<?php
declare(strict_types=1);
/**
* Example 3: ID Mapping
*
* Shows how to submit ID mapping jobs, poll for completion,
* and retrieve results using UniProt's async job model.
*
* Run from command line: php examples/map_ids.php
*/
require_once dirname(__DIR__) . '/src/autoload.php';
use UniProtPHP\Http\HttpClientFactory;
use UniProtPHP\Http\CurlClient;
use UniProtPHP\UniProt\UniProtIdMapping;
use UniProtPHP\Exception\UniProtException;
// Disable SSL verification for development/testing
CurlClient::setVerifySSL(false);
echo "=== UniProt ID Mapping Example ===\n\n";
try {
// Create HTTP client
$httpClient = HttpClientFactory::create();
echo "Using transport: " . $httpClient->getTransportName() . "\n\n";
// Create mapping object
$mapping = new UniProtIdMapping($httpClient);
// Example 1: Simple submit and wait
echo "1. Submitting ID mapping job (UniProtKB ? Ensembl)...\n";
echo " Mapping: P05067, P12345\n";
$jobId = $mapping->submitAndWait(
'UniProtKB_AC-ID',
'Ensembl',
['P05067', 'P12345'],
null, // no taxId filter
2, // poll every 2 seconds
30 // max 30 polls (1 minute)
);
echo " Job ID: {$jobId}\n";
echo " Status: COMPLETED\n\n";
// Example 2: Get results
echo "2. Retrieving mapping results...\n";
$results = $mapping->getResults($jobId);
if (isset($results['results'])) {
foreach ($results['results'] as $mapping_result) {
echo " " . $mapping_result['from'] . " ? ";
if (isset($mapping_result['to']['id'])) {
echo $mapping_result['to']['id'];
} else {
echo "NOT MAPPED";
}
echo "\n";
}
}
if (isset($results['failedIds']) && !empty($results['failedIds'])) {
echo " Failed IDs: " . implode(', ', $results['failedIds']) . "\n";
}
echo "\n";
// Example 3: Get job details
echo "3. Retrieving job details...\n";
$details = $mapping->getDetails($jobId);
echo " From DB: " . $details['from'] . "\n";
echo " To DB: " . $details['to'] . "\n";
echo " Input IDs: " . $details['ids'] . "\n";
echo "\n";
// Example 4: Different mapping (UniProtKB ? Ensembl with different IDs)
echo "4. Submitting another mapping (UniProtKB ? Gene_Name)...\n";
$jobId2 = $mapping->submitAndWait(
'UniProtKB_AC-ID',
'Gene_Name',
['P05067'],
null,
2,
30
);
$results2 = $mapping->getResults($jobId2);
if (isset($results2['results']) && !empty($results2['results'])) {
echo " Mapping result: ";
echo $results2['results'][0]['from'] . " ? " . $results2['results'][0]['to'];
echo "\n";
}
echo "\n";
// Example 5: Manual submit and poll (more control)
echo "5. Manual submit and poll workflow...\n";
$jobId3 = $mapping->submit(
'UniProtKB_AC-ID',
'Ensembl',
['P12345']
);
echo " Submitted job: {$jobId3}\n";
// Manual polling
$pollCount = 0;
$maxPolls = 20;
while ($pollCount < $maxPolls) {
$status = $mapping->status($jobId3);
if (isset($status['jobStatus'])) {
echo " Poll {$pollCount}: Status = " . $status['jobStatus'] . "\n";
if ($status['jobStatus'] === 'FINISHED') {
echo " Job completed!\n";
break;
}
} else if (isset($status['results'])) {
echo " Results ready!\n";
break;
}
sleep(2);
$pollCount++;
}
if ($pollCount >= $maxPolls) {
echo " WARNING: Job still pending after timeout\n";
}
echo "\n";
// Example 6: Stream results
echo "6. Retrieving results via stream...\n";
$streamResults = $mapping->streamResults($jobId);
if (isset($streamResults['results']) && !empty($streamResults['results'])) {
echo " Retrieved " . count($streamResults['results']) . " mappings via stream\n";
}
echo "\n";
echo "? All ID mapping 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";
echo $e->getTraceAsString() . "\n";
exit(1);
}
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