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907b200 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 | <?php
namespace App\Jobs;
use App\Models\DockingJob;
use Illuminate\Bus\Queueable;
use Illuminate\Contracts\Queue\ShouldQueue;
use Illuminate\Foundation\Bus\Dispatchable;
use Illuminate\Queue\InteractsWithQueue;
use Illuminate\Queue\SerializesModels;
use Illuminate\Support\Facades\Log;
use Illuminate\Support\Facades\Process;
class RunDockingJob implements ShouldQueue
{
use Dispatchable, InteractsWithQueue, Queueable, SerializesModels;
public $dockingJob;
public $params;
/**
* The number of seconds the job can run before timing out.
*
* @var int
*/
public $timeout = 1800;
/**
* Create a new job instance.
*/
public function __construct(DockingJob $dockingJob, array $params)
{
$this->dockingJob = $dockingJob;
$this->params = $params;
}
/**
* Execute the job.
*/
public function handle(): void
{
// Mark as processing
$this->dockingJob->update(['status' => 'processing']);
try {
$scriptPath = base_path('scripts/vina_docking.py');
$pythonPath = env('DOCKING_PYTHON_PATH', base_path('vina_env/bin/python'));
// Build command
$cmd = sprintf(
'%s %s %s %s %f %f %f %f %f %f %d %d',
escapeshellarg($pythonPath),
escapeshellarg($scriptPath),
escapeshellarg($this->dockingJob->protein_path),
escapeshellarg($this->dockingJob->ligand_path),
$this->params['center_x'],
$this->params['center_y'],
$this->params['center_z'],
$this->params['box_size_x'],
$this->params['box_size_y'],
$this->params['box_size_z'],
$this->params['exhaustiveness'] ?? 8,
$this->params['n_poses'] ?? 5
);
// Run process
$result = Process::timeout($this->timeout)->run($cmd);
// Using regex to reliably find our JSON object in the mixed python Vina logs output
$outputData = null;
$fullOutput = $result->output();
if (preg_match('/\{"status":\s*"(success|error)".*\}/s', $fullOutput, $matches)) {
$outputData = json_decode($matches[0], true);
}
// Also check standard error in case Python printed an error payload there
if (! $outputData && preg_match('/\{"status":\s*"(success|error)".*\}/s', $result->errorOutput(), $matches)) {
$outputData = json_decode($matches[0], true);
}
if (! $result->successful()) {
$errorMessage = $outputData['message'] ?? $result->errorOutput();
if (empty(trim($errorMessage))) {
$errorMessage = trim($fullOutput) ?: 'Unknown Error / Empty Output';
}
throw new \Exception(trim($errorMessage));
}
if (isset($outputData['status']) && $outputData['status'] === 'error') {
throw new \Exception($outputData['message'] ?? 'Unknown script error');
}
$vinaScores = [];
if ($outputData && isset($outputData['energies'])) {
foreach ($outputData['energies'] as $pose) {
$vinaScores[] = [
'affinity' => (float) ($pose[0] ?? 0.0),
'inter' => (float) ($pose[1] ?? 0.0),
'intra' => (float) ($pose[2] ?? 0.0),
'torsions' => (float) ($pose[3] ?? 0.0),
'unbound' => (float) ($pose[4] ?? 0.0),
];
}
unset($outputData['energies']);
}
$this->dockingJob->update([
'status' => 'completed',
'result_data' => $outputData ?: ['raw_output' => $fullOutput],
'vina_scores' => $vinaScores,
]);
} catch (\Exception $e) {
Log::error('Docking Job Failed', ['error' => $e->getMessage(), 'job_id' => $this->dockingJob->id]);
$this->dockingJob->update([
'status' => 'failed',
'result_data' => ['error' => $e->getMessage()],
]);
}
}
}
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