f"File processed! Added: {added_count}, Updated: {updated_count}, Skipped: {skipped_count}, Errors: {error_count}",
             error_message=error_message,
             error_samples=error_samples
         )
 
-    return render_template("upload.html")
+    return render_template("upload.html.jina")
 
 
 @bp.route("/download_error_log")

scipaperloader/templates/about.html.jinja

@@ -1,4 +1,4 @@
-{% extends 'base.html' %} {% block content %}
+{% extends "base.html" %} {% block content %}
 <h1 class="mb-4">📘 About This App</h1>
 
 <p class="lead">
@@ -107,4 +107,4 @@
     <li>Anyone needing a structured way to fetch and track papers in bulk</li>
   </ul>
 </section>
-{% endblock %}
+{% endblock content %}

scipaperloader/templates/base.html

@@ -1,22 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-    <meta charset="UTF-8" />
-    <title>{{ app_title }}</title>
-    <link
-      href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/css/bootstrap.min.css"
-      rel="stylesheet"
-    />
-    <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js"></script>
-    <!-- Optional Alpine.js -->
-    <script
-      defer
-      src="https://cdn.jsdelivr.net/npm/alpinejs@3.x.x/dist/cdn.min.js"
-    ></script>
-  </head>
-  <body>
-    {% include 'nav.html' %}
-    <main class="container my-5">{% block content %}{% endblock %}</main>
-    {% include 'footer.html' %}
-  </body>
-</html>

scipaperloader/templates/base.html.jinja

@@ -0,0 +1,21 @@
+<!DOCTYPE html>
+<html lang="en">
+
+<head>
+  <meta charset="UTF-8" />
+  <meta name="description" content="A platform to load scientific papers and manage metadata." />
+  <meta name="keywords" content="science, papers, research, management" />
+  <title>{{ app_title }}</title>
+  <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/css/bootstrap.min.css" rel="stylesheet" />
+  <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js"></script>
+  <!-- Optional Alpine.js -->
+  <script defer src="https://cdn.jsdelivr.net/npm/alpinejs@3.x.x/dist/cdn.min.js"></script>
+</head>
+
+<body>
+  {% include "nav.html" %}
+  <main class="container my-5">{% block content %}{% endblock content %}</main>
+  {% include "footer.html" %}
+</body>
+
+</html>

scipaperloader/templates/index.html.jinja

@@ -1,4 +1,5 @@
-{% extends 'base.html' %} {% block content %}
+{% extends "base.html" %}
+{% block content %}
 
 <div class="container text-center">
   <h1 class="display-4">Welcome to SciPaperLoader</h1>
@@ -29,7 +30,7 @@
           A daemon process runs hourly to fetch papers using Zotero API.
           Downloads are randomized to mimic human behavior and avoid detection.
         </p>
-        <a href="/logs" class="btn btn-sm btn-outline-secondary">View Logs</a>
+        <a href="{{ url_for('logger.list_logs') }}" class="btn btn-sm btn-outline-secondary">View Logs</a>
       </div>
     </div>
   </div>
@@ -43,9 +44,7 @@
           inspect errors. Files are stored on disk in structured folders per
           DOI.
         </p>
-        <a href="{{ url_for('papers.list_papers') }}" class="btn btn-sm btn-outline-success"
+        <a href="{{ url_for('papers.list_papers') }}" class="btn btn-sm btn-outline-success">Browse Papers</a>
-          >Browse Papers</a
-        >
       </div>
     </div>
   </div>
@@ -59,11 +58,9 @@
           volume (e.g. 2/hour at daytime, 0 at night) to match your bandwidth or
           usage pattern.
         </p>
-        <a href="{{ url_for('schedule.schedule') }}" class="btn btn-sm btn-outline-warning"
+        <a href="{{ url_for('schedule.schedule') }}" class="btn btn-sm btn-outline-warning">Adjust Schedule</a>
-          >Adjust Schedule</a
-        >
       </div>
     </div>
   </div>
 </div>
-{% endblock %}
+{% endblock content %}

scipaperloader/templates/nav.html.jinja

@@ -1,17 +1,8 @@
 <nav class="navbar navbar-expand-lg navbar-light bg-light">
   <div class="container-fluid">
-    <a class="navbar-brand" href="{{ url_for('main.index') }}"
+    <a class="navbar-brand" href="{{ url_for('main.index') }}">{{ app_title }}</a>
-      >{{ app_title }}</a
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarSupportedContent"
-    >
+      aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
-    <button
-      class="navbar-toggler"
-      type="button"
-      data-bs-toggle="collapse"
-      data-bs-target="#navbarSupportedContent"
-      aria-controls="navbarSupportedContent"
-      aria-expanded="false"
-      aria-label="Toggle navigation"
-    >
       <span class="navbar-toggler-icon"></span>
     </button>
     <div class="collapse navbar-collapse" id="navbarSupportedContent">
@@ -20,28 +11,22 @@
           <a class="nav-link" href="{{ url_for('upload.upload') }}">Import CSV</a>
         </li>
         <li class="nav-item">
-            <a class="nav-link" href="{{ url_for('papers.list_papers') }}">Papers</a>
+          <a class="nav-link" href="{{ url_for('papers.list_papers') }}">Papers</a>
         </li>
         <li class="nav-item">
           <a class="nav-link" href="{{ url_for('schedule.schedule') }}">Schedule</a>
         </li>
         <li class="nav-item dropdown">
-          <a
+          <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-bs-toggle="dropdown"
-            class="nav-link dropdown-toggle"
+            aria-expanded="false">
-            href="#"
-            id="navbarDropdown"
-            role="button"
-            data-bs-toggle="dropdown"
-            aria-expanded="false"
-          >
             More
           </a>
           <ul class="dropdown-menu" aria-labelledby="navbarDropdown">
             <li>
-                <a class="dropdown-item" href="{{ url_for('logger.list_logs') }}">Logs</a>
+              <a class="dropdown-item" href="{{ url_for('logger.list_logs') }}">Logs</a>
             </li>
             <li>
-                <a class="dropdown-item" href="/about">About</a>
+              <a class="dropdown-item" href="{{ url_for('main.about') }}">About</a>
             </li>
             <li>
               <a class="dropdown-item" href="https://git.mbeck.cologne">Help</a>
@@ -50,14 +35,9 @@
         </li>
       </ul>
       <form class="d-flex">
-        <input
+        <input class="form-control me-2" type="search" placeholder="Search" aria-label="Search" />
-          class="form-control me-2"
-          type="search"
-          placeholder="Search"
-          aria-label="Search"
-        />
         <button class="btn btn-outline-success" type="submit">Search</button>
       </form>
     </div>
   </div>
-</nav>
+</nav>

scipaperloader/templates/papers.html

@@ -1,273 +0,0 @@
-{% extends "base.html" %}
-{% block title %}Papers{% endblock %}
-{% block content %}
-
-{# --- Sort direction logic for each column --- #}
-{% set title_sort = 'asc' if sort_by != 'title' or sort_dir == 'desc' else 'desc' %}
-{% set journal_sort = 'asc' if sort_by != 'journal' or sort_dir == 'desc' else 'desc' %}
-{% set doi_sort = 'asc' if sort_by != 'doi' or sort_dir == 'desc' else 'desc' %}
-{% set issn_sort = 'asc' if sort_by != 'issn' or sort_dir == 'desc' else 'desc' %}
-{% set status_sort = 'asc' if sort_by != 'status' or sort_dir == 'desc' else 'desc' %}
-{% set created_sort = 'asc' if sort_by != 'created_at' or sort_dir == 'desc' else 'desc' %}
-{% set updated_sort = 'asc' if sort_by != 'updated_at' or sort_dir == 'desc' else 'desc' %}
-
-<form method="get" class="mb-4 row g-3">
-    <div class="col-md-2">
-        <label>Status</label>
-        <select name="status" class="form-select">
-            <option value="">All</option>
-            {% if request.args.get('status') == 'Pending' %}
-                <option value="Pending" selected>Pending</option>
-            {% else %}
-                <option value="Pending">Pending</option>
-            {% endif %}
-            
-            {% if request.args.get('status') == 'Done' %}
-                <option value="Done" selected>Done</option>
-            {% else %}
-                <option value="Done">Done</option>
-            {% endif %}
-            
-            {% if request.args.get('status') == 'Failed' %}
-                <option value="Failed" selected>Failed</option>
-            {% else %}
-                <option value="Failed">Failed</option>
-            {% endif %}
-        </select>
-    </div>
-    <div class="col-md-2">
-        <label>Created from</label>
-        <input type="date" name="created_from" class="form-control" value="{{ request.args.get('created_from', '') }}">
-    </div>
-    <div class="col-md-2">
-        <label>Created to</label>
-        <input type="date" name="created_to" class="form-control" value="{{ request.args.get('created_to', '') }}">
-    </div>
-    <div class="col-md-2">
-        <label>Updated from</label>
-        <input type="date" name="updated_from" class="form-control" value="{{ request.args.get('updated_from', '') }}">
-    </div>
-    <div class="col-md-2">
-        <label>Updated to</label>
-        <input type="date" name="updated_to" class="form-control" value="{{ request.args.get('updated_to', '') }}">
-    </div>
-    <div class="col-md-2 d-flex align-items-end">
-        <button type="submit" class="btn btn-primary w-100">Filter</button>
-    </div>
-</form>
-
-<div class="modal fade" id="paperDetailModal" tabindex="-1" aria-hidden="true">
-    <div class="modal-dialog modal-lg modal-dialog-scrollable">
-        <div class="modal-content" id="paper-detail-content">
-            <!-- AJAX-loaded content will go here -->
-        </div>
-    </div>
-</div>
-
-<div class="d-flex align-items-center mb-4">
-    <!-- Statistics Section -->
-    <div class="me-auto">
-        <div class="list-group list-group-horizontal">
-            <div class="list-group-item d-flex justify-content-between align-items-center">
-                <strong>Total Papers</strong>
-                <span class="badge bg-primary rounded-pill">{{ total_papers }}</span>
-            </div>
-            {% for status, count in status_counts.items() %}
-                <div class="list-group-item d-flex justify-content-between align-items-center">
-                    <strong>{{ status }}:</strong>
-                    <span class="badge bg-primary rounded-pill">{{ count }}</span>
-                </div>
-            {% endfor %}
-        </div>
-    </div>
-
-    <!-- Pagination Section -->
-    <nav aria-label="Page navigation" class="mx-auto">
-        <ul class="pagination justify-content-center mb-0">
-            {% if pagination.has_prev %}
-            <li class="page-item">
-                {% set params = request.args.to_dict() %}
-                {% set _ = params.pop('page', None) %}
-                <a class="page-link" href="{{ url_for('papers.list_papers', page=pagination.prev_num, **params) }}" aria-label="Previous">
-                    <span aria-hidden="true">&laquo;</span>
-                </a>
-            </li>
-            {% else %}
-            <li class="page-item disabled">
-                <span class="page-link" aria-hidden="true">&laquo;</span>
-            </li>
-            {% endif %}
-
-            {% for page_num in pagination.iter_pages(left_edge=2, right_edge=2, left_current=2, right_current=2) %}
-            {% if page_num %}
-            <li class="page-item {% if page_num == pagination.page %}active{% endif %}">
-                {% set params = request.args.to_dict() %}
-                {% set _ = params.pop('page', None) %}
-                <a class="page-link" href="{{ url_for('papers.list_papers', page=page_num, **params) }}">{{ page_num }}</a>
-            </li>
-            {% else %}
-            <li class="page-item disabled"><span class="page-link">…</span></li>
-            {% endif %}
-            {% endfor %}
-
-            {% if pagination.has_next %}
-            <li class="page-item">
-                {% set params = request.args.to_dict() %}
-                {% set _ = params.pop('page', None) %}
-                <a class="page-link" href="{{ url_for('papers.list_papers', page=pagination.next_num, **params) }}" aria-label="Next">
-                    <span aria-hidden="true">&raquo;</span>
-                </a>
-            </li>
-            {% else %}
-            <li class="page-item disabled">
-                <span class="page-link" aria-hidden="true">&raquo;</span>
-            </li>
-            {% endif %}
-        </ul>
-    </nav>
-
-    <!-- Buttons Section -->
-    <div class="ms-auto">
-        <a href="{{ url_for('papers.export_papers') }}" class="btn btn-outline-secondary">Export CSV</a>
-    </div>
-</div>
-    <table class="table table-striped table-bordered table-smaller">
-        <thead>
-            <tr>
-                <th>
-                    {% set params = request.args.to_dict() %}
-                    {% set params = params.update({'sort_by': 'title', 'sort_dir': title_sort}) or params %}
-                    <a href="{{ url_for('papers.list_papers', **params) }}">Title</a>
-                </th>
-                <th>
-                    {% set params = request.args.to_dict() %}
-                    {% set params = params.update({'sort_by': 'journal', 'sort_dir': journal_sort}) or params %}
-                    <a href="{{ url_for('papers.list_papers', **params) }}">Journal</a>
-                </th>
-                <th>
-                    {% set params = request.args.to_dict() %}
-                    {% set params = params.update({'sort_by': 'doi', 'sort_dir': doi_sort}) or params %}
-                    <a href="{{ url_for('papers.list_papers', **params) }}">DOI</a>
-                </th>
-                <th>
-                    {% set params = request.args.to_dict() %}
-                    {% set params = params.update({'sort_by': 'issn', 'sort_dir': issn_sort}) or params %}
-                    <a href="{{ url_for('papers.list_papers', **params) }}">ISSN</a>
-                </th>
-                <th>
-                    {% set params = request.args.to_dict() %}
-                    {% set params = params.update({'sort_by': 'status', 'sort_dir': status_sort}) or params %}
-                    <a href="{{ url_for('papers.list_papers', **params) }}">Status</a>
-                </th>
-                <th>
-                    {% set params = request.args.to_dict() %}
-                    {% set params = params.update({'sort_by': 'created_at', 'sort_dir': created_sort}) or params %}
-                    <a href="{{ url_for('papers.list_papers', **params) }}">Created</a>
-                </th>
-                <th>
-                    {% set params = request.args.to_dict() %}
-                    {% set params = params.update({'sort_by': 'updated_at', 'sort_dir': updated_sort}) or params %}
-                    <a href="{{ url_for('papers.list_papers', **params) }}">Updated</a>
-                </th>
-            </tr>
-        </thead>
-        <tbody>
-            {% for paper in papers %}
-            <tr>
-                <td>
-                    <a href="#" class="icon-link icon-link-hover paper-link" data-url="{{ url_for('papers.paper_detail', paper_id=paper.id) }}">
-                        <svg xmlns="http://www.w3.org/2000/svg" class="bi" viewBox="0 0 16 16" aria-hidden="true">
-                            <path d="M4 1.5H3a2 2 0 0 0-2 2V14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V3.5a2 2 0 0 0-2-2h-1v1h1a1 1 0 0 1 1 1V14a1 1 0 0 1-1 1H3a1 1 0 0 1-1-1V3.5a1 1 0 0 1 1-1h1v-1z"/>
-                            <path d="M9.5 1a.5.5 0 0 1 .5.5v1a.5.5 0 0 1-.5.5h-3a.5.5 0 0 1-.5-.5v-1a.5.5 0 0 1 .5-.5h3zm-3-1A1.5 1.5 0 0 0 5 1.5v1A1.5 1.5 0 0 0 6.5 4h3A1.5 1.5 0 0 0 11 2.5v-1A1.5 1.5 0 0 0 9.5 0h-3z"/>
-                          </svg>
-                        {{ paper.title }}
-                    </a>
-                </td>
-                <td>{{ paper.journal }}</td>
-                <td>
-                    <a href="http://doi.org/{{ paper.doi }}" target="_blank" class="icon-link icon-link-hover">
-                        {{ paper.doi }}   
-                        <svg xmlns="http://www.w3.org/2000/svg" class="bi" viewBox="0 0 16 16" aria-hidden="true">
-                            <path d="M1 8a.5.5 0 0 1 .5-.5h11.793l-3.147-3.146a.5.5 0 0 1 .708-.708l4 4a.5.5 0 0 1 0 .708l-4 4a.5.5 0 0 1-.708-.708L13.293 8.5H1.5A.5.5 0 0 1 1 8z"/>
-                        </svg>
-                    </a>
-                </td>
-                <td>{{ paper.issn }}</td>
-                <td>{{ paper.status }}</td>
-                <td>{{ paper.created_at.strftime('%Y-%m-%d %H:%M:%S') }}</td>
-                <td>{{ paper.updated_at.strftime('%Y-%m-%d %H:%M:%S') }}</td>
-            </tr>
-            {% endfor %}
-        </tbody>
-    </table>
-</div>
-
-<nav aria-label="Page navigation">
-    <ul class="pagination justify-content-center">
-        {% if pagination.has_prev %}
-        <li class="page-item">
-            {% set params = request.args.to_dict() %}
-            {% set _ = params.pop('page', None) %}
-            <a class="page-link" href="{{ url_for('papers.list_papers', page=pagination.prev_num, **params) }}" aria-label="Previous">
-                <span aria-hidden="true">&laquo;</span>
-            </a>
-        </li>
-        {% else %}
-        <li class="page-item disabled">
-            <span class="page-link" aria-hidden="true">&laquo;</span>
-        </li>
-        {% endif %}
-
-        {% for page_num in pagination.iter_pages(left_edge=2, right_edge=2, left_current=2, right_current=2) %}
-        {% if page_num %}
-        <li class="page-item {% if page_num == pagination.page %}active{% endif %}">
-            {% set params = request.args.to_dict() %}
-            {% set _ = params.pop('page', None) %}
-            <a class="page-link" href="{{ url_for('papers.list_papers', page=page_num, **params) }}">{{ page_num }}</a>
-        </li>
-        {% else %}
-        <li class="page-item disabled"><span class="page-link">…</span></li>
-        {% endif %}
-        {% endfor %}
-
-        {% if pagination.has_next %}
-        <li class="page-item">
-            {% set params = request.args.to_dict() %}
-            {% set _ = params.pop('page', None) %}
-            <a class="page-link" href="{{ url_for('papers.list_papers', page=pagination.next_num, **params) }}" aria-label="Next">
-                <span aria-hidden="true">&raquo;</span>
-            </a>
-        </li>
-        {% else %}
-        <li class="page-item disabled">
-            <span class="page-link" aria-hidden="true">&raquo;</span>
-        </li>
-        {% endif %}
-    </ul>
-</nav>
-
-<script>
-document.addEventListener("DOMContentLoaded", function () {
-    const modal = new bootstrap.Modal(document.getElementById('paperDetailModal'));
-    const content = document.getElementById('paper-detail-content');
-
-    document.querySelectorAll('.paper-link').forEach(link => {
-        link.addEventListener('click', function (e) {
-            e.preventDefault();
-            const url = this.getAttribute('data-url');
-
-            fetch(url)
-                .then(response => response.text())
-                .then(html => {
-                    content.innerHTML = html;
-                    modal.show();
-                })
-                .catch(err => {
-                    content.innerHTML = '<div class="modal-body text-danger">Error loading details.</div>';
-                    modal.show();
-                });
-        });
-    });
-});
-</script>
-{% endblock %}

scipaperloader/templates/papers.html.jinja

@@ -0,0 +1,281 @@
+{% extends "base.html" %}
+{% block title %}Papers{% endblock title %}
+{% block content %}
+
+{# --- Sort direction logic for each column --- #}
+{% set title_sort = 'asc' if sort_by != 'title' or sort_dir == 'desc' else 'desc' %}
+{% set journal_sort = 'asc' if sort_by != 'journal' or sort_dir == 'desc' else 'desc' %}
+{% set doi_sort = 'asc' if sort_by != 'doi' or sort_dir == 'desc' else 'desc' %}
+{% set issn_sort = 'asc' if sort_by != 'issn' or sort_dir == 'desc' else 'desc' %}
+{% set status_sort = 'asc' if sort_by != 'status' or sort_dir == 'desc' else 'desc' %}
+{% set created_sort = 'asc' if sort_by != 'created_at' or sort_dir == 'desc' else 'desc' %}
+{% set updated_sort = 'asc' if sort_by != 'updated_at' or sort_dir == 'desc' else 'desc' %}
+
+<form method="get" class="mb-4 row g-3">
+    <div class="col-md-2">
+        <label>Status</label>
+        <select name="status" class="form-select">
+            <option value="">All</option>
+            {% if request.args.get('status') == 'Pending' %}
+            <option value="Pending" selected>Pending</option>
+            {% else %}
+            <option value="Pending">Pending</option>
+            {% endif %}
+
+            {% if request.args.get('status') == 'Done' %}
+            <option value="Done" selected>Done</option>
+            {% else %}
+            <option value="Done">Done</option>
+            {% endif %}
+
+            {% if request.args.get('status') == 'Failed' %}
+            <option value="Failed" selected>Failed</option>
+            {% else %}
+            <option value="Failed">Failed</option>
+            {% endif %}
+        </select>
+    </div>
+    <div class="col-md-2">
+        <label>Created from</label>
+        <input type="date" name="created_from" class="form-control" value="{{ request.args.get('created_from', '') }}">
+    </div>
+    <div class="col-md-2">
+        <label>Created to</label>
+        <input type="date" name="created_to" class="form-control" value="{{ request.args.get('created_to', '') }}">
+    </div>
+    <div class="col-md-2">
+        <label>Updated from</label>
+        <input type="date" name="updated_from" class="form-control" value="{{ request.args.get('updated_from', '') }}">
+    </div>
+    <div class="col-md-2">
+        <label>Updated to</label>
+        <input type="date" name="updated_to" class="form-control" value="{{ request.args.get('updated_to', '') }}">
+    </div>
+    <div class="col-md-2 d-flex align-items-end">
+        <button type="submit" class="btn btn-primary w-100">Filter</button>
+    </div>
+</form>
+
+<div class="modal fade" id="paperDetailModal" tabindex="-1" aria-hidden="true">
+    <div class="modal-dialog modal-lg modal-dialog-scrollable">
+        <div class="modal-content" id="paper-detail-content">
+            <!-- AJAX-loaded content will go here -->
+        </div>
+    </div>
+</div>
+
+<div class="d-flex align-items-center mb-4">
+    <!-- Statistics Section -->
+    <div class="me-auto">
+        <div class="list-group list-group-horizontal">
+            <div class="list-group-item d-flex justify-content-between align-items-center">
+                <strong>Total Papers</strong>
+                <span class="badge bg-primary rounded-pill">{{ total_papers }}</span>
+            </div>
+            {% for status, count in status_counts.items() %}
+            <div class="list-group-item d-flex justify-content-between align-items-center">
+                <strong>{{ status }}:</strong>
+                <span class="badge bg-primary rounded-pill">{{ count }}</span>
+            </div>
+            {% endfor %}
+        </div>
+    </div>
+
+    <!-- Pagination Section -->
+    <nav aria-label="Page navigation" class="mx-auto">
+        <ul class="pagination justify-content-center mb-0">
+            {% if pagination.has_prev %}
+            <li class="page-item">
+                {% set params = request.args.to_dict() %}
+                {% set _ = params.pop('page', None) %}
+                <a class="page-link" href="{{ url_for('papers.list_papers', page=pagination.prev_num, **params) }}"
+                    aria-label="Previous">
+                    <span aria-hidden="true">«</span>
+                </a>
+            </li>
+            {% else %}
+            <li class="page-item disabled">
+                <span class="page-link" aria-hidden="true">«</span>
+            </li>
+            {% endif %}
+
+            {% for page_num in pagination.iter_pages(left_edge=2, right_edge=2, left_current=2, right_current=2) %}
+            {% if page_num %}
+            <li class="page-item {% if page_num == pagination.page %}active{% endif %}">
+                {% set params = request.args.to_dict() %}
+                {% set _ = params.pop('page', None) %}
+                <a class="page-link" href="{{ url_for('papers.list_papers', page=page_num, **params) }}">{{ page_num
+                    }}</a>
+            </li>
+            {% else %}
+            <li class="page-item disabled"><span class="page-link">…</span></li>
+            {% endif %}
+            {% endfor %}
+
+            {% if pagination.has_next %}
+            <li class="page-item">
+                {% set params = request.args.to_dict() %}
+                {% set _ = params.pop('page', None) %}
+                <a class="page-link" href="{{ url_for('papers.list_papers', page=pagination.next_num, **params) }}"
+                    aria-label="Next">
+                    <span aria-hidden="true">»</span>
+                </a>
+            </li>
+            {% else %}
+            <li class="page-item disabled">
+                <span class="page-link" aria-hidden="true">»</span>
+            </li>
+            {% endif %}
+        </ul>
+    </nav>
+
+    <!-- Buttons Section -->
+    <div class="ms-auto">
+        <a href="{{ url_for('papers.export_papers') }}" class="btn btn-outline-secondary">Export CSV</a>
+    </div>
+</div>
+<table class="table table-striped table-bordered table-smaller">
+    <thead>
+        <tr>
+            <th>
+                {% set params = request.args.to_dict() %}
+                {% set params = params.update({'sort_by': 'title', 'sort_dir': title_sort}) or params %}
+                <a href="{{ url_for('papers.list_papers', **params) }}">Title</a>
+            </th>
+            <th>
+                {% set params = request.args.to_dict() %}
+                {% set params = params.update({'sort_by': 'journal', 'sort_dir': journal_sort}) or params %}
+                <a href="{{ url_for('papers.list_papers', **params) }}">Journal</a>
+            </th>
+            <th>
+                {% set params = request.args.to_dict() %}
+                {% set params = params.update({'sort_by': 'doi', 'sort_dir': doi_sort}) or params %}
+                <a href="{{ url_for('papers.list_papers', **params) }}">DOI</a>
+            </th>
+            <th>
+                {% set params = request.args.to_dict() %}
+                {% set params = params.update({'sort_by': 'issn', 'sort_dir': issn_sort}) or params %}
+                <a href="{{ url_for('papers.list_papers', **params) }}">ISSN</a>
+            </th>
+            <th>
+                {% set params = request.args.to_dict() %}
+                {% set params = params.update({'sort_by': 'status', 'sort_dir': status_sort}) or params %}
+                <a href="{{ url_for('papers.list_papers', **params) }}">Status</a>
+            </th>
+            <th>
+                {% set params = request.args.to_dict() %}
+                {% set params = params.update({'sort_by': 'created_at', 'sort_dir': created_sort}) or params %}
+                <a href="{{ url_for('papers.list_papers', **params) }}">Created</a>
+            </th>
+            <th>
+                {% set params = request.args.to_dict() %}
+                {% set params = params.update({'sort_by': 'updated_at', 'sort_dir': updated_sort}) or params %}
+                <a href="{{ url_for('papers.list_papers', **params) }}">Updated</a>
+            </th>
+        </tr>
+    </thead>
+    <tbody>
+        {% for paper in papers %}
+        <tr>
+            <td>
+                <a href="#" class="icon-link icon-link-hover paper-link"
+                    data-url="{{ url_for('papers.paper_detail', paper_id=paper.id) }}">
+                    <svg xmlns="http://www.w3.org/2000/svg" class="bi" viewBox="0 0 16 16" aria-hidden="true">
+                        <path
+                            d="M4 1.5H3a2 2 0 0 0-2 2V14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V3.5a2 2 0 0 0-2-2h-1v1h1a1 1 0 0 1 1 1V14a1 1 0 0 1-1 1H3a1 1 0 0 1-1-1V3.5a1 1 0 0 1 1-1h1v-1z" />
+                        <path
+                            d="M9.5 1a.5.5 0 0 1 .5.5v1a.5.5 0 0 1-.5.5h-3a.5.5 0 0 1-.5-.5v-1a.5.5 0 0 1 .5-.5h3zm-3-1A1.5 1.5 0 0 0 5 1.5v1A1.5 1.5 0 0 0 6.5 4h3A1.5 1.5 0 0 0 11 2.5v-1A1.5 1.5 0 0 0 9.5 0h-3z" />
+                    </svg>
+                    {{ paper.title }}
+                </a>
+            </td>
+            <td>{{ paper.journal }}</td>
+            <td>
+                <a href="https://doi.org/{{ paper.doi }}" target="_blank" class="icon-link icon-link-hover">
+                    {{ paper.doi }}
+                    <svg xmlns="http://www.w3.org/2000/svg" class="bi" viewBox="0 0 16 16" aria-hidden="true">
+                        <path
+                            d="M1 8a.5.5 0 0 1 .5-.5h11.793l-3.147-3.146a.5.5 0 0 1 .708-.708l4 4a.5.5 0 0 1 0 .708l-4 4a.5.5 0 0 1-.708-.708L13.293 8.5H1.5A.5.5 0 0 1 1 8z" />
+                    </svg>
+                </a>
+            </td>
+            <td>{{ paper.issn }}</td>
+            <td>{{ paper.status }}</td>
+            <td>{{ paper.created_at.strftime('%Y-%m-%d %H:%M:%S') }}</td>
+            <td>{{ paper.updated_at.strftime('%Y-%m-%d %H:%M:%S') }}</td>
+        </tr>
+        {% endfor %}
+    </tbody>
+</table>
+
+<nav aria-label="Page navigation">
+    <ul class="pagination justify-content-center">
+        {% if pagination.has_prev %}
+        <li class="page-item">
+            {% set params = request.args.to_dict() %}
+            {% set _ = params.pop('page', None) %}
+            <a class="page-link" href="{{ url_for('papers.list_papers', page=pagination.prev_num, **params) }}"
+                aria-label="Previous">
+                <span aria-hidden="true">«</span>
+            </a>
+        </li>
+        {% else %}
+        <li class="page-item disabled">
+            <span class="page-link" aria-hidden="true">«</span>
+        </li>
+        {% endif %}
+
+        {% for page_num in pagination.iter_pages(left_edge=2, right_edge=2, left_current=2, right_current=2) %}
+        {% if page_num %}
+        <li class="page-item {% if page_num == pagination.page %}active{% endif %}">
+            {% set params = request.args.to_dict() %}
+            {% set _ = params.pop('page', None) %}
+            <a class="page-link" href="{{ url_for('papers.list_papers', page=page_num, **params) }}">{{ page_num }}</a>
+        </li>
+        {% else %}
+        <li class="page-item disabled"><span class="page-link">…</span></li>
+        {% endif %}
+        {% endfor %}
+
+        {% if pagination.has_next %}
+        <li class="page-item">
+            {% set params = request.args.to_dict() %}
+            {% set _ = params.pop('page', None) %}
+            <a class="page-link" href="{{ url_for('papers.list_papers', page=pagination.next_num, **params) }}"
+                aria-label="Next">
+                <span aria-hidden="true">»</span>
+            </a>
+        </li>
+        {% else %}
+        <li class="page-item disabled">
+            <span class="page-link" aria-hidden="true">»</span>
+        </li>
+        {% endif %}
+    </ul>
+</nav>
+
+<script>
+    document.addEventListener("DOMContentLoaded", function () {
+        const modal = new bootstrap.Modal(document.getElementById('paperDetailModal'));
+        const content = document.getElementById('paper-detail-content');
+
+        document.querySelectorAll('.paper-link').forEach(link => {
+            link.addEventListener('click', function (e) {
+                e.preventDefault();
+                const url = this.getAttribute('data-url');
+
+                fetch(url)
+                    .then(response => response.text())
+                    .then(html => {
+                        content.innerHTML = html;
+                        modal.show();
+                    })
+                    .catch(err => {
+                        content.innerHTML = '<div class="modal-body text-danger">Error loading details.</div>';
+                        modal.show();
+                    });
+            });
+        });
+    });
+</script>
+{% endblock content %}

scipaperloader/templates/partials/paper_detail_modal.html.jinja

@@ -12,18 +12,13 @@
   <p>
     <strong>ISSN:</strong>
     {% for issn in value.split(',') %}
-    <a
+    <a href="https://www.worldcat.org/search?q=issn:{{ issn.strip() }}" target="_blank">{{ issn.strip() }}</a>{% if not
-      href="https://www.worldcat.org/search?q=issn:{{ issn.strip() }}"
+    loop.last %}, {% endif %} {% endfor %}
-      target="_blank"
-      >{{ issn.strip() }}</a
-    >{% if not loop.last %}, {% endif %} {% endfor %}
   </p>
   {% else %}
   <p>
     <strong>ISSN:</strong>
-    <a href="https://www.worldcat.org/search?q=issn:{{ value }}" target="_blank"
+    <a href="https://www.worldcat.org/search?q=issn:{{ value }}" target="_blank">{{ value }}</a>
-      >{{ value }}</a
-    >
   </p>
   {% endif %} {% endif %} {% if not key.startswith('_') and key != 'metadata'
   and key != 'doi' and key != 'issn' %}
@@ -34,4 +29,4 @@
   <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">
     Close
   </button>
-</div>
+</div>

scipaperloader/templates/schedule.html.jinja

@@ -1,15 +1,17 @@
-{% extends 'base.html' %} {% block content %}
+{% extends "base.html" %} {% block content %}
 <style>
   .timeline {
     display: flex;
     flex-wrap: wrap;
     gap: 3px;
-    user-select: none; /* Prevent text selection during drag */
+    user-select: none;
+    /* Prevent text selection during drag */
   }
 
   .hour-block {
     width: 49px;
-    height: 70px; /* Increased height to fit additional text */
+    height: 70px;
+    /* Increased height to fit additional text */
     border-radius: 5px;
     text-align: center;
     line-height: 1.2;
@@ -76,11 +78,8 @@
   messages %}
   <div id="flash-messages">
     {% for category, message in messages %}
-    <div
+    <div class="flash-message {{ category }}" x-data="{}"
-      class="flash-message {{ category }}"
+      x-init="setTimeout(() => $el.classList.add('fade'), 100); setTimeout(() => $el.remove(), 5000)">
-      x-data="{}"
-      x-init="setTimeout(() => $el.classList.add('fade'), 100); setTimeout(() => $el.remove(), 5000)"
-    >
       {{ message }}
     </div>
     {% endfor %}
@@ -118,39 +117,21 @@
       <strong x-text="volume"></strong> papers.
     </p>
     <div class="d-flex align-items-center mb-3">
-      <form
+      <form method="post" action="{{ url_for('schedule.schedule') }}" class="input-group w-50">
-        method="POST"
-        action="{{ url_for('schedule.schedule') }}"
-        class="input-group w-50"
-      >
         <label class="input-group-text">Papers per day:</label>
-        <input
+        <input type="number" class="form-control" name="total_volume" value="{{ volume }}" min="1" max="1000"
-          type="number"
+          required />
-          class="form-control"
-          name="total_volume"
-          value="{{ volume }}"
-          min="1"
-          max="1000"
-          required
-        />
         <button type="submit" class="btn btn-primary">Update Volume</button>
       </form>
     </div>
   </div>
 
   <h2 class="mt-4">Current Schedule</h2>
-  <form method="POST" action="{{ url_for('schedule.schedule') }}">
+  <form method="post" action="{{ url_for('schedule.schedule') }}">
     <div class="timeline mb-3" @mouseup="endDrag()" @mouseleave="endDrag()">
       <template x-for="hour in Object.keys(schedule)" :key="hour">
-        <div
+        <div class="hour-block" :id="'hour-' + hour" :data-hour="hour" :style="getBackgroundStyle(hour)"
-          class="hour-block"
+          :class="{'selected': isSelected(hour)}" @mousedown="startDrag($event, hour)" @mouseover="dragSelect(hour)">
-          :id="'hour-' + hour"
-          :data-hour="hour"
-          :style="getBackgroundStyle(hour)"
-          :class="{'selected': isSelected(hour)}"
-          @mousedown="startDrag($event, hour)"
-          @mouseover="dragSelect(hour)"
-        >
           <div><strong x-text="formatHour(hour)"></strong></div>
           <div class="weight"><span x-text="schedule[hour]"></span></div>
           <div class="papers">
@@ -163,25 +144,14 @@
 
     <div class="input-group mb-4 w-50">
       <label class="input-group-text">Set Weight:</label>
-      <input
+      <input type="number" step="0.1" min="0" max="5" x-model="newWeight" class="form-control" />
-        type="number"
+      <button type="button" class="btn btn-outline-primary" @click="applyWeight()">
-        step="0.1"
-        min="0"
-        max="5"
-        x-model="newWeight"
-        class="form-control"
-      />
-      <button
-        type="button"
-        class="btn btn-outline-primary"
-        @click="applyWeight()"
-      >
         Apply to Selected
       </button>
     </div>
 
     <div class="d-flex justify-content-between">
-      <a href="/" class="btn btn-outline-secondary">⬅ Back</a>
+      <a href="{{ url_for(main.index) }}" class="btn btn-outline-secondary">⬅ Back</a>
       <button type="submit" class="btn btn-success">💾 Save Schedule</button>
     </div>
   </form>
@@ -297,4 +267,4 @@
     };
   }
 </script>
-{% endblock %}
+{% endblock content %}

scipaperloader/templates/upload.html

@@ -1,73 +0,0 @@
-{% extends 'base.html' %}
-{% block content %}
-<h1>Welcome to SciPaperLoader</h1>
-
-{% if success %}
-    <div class="alert alert-success mt-3">{{ success }}</div>
-{% endif %}
-
-{% if error_message %}
-    <div class="alert alert-warning mt-3">
-        <h4>{{ error_message }}</h4>
-        <table class="table table-sm table-bordered">
-            <thead>
-                <tr>
-                    <th>Row</th>
-                    <th>DOI</th>
-                    <th>Error</th>
-                </tr>
-            </thead>
-            <tbody>
-                {% for error in error_samples %}
-                <tr>
-                    <td>{{ error.row }}</td>
-                    <td>{{ error.doi }}</td>
-                    <td>{{ error.error }}</td>
-                </tr>
-                {% endfor %}
-            </tbody>
-        </table>
-        <a href="{{ url_for('upload.download_error_log') }}" class="btn btn-outline-secondary">Download Full Error Log</a>
-    </div>
-{% endif %}
-
-<div class="alert alert-info">
-    <p><strong>Instructions:</strong> Please upload a CSV file containing academic paper metadata. The file must include the following columns:</p>
-    <ul>
-        <li><code>alternative_id</code> – an alternative title or abbreviation</li>
-        <li><code>journal</code> – the journal name</li>
-        <li><code>doi</code> – the digital object identifier</li>
-        <li><code>issn</code> – the ISSN of the journal</li>
-        <li><code>title</code> – the title of the paper</li>
-    </ul>
-    <p>The format of your CSV should resemble the response structure of the Crossref API's <code>/journals/{issn}/works</code> endpoint.</p>
-</div>
-
-<form method="POST" action="{{ url_for('upload.upload') }}" enctype="multipart/form-data">
-    <div class="mb-3">
-        <label class="form-label">How to handle duplicate DOIs:</label>
-        <div class="form-check">
-            <input class="form-check-input" type="radio" name="duplicate_strategy" value="skip" id="skip" checked>
-            <label class="form-check-label" for="skip">Skip duplicate entries</label>
-        </div>
-        <div class="form-check">
-            <input class="form-check-input" type="radio" name="duplicate_strategy" value="update" id="update">
-            <label class="form-check-label" for="update">Update existing entries</label>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="file">Upload CSV File</label>
-        <input type="file" name="file" id="file" class="form-control" required>
-    </div>
-    <div class="form-group mt-3">
-        <label for="delimiter">Choose CSV Delimiter</label>
-        <select name="delimiter" id="delimiter" class="form-control">
-            <option value=",">Comma (,)</option>
-            <option value=";">Semicolon (;)</option>
-            <option value="\t">Tab (\\t)</option>
-            <option value="|">Pipe (|)</option>
-        </select>
-    </div>
-    <button type="submit" class="btn btn-primary mt-3">Upload</button>
-</form>
-{% endblock %}

scipaperloader/templates/upload.html.jinja

@@ -0,0 +1,76 @@
+{% extends "base.html" %} {% block content %}
+<h1>Welcome to SciPaperLoader</h1>
+
+{% if success %}
+<div class="alert alert-success mt-3">{{ success }}</div>
+{% endif %} {% if error_message %}
+<div class="alert alert-warning mt-3">
+  <h4>{{ error_message }}</h4>
+  <table class="table table-sm table-bordered">
+    <thead>
+      <tr>
+        <th>Row</th>
+        <th>DOI</th>
+        <th>Error</th>
+      </tr>
+    </thead>
+    <tbody>
+      {% for error in error_samples %}
+      <tr>
+        <td>{{ error.row }}</td>
+        <td>{{ error.doi }}</td>
+        <td>{{ error.error }}</td>
+      </tr>
+      {% endfor %}
+    </tbody>
+  </table>
+  <a href="{{ url_for('upload.download_error_log') }}" class="btn btn-outline-secondary">Download Full Error Log</a>
+</div>
+{% endif %}
+
+<div class="alert alert-info">
+  <p>
+    <strong>Instructions:</strong> Please upload a CSV file containing academic
+    paper metadata. The file must include the following columns:
+  </p>
+  <ul>
+    <li><code>alternative_id</code> – an alternative title or abbreviation</li>
+    <li><code>journal</code> – the journal name</li>
+    <li><code>doi</code> – the digital object identifier</li>
+    <li><code>issn</code> – the ISSN of the journal</li>
+    <li><code>title</code> – the title of the paper</li>
+  </ul>
+  <p>
+    The format of your CSV should resemble the response structure of the
+    Crossref API's <code>/journals/{issn}/works</code> endpoint.
+  </p>
+</div>
+
+<form method="post" action="{{ url_for('upload.upload') }}" enctype="multipart/form-data">
+  <div class="mb-3">
+    <label class="form-label">How to handle duplicate DOIs:</label>
+    <div class="form-check">
+      <input class="form-check-input" type="radio" name="duplicate_strategy" value="skip" id="skip" checked />
+      <label class="form-check-label" for="skip">Skip duplicate entries</label>
+    </div>
+    <div class="form-check">
+      <input class="form-check-input" type="radio" name="duplicate_strategy" value="update" id="update" />
+      <label class="form-check-label" for="update">Update existing entries</label>
+    </div>
+  </div>
+  <div class="form-group">
+    <label for="file">Upload CSV File</label>
+    <input type="file" name="file" id="file" class="form-control" required />
+  </div>
+  <div class="form-group mt-3">
+    <label for="delimiter">Choose CSV Delimiter</label>
+    <select name="delimiter" id="delimiter" class="form-control">
+      <option value=",">Comma (,)</option>
+      <option value=";">Semicolon (;)</option>
+      <option value="\t">Tab (\\t)</option>
+      <option value="|">Pipe (|)</option>
+    </select>
+  </div>
+  <button type="submit" class="btn btn-primary mt-3">Upload</button>
+</form>
+{% endblock content %}