web/dev.html at main · snipe-bio/web · GitHub

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<!DOCTYPE html>
<html lang="en">

<head>
    <!-- Google Tag Manager -->
    <script>(function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':
        new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],
        j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src=
        'https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);
        })(window,document,'script','dataLayer','GTM-N5RW3TB3');</script>
        <!-- End Google Tag Manager -->

    <meta charset="UTF-8">
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <title>Snipe Web</title>

    <!-- Bootstrap 5 CSS -->
    <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-QWTKZyjpPEjISv5WaRU9OFeRpok6YctnYmDr5pNlyT2bRjXh0JMhjY6hW+ALEwIH" crossorigin="anonymous">

    <!-- Font Awesome for Icons -->
    <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.6.0/css/all.min.css">

    <!-- Dropzone CSS -->
    <link rel="stylesheet" href="https://unpkg.com/dropzone@5/dist/min/dropzone.min.css" type="text/css" />

    <!-- Custom Styles -->
    <link href="styles/main.css" rel="stylesheet">

    <style>
        /* Custom Styles */
        body {
            font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;
            background: linear-gradient(135deg, #f5f7fa 0%, #c3cfe2 100%);
            min-height: 100vh;
        }

        .container {
            background-color: white;
            padding: 2rem;
            border-radius: 15px;
            box-shadow: 0 10px 30px rgba(0, 0, 0, 0.1);
            width: 90%;
            max-width: 1200px;
            margin: 2rem auto;
        }

        h1 {
            color: #2c3e50;
            text-align: center;
            margin-bottom: 2rem;
            font-size: 2.5rem;
            text-transform: uppercase;
            letter-spacing: 2px;
        }

        .control-group label {
            font-weight: bold;
            margin-bottom: 0.5rem;
            color: #34495e;
        }

        .dropzone {
            border: 2px dashed #3498db;
            border-radius: 10px;
            padding: 20px;
            text-align: center;
            color: #3498db;
            cursor: pointer;
        }

        .file-info {
            margin-top: 10px;
        }

        .file-info .remove-file {
            margin-left: 10px;
            color: rgb(255, 255, 255);
            cursor: pointer;
        }

        #loadingAnimation {
            position: fixed;
            top: 0;
            left: 0;
            width: 100%;
            height: 100%;
            background: rgba(255, 255, 255, 0.8);
            display: flex;
            align-items: center;
            justify-content: center;
            z-index: 1000;
        }

        .loader {
            border: 12px solid #f3f3f3;
            border-top: 12px solid #3498db;
            border-radius: 50%;
            width: 60px;
            height: 60px;
            animation: spin 1s linear infinite;
        }

        @keyframes spin {
            0% {
                transform: rotate(0deg);
            }

            100% {
                transform: rotate(360deg);
            }
        }

        /* Footer Styling */
        footer.footer {
            background-color: #f8f9fa;
            padding: 1rem 0;
            margin-top: 2rem;
            text-align: center;
            color: #6c757d;
        }

        /* Enhanced Table Styling */
        table.table-striped thead {
            background-color: #3498db;
            color: white;
        }

        table.table-striped tbody tr:nth-of-type(odd) {
            background-color: #f9f9f9;
        }

        table.table-striped tbody tr:nth-of-type(even) {
            background-color: #ffffff;
        }

        .progress {
            height: 20px;
        }

        .progress-bar {
            font-size: 0.8rem;
            line-height: 20px;
        }
    </style>
</head>

<body>
    <!-- Google Tag Manager (noscript) -->
    <noscript><iframe src="https://www.googletagmanager.com/ns.html?id=GTM-N5RW3TB3"
        height="0" width="0" style="display:none;visibility:hidden"></iframe></noscript>
        <!-- End Google Tag Manager (noscript) -->

    <!-- Help Modal -->
    <div id="help-modal" class="modal" tabindex="-1" role="dialog">
        <div class="modal-dialog modal-lg" role="document">
            <div class="modal-content">
                <div class="modal-header">
                    <h5 class="modal-title">Snipe Metrics Description</h5>
                    <button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
                </div>
                <div class="modal-body">
                    <p>Here you can describe the metrics used in Snipe...</p>
                    <!-- Add more detailed descriptions as needed -->
                </div>
                <div class="modal-footer">
                    <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
                </div>
            </div>
        </div>
    </div>

    <!-- Main Container -->
    <div class="container">
        <h1>Snipe Processing App</h1>

        <!-- Data Selection Section -->
        <div id="data-selection-container" class="species-selection">
            <div class="row">
                <div class="col-md-3 mb-3">
                    <label for="species-select" class="form-label">Species:</label>
                    <select id="species-select" class="form-select">
                        <option value="" disabled selected>Select Species</option>
                        <!-- Options will be populated dynamically -->
                    </select>
                </div>
                <div class="col-md-3 mb-3">
                    <label for="genome-select" class="form-label">Reference Genome:</label>
                    <select id="genome-select" class="form-select" disabled>
                        <option value="" disabled selected>Select Reference Genome</option>
                        <!-- Options will be populated dynamically -->
                    </select>
                </div>
                <div class="col-md-3 mb-3">
                    <label for="ychr-select" class="form-label">Y Chromosome:</label>
                    <select id="ychr-select" class="form-select" disabled>
                        <option value="" disabled selected>Select Y Chromosome</option>
                        <!-- Options will be populated dynamically -->
                    </select>
                </div>
                <div class="col-md-3 mb-3">
                    <label for="amplicon-select" class="form-label">Amplicon (Optional):</label>
                    <select id="amplicon-select" class="form-select" disabled>
                        <option value="" disabled selected>Select Amplicon (Optional)</option>
                        <!-- Options will be populated dynamically -->
                    </select>
                </div>
            </div>
            <button id="load-data-button" class="btn btn-success" disabled>Load Data</button>
            <div id="log-info" class="log-info mt-3" style="display: none;">
                <!-- Log information will be displayed here -->
            </div>
        </div>

        <!-- File Upload Section -->
        <div class="mt-4">
            <h2>Upload Sample Files</h2>
            <form id="sample-upload-form" class="dropzone">
                <div class="dz-message">Drop files here or click to upload.</div>
            </form>
            <!-- Container for Uploaded Files and Their Progress -->
            <div id="uploaded-files" class="mt-3">
                <!-- Individual file progress will be appended here -->
            </div>
        </div>


        <!-- Results Table -->
        <div id="resultsTableContainer" class="mt-4" style="display: none;">
            <div class="mb-3">
                <label for="bioprojectInput" class="form-label"><b>Update BioProject Accession:</b></label>
                <input type="text" id="bioprojectInput" class="form-control" placeholder="Enter BioProject Accession">
            </div>
            <h3>Results</h3>
            <button id="exportButton" class="btn btn-primary">Export as TSV</button>
            <div class="table-responsive">
                <table class="table table-striped">
                    <thead id="resultsTableHead"></thead>
                    <tbody id="resultsTableBody"></tbody>
                </table>
            </div>
        </div>


        <!-- Loading Animation -->
        <div id="loadingAnimation" style="display: none;">
            <div class="loader"></div>
        </div>
    </div>
        <!-- Footer -->
        <footer class="footer mt-auto py-3 bg-light">
                <p class="text-center">© 2024 Snipe. All rights reserved.</p>
        </footer>
</body>
</html>


    <!-- Required Scripts -->
    <script src="https://code.jquery.com/jquery-3.6.0.min.js"></script>
    <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js" integrity="sha384-YvpcrYf0tY3lHB60NNkmXc5s9fDVZLESaAA55NDzOxhy9GkcIdslK1eN7N6jIeHz" crossorigin="anonymous"></script>

    <!-- Dropzone JS -->
    <script src="https://unpkg.com/dropzone@5/dist/min/dropzone.min.js"></script>

    <!-- JSZip for ZIP file handling -->
    <script src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.10.1/jszip.min.js"></script>

    <!-- Pyodide for Python integration -->
    <script src="https://cdn.jsdelivr.net/pyodide/v0.26.2/full/pyodide.js"></script>

    <!-- Plotly for plotting -->
    <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>

    <!-- Custom Script -->
    <script src="./scripts/main.js" defer></script>