<?php
declare(strict_types=1);
/**
* Example 2: Search with Pagination
*
* Shows how to search UniProtKB with complex queries and handle pagination.
* Demonstrates both automatic cursor-based pagination and manual offset-based pagination.
*
* Run from command line: php examples/search_entries.php
*/
require_once dirname(__DIR__) . '/src/autoload.php';
use UniProtPHP\Http\HttpClientFactory;
use UniProtPHP\Http\CurlClient;
use UniProtPHP\UniProt\UniProtSearch;
use UniProtPHP\Exception\UniProtException;
// Disable SSL verification for development/testing
CurlClient::setVerifySSL(false);
echo "=== UniProt Search with Pagination Example ===\n\n";
try {
// Create HTTP client
$httpClient = HttpClientFactory::create();
echo "Using transport: " . $httpClient->getTransportName() . "\n\n";
// Create search object
$search = new UniProtSearch($httpClient);
// Example 1: Simple search
echo "1. Simple search for human insulin...\n";
$results = $search->search('insulin AND organism_id:9606 AND reviewed:true', [
'size' => 10
]);
$count = 0;
foreach ($results as $entry) {
echo " " . $entry['primaryAccession'] . " - ";
echo (isset($entry['uniProtkbId']) ? $entry['uniProtkbId'] : 'N/A') . "\n";
if (++$count >= 5) {
echo " ... (limited to 5 results)\n";
break;
}
}
echo "\n";
// Example 2: Search with specific fields
echo "2. Search with selected fields...\n";
$results = $search->search('organism_id:9606 AND reviewed:true', [
'size' => 10,
'fields' => [
'accession',
'protein_name',
'organism_name',
'length'
]
]);
$count = 0;
foreach ($results as $entry) {
echo " " . $entry['primaryAccession'];
if (isset($entry['proteinName']['recommendedName']['fullName']['value'])) {
echo " - " . substr($entry['proteinName']['recommendedName']['fullName']['value'], 0, 30);
}
echo "\n";
if (++$count >= 3) {
break;
}
}
echo "\n";
// Example 3: Complex query with boolean operators
echo "3. Complex query - kinases in human...\n";
$results = $search->search(
'organism_id:9606 AND reviewed:true AND (protein_name:kinase OR gene:*kinase)',
['size' => 5]
);
$count = 0;
foreach ($results as $entry) {
echo " " . $entry['primaryAccession'];
if (isset($entry['genes'][0]['geneName']['value'])) {
echo " (" . $entry['genes'][0]['geneName']['value'] . ")";
}
echo "\n";
if (++$count >= 3) {
break;
}
}
echo "\n";
// Example 4: Query with filters - proteins by size
echo "4. Search - proteins with specific mass range...\n";
$results = $search->search(
'organism_id:9606 AND reviewed:true AND mass:[50000 TO 100000]',
['size' => 5]
);
$count = 0;
foreach ($results as $entry) {
if (isset($entry['sequence']['molWeight'])) {
echo " " . $entry['primaryAccession'] . " - ";
echo number_format($entry['sequence']['molWeight'], 0) . " Da\n";
}
if (++$count >= 3) {
break;
}
}
echo "\n";
// Example 5: First page only (without iterating all results)
echo "5. Get first page only...\n";
$firstPage = $search->getFirstPage('organism_id:9606 AND reviewed:true', [
'size' => 3,
'fields' => ['accession', 'protein_name']
]);
if (isset($firstPage['results'])) {
foreach ($firstPage['results'] as $entry) {
echo " " . $entry['primaryAccession'] . "\n";
}
}
echo "\n";
// Example 6: Query with NOT and exclusions
echo "6. Search - proteins NOT in PDB...\n";
$results = $search->search(
'organism_id:9606 AND reviewed:true AND NOT xref:pdb',
['size' => 5]
);
$count = 0;
foreach ($results as $entry) {
echo " " . $entry['primaryAccession'] . "\n";
if (++$count >= 2) {
break;
}
}
echo "\n";
// Example 7: Full pagination - retrieve ALL results (e.g., ~22,400 human proteins)
// This demonstrates automatic pagination for large result sets
echo "7. Full pagination example - ALL human reviewed proteins...\n";
echo " ?? NOTE: This will fetch ~22,400 results (45 requests of 500 each)\n";
echo " Starting pagination (showing first 10 + last 10 results)...\n\n";
$results = $search->search(
'organism_id:9606 AND reviewed:true',
['size' => 500] // Max allowed per request
);
$count = 0;
$firstResults = [];
$lastResults = [];
foreach ($results as $entry) {
$count++;
// Store first 10
if ($count <= 10) {
$firstResults[] = $entry['primaryAccession'];
}
// Keep last 10 in memory
$lastResults[] = $entry['primaryAccession'];
if (count($lastResults) > 10) {
array_shift($lastResults);
}
}
echo " First 10 results:\n";
foreach ($firstResults as $i => $acc) {
echo " " . ($i + 1) . ". $acc\n";
}
echo "\n ... [" . ($count - 20) . " results in between] ...\n\n";
echo " Last 10 results:\n";
foreach ($lastResults as $i => $acc) {
echo " " . ($count - 9 + $i) . ". $acc\n";
}
echo "\n ? Total retrieved: $count entries\n";
echo " ? Automatic cursor-based pagination completed!\n\n";
echo "? All search examples completed successfully!\n";
} catch (UniProtException $e) {
echo "? Error: " . $e->getDetailedMessage() . "\n";
if ($e->getApiErrorMessage()) {
echo " API Error: " . $e->getApiErrorMessage() . "\n";
}
exit(1);
} catch (Exception $e) {
echo "? Unexpected error: " . $e->getMessage() . "\n";
exit(1);
}
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