routes/api.php

<?php

use App\Http\Controllers\Api\AdmetController;
use App\Http\Controllers\Api\AiServicesIntegrationController;
use App\Http\Controllers\Api\AuthController;
use App\Http\Controllers\Api\AwardController;
use App\Http\Controllers\Api\ChemicalSearchController;
use App\Http\Controllers\Api\ChemistryController;
use App\Http\Controllers\Api\ConvertSmilesController;
use App\Http\Controllers\Api\DockingController;
use App\Http\Controllers\Api\EmailVerificationController;
use App\Http\Controllers\Api\GenerationController;
use App\Http\Controllers\Api\LigandsController;
use App\Http\Controllers\Api\MdSimulationController;
use App\Http\Controllers\Api\NewsController;
use App\Http\Controllers\Api\PasswordResetController;
use App\Http\Controllers\Api\ScientistController;
use App\Http\Controllers\Api\ScreeningController;
use App\Http\Controllers\Api\SubscriptionController;
use App\Http\Controllers\Api\UserController;
use App\Http\Controllers\StripeWebhookController;
use Cloudinary\Cloudinary;
use Illuminate\Http\Request;
use Illuminate\Support\Facades\Route;

/*
|--------------------------------------------------------------------------
| API Routes
|--------------------------------------------------------------------------
|
| Here is where you can register API routes for your application. These
| routes are loaded by the RouteServiceProvider within a group which
| is assigned the "api" middleware group. Enjoy building your API!
|
*/

// ==================== AI INTEGRATION (Docker / CI) ====================
if (config('app.enable_ai_integration_routes')) {
    Route::prefix('ai-services')->group(function () {
        Route::get('/health', [AiServicesIntegrationController::class, 'health']);
        Route::post('/test/admet', [AiServicesIntegrationController::class, 'testAdmet']);
        Route::post('/test/chemical-search', [AiServicesIntegrationController::class, 'testChemicalSearch']);
        Route::get('/test/drug-repurposing', [AiServicesIntegrationController::class, 'testDrugRepurposing']);
    });
}

// ==================== AWARDS ====================
Route::get('/awards', [AwardController::class, 'index']);
Route::get('/awards/{id}', [AwardController::class, 'show']);
Route::get('/awards/{id}/scientists', [AwardController::class, 'getScientistsByAward']);
// ==================== SCIENTISTS ====================
Route::get('/scientists', [ScientistController::class, 'index']);
Route::get('/scientists/{id}', [ScientistController::class, 'show']);
Route::get('/scientists/{id}/awards', [ScientistController::class, 'getAwardsByScientist']);
// ==================== USER ====================

// ==================== USERS & AUTHENTICATION ====================
Route::prefix('user')->group(function () {
    Route::post('register', [AuthController::class, 'register']);
    Route::post('login', [AuthController::class, 'login']);

    // email verification
    Route::post('/verify-email', [EmailVerificationController::class, 'verify']);
    Route::post('/resend-verification', [EmailVerificationController::class, 'resend']);

    // password reset
    Route::post('forgot-password', [PasswordResetController::class, 'sendForgotPasswordOtp']);
    Route::post('reset-password', [PasswordResetController::class, 'resetPassword']);
    Route::post('/resend-reset-password-otp', [PasswordResetController::class, 'resendResetPasswordOtp']);

    // login google
    Route::post('auth/google', [AuthController::class, 'handleGoogleCallback']);

    // profile and logout routes
    Route::middleware('auth:sanctum')->group(function () {
        Route::get('profile', [UserController::class, 'profile']);
        Route::post('update-profile', [UserController::class, 'updateProfile']);
        Route::post('logout', [AuthController::class, 'logout']);
    });
});
// ====================NEWS====================

Route::middleware('auth:sanctum')->group(function () {
    Route::get('/news', [NewsController::class, 'index']);
    Route::get('/news/refresh', [NewsController::class, 'refresh']);
    Route::get('/news/categories', [NewsController::class, 'getCategories']);
    Route::post('/news/{articleId}/share', [NewsController::class, 'shareArticle']);
    Route::post('/news/{articleId}/save', [NewsController::class, 'saveArticle']);
    Route::get('/news/saved', [NewsController::class, 'getSavedArticles']);
    Route::delete('/news/saved/{savedArticleId}', [NewsController::class, 'unsaveArticle']);
});

// ====================DOCKING====================

Route::middleware('auth:sanctum')->prefix('docking')->group(function () {
    Route::get('history', [DockingController::class, 'history']);
    Route::post('submit', [DockingController::class, 'submit']);
    Route::get('{id}', [DockingController::class, 'status']);
});

Route::get('docking/download/{id}', [DockingController::class, 'download']);

// ====================CONVERT SMILES====================

Route::middleware('auth:sanctum')->prefix('convert-smiles')->group(function () {
    Route::get('history', [ConvertSmilesController::class, 'history']);
    Route::post('convert', [ConvertSmilesController::class, 'convert']);
    Route::get('download/{id}', [ConvertSmilesController::class, 'download']);
});

// ==================== DRUG REPURPOSING / SCREENING ====================

Route::prefix('drug-repurposing')->middleware('auth:sanctum')->group(function () {
    Route::get('targets/history', [ScreeningController::class, 'historyTargets']);
    Route::post('targets', [ScreeningController::class, 'targets']);
    Route::get('targets/{id}', [ScreeningController::class, 'statusTargets'])->whereNumber('id');

    Route::get('screen/history', [ScreeningController::class, 'historyScreening']);
    Route::get('screen/{id}', [ScreeningController::class, 'statusScreening'])->whereNumber('id');
    Route::post('screen', [ScreeningController::class, 'screen']);
});

// ==================== CHEMICAL SEARCH ====================
Route::middleware('auth:sanctum')->prefix('chemical-search')->group(function () {
    Route::post('/', [ChemicalSearchController::class, 'store']);
    Route::post('/full-rag', [ChemicalSearchController::class, 'fullRag']);
});

// ==================== MD SIMULATION ====================
Route::get('/md-simulation/health', [MdSimulationController::class, 'health']);

Route::middleware('auth:sanctum')->prefix('md-simulation')->group(function () {
    Route::post('/process', [MdSimulationController::class, 'process']);
    Route::get('/history', [MdSimulationController::class, 'history']);
    Route::get('/status/{remoteJobId}', [MdSimulationController::class, 'status']);
    Route::post('/analyze/{remoteJobId}', [MdSimulationController::class, 'analyze']);
    Route::get('/download/{remoteJobId}', [MdSimulationController::class, 'download']);
    Route::get('/download-analysis/{remoteJobId}', [MdSimulationController::class, 'downloadAnalysis']);
});

// ==================== AI Agent ====================
Route::get('chemistry/health', [ChemistryController::class, 'health']);

Route::middleware('auth:sanctum')->group(function () {

    Route::prefix('chemistry')->group(function () {
        // Threads
        Route::post('thread', [ChemistryController::class, 'createThread']);
        Route::get('threads', [ChemistryController::class, 'listThreads']);
        Route::post('/thread-messages', [ChemistryController::class, 'threadMessages']);

        // Chat
        Route::post('chat', [ChemistryController::class, 'chat']);

        // Analysis
        Route::post('analyze/smiles', [ChemistryController::class, 'analyzeSmiles']);
        Route::post('analyze/compare', [ChemistryController::class, 'compare']);
        Route::post('analyze/docking', [ChemistryController::class, 'docking']);

        // CSV Batch
        Route::post('csv/upload', [ChemistryController::class, 'uploadCsv']);
        Route::get('csv/status/{job_id}', [ChemistryController::class, 'csvStatus']);
        Route::get('csv/results/{job_id}', [ChemistryController::class, 'csvResults']);
        Route::get('csv/jobs', [ChemistryController::class, 'listJobs']);
        Route::delete('csv/jobs/{job_id}', [ChemistryController::class, 'deleteJob']);

        // User History
        Route::get('history', [ChemistryController::class, 'userHistory']);
    });
});

// ==================== ADMET PREDICTION ====================
Route::middleware('auth:sanctum')->post('/admet/predict', [AdmetController::class, 'predict']);

// ==================== AI-GENERATION ====================
Route::middleware('auth:sanctum')->prefix('ai')->group(function () {

    Route::prefix('generation')->group(function () {
        Route::post('/run', [GenerationController::class, 'run']);
        Route::get('/history', [GenerationController::class, 'history']);
        Route::middleware('job.owner')->group(function () {
            Route::get('/status/{job_id}', [GenerationController::class, 'status']);
            Route::get('/jobs/{job_id}/results', [GenerationController::class, 'results']);
            Route::post('/jobs/{job_id}/cancel', [GenerationController::class, 'cancel']);
        });
    });

    // ========== Files ==========
    Route::middleware('job.owner')->get('/files/{job_id}/{filename}', [GenerationController::class, 'downloadFile']);

    // ========== Ligands Export ==========
    Route::post('/ligands/export', [LigandsController::class, 'exportLigands']);
});


// ==================== STRIPE ====================
Route::post('/stripe/webhook', [StripeWebhookController::class, 'handleWebhook']);

Route::middleware('auth:sanctum')->group(function () {
    Route::get('/plans', [SubscriptionController::class, 'plans']);

    Route::prefix('subscription')->group(function () {
        Route::post('/checkout', [SubscriptionController::class, 'checkout']);
        Route::get('/status', [SubscriptionController::class, 'status']);
        Route::post('/swap', [SubscriptionController::class, 'swap']);
        Route::post('/cancel', [SubscriptionController::class, 'cancel']);
        Route::post('/resume', [SubscriptionController::class, 'resume']);
        Route::get('/invoices', [SubscriptionController::class, 'invoices']);
        Route::get('/billing-portal', [SubscriptionController::class, 'billingPortal']);
    });
});

// cloudinary file upload test route

Route::post('/upload-file', function (Request $request) {

    $request->validate([
        'file' => 'required|file',
    ]);

    try {
        $file = $request->file('file');
        $originalName = pathinfo($file->getClientOriginalName(), PATHINFO_FILENAME);
        $extension = $file->getClientOriginalExtension();

        $cloudinary = new Cloudinary([
            'cloud' => [
                'cloud_name' => env('CLOUDINARY_CLOUD_NAME'),
                'api_key' => env('CLOUDINARY_API_KEY'),
                'api_secret' => env('CLOUDINARY_API_SECRET'),
            ],
            'url' => ['secure' => true],
        ]);

        $result = $cloudinary->uploadApi()->upload(
            $file->getRealPath(),
            [
                'resource_type' => 'raw',
                'public_id' => $originalName,
                'filename_override' => $originalName . '.' . $extension,
            ]
        );

        return response()->json([
            'url' => $result['secure_url'],
        ]);
    } catch (\Exception $e) {
        return response()->json([
            'error' => $e->getMessage(),
        ], 500);
    }
});