<?php
declare(strict_types=1);
/**
* Example 1: Single Entry Retrieval
*
* Shows how to fetch individual UniProtKB entries by accession number.
* Demonstrates basic retrieval, field selection, and batch operations.
*
* Run from command line: php examples/get_entry.php
*/
require_once dirname(__DIR__) . '/src/autoload.php';
use UniProtPHP\Http\HttpClientFactory;
use UniProtPHP\Http\CurlClient;
use UniProtPHP\UniProt\UniProtEntry;
use UniProtPHP\Exception\UniProtException;
// Disable SSL verification for development/testing
CurlClient::setVerifySSL(false);
echo "=== UniProt Entry Retrieval Example ===\n\n";
try {
// Create HTTP client (automatically chooses cURL or streams)
$httpClient = HttpClientFactory::create();
echo "Using transport: " . $httpClient->getTransportName() . "\n\n";
// Create entry retriever
$entry = new UniProtEntry($httpClient);
// Example 1: Get a single entry (from P12345.json in reference)
echo "1. Retrieving entry P12345...\n";
$protein = $entry->get('P12345');
echo " Accession: " . $protein['primaryAccession'] . "\n";
echo " Name: " . $protein['uniProtkbId'] . "\n";
echo " Organism: " . $protein['organism']['commonName'] . "\n";
if (isset($protein['sequence'])) {
echo " Sequence length: " . $protein['sequence']['length'] . " amino acids\n";
}
echo "\n";
// Example 2: Check if entry exists
echo "2. Checking if entries exist...\n";
$exists = $entry->exists('P12345');
echo " P12345 exists: " . ($exists ? 'Yes' : 'No') . "\n";
$notExists = $entry->exists('P99999999');
echo " P99999999 exists: " . ($notExists ? 'Yes' : 'No') . "\n";
echo "\n";
// Example 3: Get specific fields
echo "3. Getting specific fields for P12345...\n";
$data = $entry->getWithFields('P12345', [
'accession',
'protein_name',
'organism_name',
'sequence'
]);
echo " Protein: " . $data['uniProtkbId'] . "\n";
echo " Sequence: " . substr($data['sequence']['value'], 0, 50) . "...\n";
echo "\n";
// Example 4: Get entry in different formats
echo "4. Retrieving entry in different formats...\n";
$fasta = $entry->get('P12345', 'fasta');
echo " FASTA format (first 100 chars):\n";
echo " " . substr($fasta['body'], 0, 100) . "...\n";
echo "\n";
// Example 5: Batch retrieval
echo "5. Batch retrieving multiple entries...\n";
$results = $entry->getBatch(['P12345', 'P00750', 'INVALID123']);
foreach ($results as $result) {
if (isset($result['error'])) {
echo " " . $result['accession'] . ": ERROR - " . $result['error'] . "\n";
} else {
echo " " . $result['primaryAccession'] . " - " . $result['organism']['commonName'] . "\n";
}
}
echo "\n";
echo "? All examples completed successfully!\n";
} catch (UniProtException $e) {
echo "? Error: " . $e->getDetailedMessage() . "\n";
if ($e->getHttpStatus() > 0) {
echo " HTTP Status: " . $e->getHttpStatus() . "\n";
}
exit(1);
} catch (Exception $e) {
echo "? Unexpected error: " . $e->getMessage() . "\n";
exit(1);
}
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