<?php
declare(strict_types=1);
require_once dirname(__DIR__) . '/src/Exception/UniProtException.php';
require_once dirname(__DIR__) . '/src/Http/HttpClientInterface.php';
require_once dirname(__DIR__) . '/src/Http/CurlClient.php';
require_once dirname(__DIR__) . '/src/Http/StreamClient.php';
require_once dirname(__DIR__) . '/src/Http/HttpClientFactory.php';
require_once dirname(__DIR__) . '/src/UniProt/UniProtIdMapping.php';
use UniProtPHP\Http\CurlClient;
use UniProtPHP\Http\HttpClientFactory;
use UniProtPHP\UniProt\UniProtIdMapping;
use UniProtPHP\Exception\UniProtException;
// Disable SSL verification for development
CurlClient::setVerifySSL(false);
$submitResult = null;
$retrieveResult = null;
$error = null;
$jobId = '';
$ids = "P05067\nP12345";
$fromDb = 'UniProtKB_AC-ID';
$toDb = 'Ensembl';
// Handle ID submission
if ($_SERVER['REQUEST_METHOD'] === 'POST' && isset($_POST['action'])) {
$action = $_POST['action'];
if ($action === 'submit') {
$ids = trim($_POST['ids']);
$fromDb = $_POST['from_db'] ?? 'UniProtKB_AC-ID';
$toDb = $_POST['to_db'] ?? 'Ensembl';
if (empty($ids)) {
$error = 'Please enter at least one ID';
} else {
try {
$idArray = array_filter(array_map('trim', explode("\n", $ids)));
if (empty($idArray)) {
throw new Exception('No valid IDs provided');
}
$httpClient = HttpClientFactory::create();
$mapping = new UniProtIdMapping($httpClient);
$jobId = $mapping->submit($fromDb, $toDb, $idArray);
$submitResult = ['jobId' => $jobId];
} catch (UniProtException $e) {
$error = $e->getMessage();
} catch (Exception $e) {
$error = $e->getMessage();
}
}
}
elseif ($action === 'retrieve') {
$jobId = trim($_POST['job_id']);
if (empty($jobId)) {
$error = 'Please enter a job ID';
} else {
try {
$httpClient = HttpClientFactory::create();
$mapping = new UniProtIdMapping($httpClient);
// Check status first
$statusResponse = $mapping->status($jobId);
$status = $statusResponse['jobStatus'] ?? 'UNKNOWN';
if ($status !== 'FINISHED') {
$error = "Job status: {$status}. Please wait for job to complete.";
} else {
$results = $mapping->getResults($jobId);
$details = $mapping->getDetails($jobId);
$retrieveResult = [
'details' => $details,
'results' => $results
];
}
} catch (UniProtException $e) {
$error = $e->getMessage();
} catch (Exception $e) {
$error = $e->getMessage();
}
}
}
}
?>
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>ID Mapping - UniProt PHP Library</title>
<style>
* {
margin: 0;
padding: 0;
box-sizing: border-box;
}
body {
font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
background: #f5f7fa;
padding: 20px;
}
.container {
max-width: 1200px;
margin: 0 auto;
}
.header {
background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
color: white;
padding: 30px;
border-radius: 12px;
margin-bottom: 30px;
box-shadow: 0 10px 30px rgba(0,0,0,0.2);
}
.header h1 {
margin-bottom: 10px;
}
.back-btn {
display: inline-block;
background: white;
color: #667eea;
padding: 8px 15px;
border-radius: 6px;
text-decoration: none;
font-weight: 600;
margin-top: 10px;
}
.grid {
display: grid;
grid-template-columns: 1fr 1fr;
gap: 30px;
margin-bottom: 30px;
}
.card {
background: white;
padding: 30px;
border-radius: 12px;
box-shadow: 0 5px 15px rgba(0,0,0,0.1);
}
.card h2 {
color: #333;
margin-bottom: 20px;
padding-bottom: 10px;
border-bottom: 2px solid #667eea;
}
.form-group {
margin-bottom: 20px;
}
.form-group label {
display: block;
color: #333;
font-weight: 600;
margin-bottom: 8px;
}
.form-group textarea,
.form-group select {
width: 100%;
padding: 12px;
border: 2px solid #ddd;
border-radius: 6px;
font-size: 1em;
font-family: inherit;
transition: border-color 0.3s;
}
.form-group textarea:focus,
.form-group select:focus {
outline: none;
border-color: #667eea;
}
.form-group textarea {
min-height: 120px;
resize: vertical;
}
.form-group input {
width: 100%;
padding: 12px;
border: 2px solid #ddd;
border-radius: 6px;
font-size: 1em;
transition: border-color 0.3s;
}
.form-group input:focus {
outline: none;
border-color: #667eea;
}
.form-row {
display: grid;
grid-template-columns: 1fr 1fr;
gap: 15px;
}
.button-group {
display: flex;
gap: 10px;
}
button {
flex: 1;
padding: 12px;
background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
color: white;
border: none;
border-radius: 6px;
cursor: pointer;
font-weight: 600;
transition: opacity 0.3s;
}
button:hover {
opacity: 0.9;
}
.hint {
color: #888;
font-size: 0.9em;
margin-top: 8px;
}
.success {
background: #efe;
color: #3c3;
padding: 15px;
border-radius: 6px;
margin-bottom: 20px;
border-left: 4px solid #3c3;
}
.error {
background: #fee;
color: #c33;
padding: 15px;
border-radius: 6px;
margin-bottom: 20px;
border-left: 4px solid #c33;
}
.job-result {
background: #f0f7ff;
padding: 15px;
border-radius: 6px;
margin-top: 15px;
border-left: 4px solid #667eea;
}
.tabs {
display: flex;
gap: 10px;
margin-bottom: 20px;
border-bottom: 2px solid #ddd;
}
.tab-btn {
padding: 12px 20px;
background: none;
border: none;
cursor: pointer;
font-weight: 600;
color: #999;
border-bottom: 3px solid transparent;
transition: all 0.3s;
}
.tab-btn.active {
color: #667eea;
border-bottom-color: #667eea;
}
.tab-content {
display: none;
}
.tab-content.active {
display: block;
}
.results-table {
width: 100%;
border-collapse: collapse;
}
.results-table th {
background: #f0f0f0;
padding: 12px;
text-align: left;
font-weight: 600;
border-bottom: 2px solid #ddd;
}
.results-table td {
padding: 12px;
border-bottom: 1px solid #eee;
}
.results-table tr:hover {
background: #f9f9f9;
}
.json-viewer {
background: #f8f9fa;
padding: 15px;
border-radius: 6px;
overflow-x: auto;
font-family: 'Courier New', monospace;
font-size: 0.85em;
line-height: 1.6;
color: #333;
max-height: 400px;
overflow-y: auto;
}
.copyable {
user-select: all;
padding: 8px;
background: #f0f0f0;
border-radius: 4px;
font-family: monospace;
}
.accordion {
background: white;
padding: 30px;
border-radius: 12px;
box-shadow: 0 5px 15px rgba(0,0,0,0.1);
margin-bottom: 30px;
}
.accordion-item {
border: 1px solid #ddd;
border-radius: 6px;
margin-bottom: 15px;
}
.accordion-btn {
width: 100%;
padding: 15px 20px;
background: #f8f9fa;
border: none;
border-radius: 6px;
cursor: pointer;
font-weight: 600;
text-align: left;
color: #333;
display: flex;
justify-content: space-between;
align-items: center;
transition: all 0.3s;
}
.accordion-btn:hover {
background: #f0f0f0;
}
.accordion-btn.active {
background: #667eea;
color: white;
}
.accordion-content {
display: none;
padding: 20px;
background: #f9f9f9;
border-top: 1px solid #ddd;
}
.accordion-content.active {
display: block;
}
.accordion-content pre {
background: white;
padding: 15px;
border-radius: 4px;
overflow-x: auto;
font-size: 0.9em;
line-height: 1.5;
border: 1px solid #ddd;
}
@media (max-width: 768px) {
.grid {
grid-template-columns: 1fr;
}
.form-row {
grid-template-columns: 1fr;
}
}
</style>
</head>
<body>
<div class="container">
<div class="header">
<h1>? ID Mapping</h1>
<p>Map protein IDs between different databases</p>
<a href="index.php" class="back-btn">? Back to Home</a>
</div>
<?php if ($error): ?>
<div class="error">? Error: <?php echo htmlspecialchars($error); ?></div>
<?php endif; ?>
<div class="accordion">
<div class="accordion-item">
<button class="accordion-btn" onclick="toggleAccordion(this)">
<span>? ID Mapping Code Example</span>
<span>?</span>
</button>
<div class="accordion-content">
<pre><?php
require_once 'src/Http/HttpClientFactory.php';
require_once 'src/UniProt/UniProtIdMapping.php';
use UniProtPHP\Http\HttpClientFactory;
use UniProtPHP\UniProt\UniProtIdMapping;
use UniProtPHP\Exception\UniProtException;
// Create HTTP client and mapping instance
$httpClient = HttpClientFactory::create();
$mapping = new UniProtIdMapping($httpClient);
// Step 1: Submit mapping job
$jobId = $mapping->submit(
'UniProtKB_AC-ID', // from database
'Ensembl', // to database
['P05067', 'P12345'] // protein IDs
);
echo "Job ID: {$jobId}\n";
// Step 2: Check job status (wait for completion)
$statusResponse = $mapping->status($jobId);
$status = $statusResponse['jobStatus']; // 'RUNNING' or 'FINISHED'
// Step 3: Wait for job to complete and get results
$results = $mapping->waitForCompletion($jobId);
// Step 4: Get detailed mapping information
$details = $mapping->getDetails($jobId);
// Process results
foreach ($results as $mapping_entry) {
echo $mapping_entry['from'] . " -> " .
$mapping_entry['to'] . "\n";
}
?></pre>
</div>
</div>
</div>
<?php if ($error): ?>
<div class="error">? Error: <?php echo htmlspecialchars($error); ?></div>
<?php endif; ?>
<div class="grid">
<!-- Submit Mapping -->
<div class="card">
<h2>? Submit Mapping Job</h2>
<form method="POST">
<input type="hidden" name="action" value="submit">
<div class="form-group">
<label>From Database</label>
<select name="from_db">
<option value="UniProtKB_AC-ID" selected>UniProtKB AC/ID</option>
<option value="Ensembl">Ensembl</option>
<option value="GeneID">GeneID (NCBI)</option>
</select>
<div class="hint">Source database for your IDs</div>
</div>
<div class="form-group">
<label>To Database</label>
<select name="to_db">
<option value="UniProtKB_AC-ID">UniProtKB AC/ID</option>
<option value="Ensembl" selected>Ensembl</option>
<option value="GeneID">GeneID (NCBI)</option>
</select>
<div class="hint">Target database for mapping</div>
</div>
<div class="form-group">
<label>Input IDs (one per line)</label>
<textarea name="ids" required><?php echo htmlspecialchars($ids); ?></textarea>
<div class="hint">Max 100,000 IDs per job. Examples: P05067, P12345, Q96QH7</div>
</div>
<button type="submit">Submit Mapping Job</button>
</form>
<?php if ($submitResult): ?>
<div class="success">
? Job submitted successfully!
<div class="job-result">
<strong>Job ID:</strong><br>
<div class="copyable"><?php echo htmlspecialchars($submitResult['jobId']); ?></div>
<div class="hint" style="margin-top: 10px;">? Copy this ID to retrieve results. Check back in a few seconds!</div>
</div>
</div>
<?php endif; ?>
</div>
<!-- Retrieve Results -->
<div class="card">
<h2>? Retrieve Results</h2>
<form method="POST">
<input type="hidden" name="action" value="retrieve">
<div class="form-group">
<label>Job ID</label>
<input type="text" name="job_id" value="<?php echo htmlspecialchars($jobId); ?>" placeholder="Paste job ID here" required>
<div class="hint">The job ID returned from the submission above</div>
</div>
<button type="submit">Retrieve Results</button>
</form>
<?php if ($retrieveResult): ?>
<div class="success">
? Results retrieved!
</div>
<?php endif; ?>
</div>
</div>
<!-- Results Display -->
<?php if ($retrieveResult): ?>
<div class="card" style="margin-top: 30px;">
<h2>? Mapping Results</h2>
<div class="tabs">
<button class="tab-btn active" onclick="switchTab('table')">? Results Table</button>
<button class="tab-btn" onclick="switchTab('details')">?? Job Details</button>
<button class="tab-btn" onclick="switchTab('raw')">? Raw JSON</button>
</div>
<div id="table" class="tab-content active">
<?php
$results = $retrieveResult['results']['results'] ?? [];
if (!empty($results)):
?>
<table class="results-table">
<thead>
<tr>
<th>From ID</th>
<th>To ID</th>
</tr>
</thead>
<tbody>
<?php foreach ($results as $result): ?>
<tr>
<td><?php echo htmlspecialchars($result['from'] ?? 'N/A'); ?></td>
<td><?php echo htmlspecialchars($result['to'] ?? 'N/A'); ?></td>
</tr>
<?php endforeach; ?>
</tbody>
</table>
<?php else: ?>
<p style="color: #999;">No mapping results found.</p>
<?php endif; ?>
<?php if (!empty($retrieveResult['results']['failedIds'])): ?>
<div style="margin-top: 20px; padding: 15px; background: #fef3cd; border-radius: 6px; border-left: 4px solid #ffc107;">
<strong>?? Failed IDs:</strong>
<ul>
<?php foreach ($retrieveResult['results']['failedIds'] as $failed): ?>
<li><?php echo htmlspecialchars($failed); ?></li>
<?php endforeach; ?>
</ul>
</div>
<?php endif; ?>
</div>
<div id="details" class="tab-content">
<table class="results-table">
<tr>
<td><strong>From Database:</strong></td>
<td><?php echo htmlspecialchars($retrieveResult['details']['from'] ?? 'N/A'); ?></td>
</tr>
<tr>
<td><strong>To Database:</strong></td>
<td><?php echo htmlspecialchars($retrieveResult['details']['to'] ?? 'N/A'); ?></td>
</tr>
<tr>
<td><strong>Input IDs:</strong></td>
<td><?php echo count($retrieveResult['details']['ids'] ?? []); ?> IDs</td>
</tr>
<tr>
<td><strong>Mapped:</strong></td>
<td><?php echo count($retrieveResult['results']['results'] ?? []); ?> results</td>
</tr>
</table>
</div>
<div id="raw" class="tab-content">
<div class="json-viewer">
<pre><?php echo htmlspecialchars(json_encode($retrieveResult, JSON_PRETTY_PRINT | JSON_UNESCAPED_SLASHES)); ?></pre>
</div>
</div>
</div>
<?php endif; ?>
</div>
<script>
function switchTab(tabName) {
document.querySelectorAll('.tab-content').forEach(el => el.classList.remove('active'));
document.querySelectorAll('.tab-btn').forEach(el => el.classList.remove('active'));
document.getElementById(tabName).classList.add('active');
event.target.classList.add('active');
}
function toggleAccordion(btn) {
btn.classList.toggle('active');
btn.nextElementSibling.classList.toggle('active');
}
</script>
</body>
</html>
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