File: docs/hosting-notes.md

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docs/hosting-notes.md

File:	`docs/hosting-notes.md`
Role:	Auxiliary data
Content type:	`text/markdown`
Description:	Auxiliary data
Class:	Uniprot PHP Class Access a UniProt Protein sequence REST API.
Author:	By Saurabh Gayali
Last change:
Date:	2 months ago
Size:	`6,765 bytes`

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Shared Hosting Compatibility

This library is designed to work on shared hosting environments with minimal dependencies.

Transport Layer

The library automatically selects the best available HTTP transport:

1. cURL (Preferred)

Fastest - Optimized C implementation
Most Compatible - Works everywhere
Required: `php.ini` has `extension=curl`

$httpClient = HttpClientFactory::create();
echo $httpClient->getTransportName();  // "cURL"

2. PHP Streams (Fallback)

Always Available - Part of core PHP
Slower - Pure PHP implementation
Required: Nothing (enabled by default)

$httpClient = HttpClientFactory::create();
echo $httpClient->getTransportName();  // "PHP Streams"

Checking Available Transports

$available = HttpClientFactory::getAvailableTransports();

echo "cURL: " . ($available['cURL'] ? 'Available' : 'Not available') . "\n";
echo "Streams: " . ($available['PHP Streams'] ? 'Available' : 'Not available') . "\n";

if (!$available['cURL'] && !$available['PHP Streams']) {
    die("No HTTP transport available on this server\n");
}

Enabling cURL on Shared Hosting

Check if Installed

php -m | grep curl

Or via PHP:

if (extension_loaded('curl')) {
    echo "cURL is available\n";
} else {
    echo "cURL is not available\n";
}

Enable in php.ini

Access your hosting control panel (cPanel, Plesk, etc.)
Find PHP configuration
Ensure `extension=curl.so` (Linux) or `extension=php_curl.dll` (Windows)
Restart PHP

If Not Available

Contact your hosting provider - most modern hosts enable cURL by default.

Shared Hosting Considerations

1. File Permissions

// Don't need write permissions, only read
$httpClient = HttpClientFactory::create();

2. Outbound Network Access

Ensure your host allows outbound HTTPS:

// Test connectivity
try {
    $httpClient = HttpClientFactory::create();
    $entry = new UniProtEntry($httpClient);
    $protein = $entry->get('P12345');
    echo "? Network access working\n";
} catch (UniProtException $e) {
    if ($e->isTransportError()) {
        echo "? No outbound network access\n";
    }
}

3. Timeout Considerations

Shared hosting may have strict timeouts:

// Use shorter polling intervals
$mapping->waitForCompletion(
    $jobId,
    2,   // 2 second polling interval
    15   // max 15 polls (30 seconds total)
);

4. Memory Usage

Large search results can consume memory:

// Stop iteration early
$results = $search->search('organism_id:9606');

$count = 0;
foreach ($results as $entry) {
    // Process entry
    
    if (++$count >= 1000) {
        break;  // Stop to save memory
    }
}

5. CPU Limits

Batch operations in smaller chunks:

// Process in smaller batches
$allIds = [...]; // millions of IDs

foreach (array_chunk($allIds, 10000) as $chunk) {
    $jobId = $mapping->submitAndWait(
        'UniProtKB_AC-ID',
        'Ensembl',
        $chunk
    );
    
    // Process results
}

Performance Optimization

Cache Results

$cacheDir = sys_get_temp_dir() . '/uniprot_cache';
if (!is_dir($cacheDir)) {
    mkdir($cacheDir, 0755, true);
}

function getCachedEntry($accession, $maxAge = 86400) {
    global $cacheDir;
    
    $cacheFile = $cacheDir . '/' . $accession . '.json';
    
    if (file_exists($cacheFile)) {
        $age = time() - filemtime($cacheFile);
        if ($age < $maxAge) {
            return json_decode(file_get_contents($cacheFile), true);
        }
    }
    
    // Fetch from API
    $httpClient = HttpClientFactory::create();
    $entry = new UniProtEntry($httpClient);
    $protein = $entry->get($accession);
    
    // Cache result
    file_put_contents($cacheFile, json_encode($protein));
    
    return $protein;
}

Batch Operations

// Combine requests
$results = [];

foreach (array_chunk($accessions, 10) as $batch) {
    $batchResults = $entry->getBatch($batch);
    $results = array_merge($results, $batchResults);
    
    // Small delay between batches
    sleep(1);
}

Efficient Pagination

// Use larger page sizes when possible
$results = $search->search('organism_id:9606', [
    'size' => 500  // Maximum
]);

foreach ($results as $entry) {
    // Process
}

Debugging on Shared Hosting

Check Transport

echo "Using transport: " . HttpClientFactory::getInstance()->getTransportName() . "\n";

Verify API Access

try {
    $httpClient = HttpClientFactory::create();
    $entry = new UniProtEntry($httpClient);
    $protein = $entry->get('P12345');
    echo "? API access working\n";
} catch (UniProtException $e) {
    echo "? API access failed: " . $e->getMessage() . "\n";
}

Check Available Functions

echo "stream_context_create: " . (function_exists('stream_context_create') ? 'Yes' : 'No') . "\n";
echo "file_get_contents: " . (function_exists('file_get_contents') ? 'Yes' : 'No') . "\n";
echo "curl_init: " . (function_exists('curl_init') ? 'Yes' : 'No') . "\n";
echo "json_decode: " . (function_exists('json_decode') ? 'Yes' : 'No') . "\n";

Error Logging

ini_set('log_errors', '1');
ini_set('error_log', '/path/to/error.log');

try {
    // API call
} catch (UniProtException $e) {
    error_log($e->getDetailedMessage());
}