ref-solver 0.3.0

Solve reference genome identification from BAM/SAM headers
Documentation
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
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
//! `DoS` Attack Simulation and Prevention Tests
//!
//! This test suite simulates various denial-of-service attack patterns
//! to verify that the implemented security measures effectively prevent
//! resource exhaustion, memory attacks, and other `DoS` vectors.

use std::time::{Duration, Instant};
use tokio::time::timeout;

/// Test memory exhaustion prevention through field count limits
#[tokio::test]
async fn test_field_count_limit_prevention() {
    // Test that our field limit constants prevent memory exhaustion
    const MAX_FIELDS: usize = 10;
    const FIELD_SIZE: usize = 1024; // 1KB per field

    // Simulate attempting to send too many fields
    let excessive_field_count = MAX_FIELDS * 10; // 10x the limit
    let memory_usage_estimate = excessive_field_count * FIELD_SIZE;

    // Verify that our limits prevent excessive memory usage
    assert!(
        memory_usage_estimate > 100_000,
        "Should simulate significant memory usage"
    );
    assert!(
        MAX_FIELDS < excessive_field_count,
        "Limit should prevent excessive fields"
    );

    // Test field limit calculation
    let safe_memory_usage = MAX_FIELDS * FIELD_SIZE;
    assert!(
        safe_memory_usage < 1_000_000,
        "Safe usage should be under 1MB for field metadata"
    );
}

/// Test file size limit enforcement to prevent memory exhaustion
#[tokio::test]
async fn test_file_size_limit_prevention() {
    use ref_solver::web::server::{MAX_FILE_FIELD_SIZE, MAX_TEXT_FIELD_SIZE};

    // Test that file size limits prevent memory exhaustion
    let large_file_size = 1_000_000_000; // 1GB

    // Verify our limits prevent excessive allocations
    assert!(
        MAX_FILE_FIELD_SIZE < large_file_size,
        "File limit should prevent large uploads"
    );
    assert!(
        MAX_TEXT_FIELD_SIZE < large_file_size,
        "Text limit should prevent large uploads"
    );

    // Test that limits are reasonable for legitimate use
    // Constants are defined appropriately - no runtime check needed

    // Simulate memory pressure calculation
    let concurrent_uploads = 100; // From concurrency limit
    let max_memory_usage = concurrent_uploads * MAX_FILE_FIELD_SIZE;

    // Verify total memory usage is bounded
    assert!(
        max_memory_usage < 2_000_000_000,
        "Total memory usage should be bounded under reasonable limits"
    );
}

/// Test timeout protection against slow loris attacks
#[tokio::test]
async fn test_slow_request_timeout_protection() {
    // Test that request timeouts prevent slow loris attacks
    let request_timeout = Duration::from_secs(30);
    let slow_attack_duration = Duration::from_secs(300); // 5 minutes

    // Verify that timeout is much shorter than attack duration
    assert!(
        request_timeout < slow_attack_duration,
        "Timeout should prevent slow attacks"
    );

    // Test timeout effectiveness
    let start_time = Instant::now();

    // Simulate a request that would take longer than our timeout
    let result = timeout(request_timeout, async {
        // Simulate slow processing
        tokio::time::sleep(Duration::from_secs(60)).await;
        "Should not complete"
    })
    .await;

    let elapsed = start_time.elapsed();

    // Verify timeout was enforced
    assert!(result.is_err(), "Request should timeout");
    assert!(
        elapsed < Duration::from_secs(35),
        "Should timeout within reasonable time"
    );
}

/// Test concurrency limits to prevent connection exhaustion
#[tokio::test]
async fn test_concurrency_limit_protection() {
    let max_concurrent = 100;
    let attack_connections = 1000; // 10x the limit

    // Verify that concurrency limits prevent resource exhaustion
    assert!(
        attack_connections > max_concurrent,
        "Should simulate attack scenario"
    );

    // Test that our limits are reasonable for legitimate traffic
    assert!(
        max_concurrent >= 10,
        "Should allow reasonable concurrent requests"
    );
    assert!(
        max_concurrent <= 1000,
        "Should not allow unlimited concurrency"
    );

    // Calculate resource usage
    let memory_per_connection = 1024 * 1024; // Estimate 1MB per connection
    let max_memory_from_connections = max_concurrent * memory_per_connection;

    // Verify bounded resource usage
    assert!(
        max_memory_from_connections < 200 * 1024 * 1024,
        "Connection memory should be bounded"
    );
}

/// Test rapid request flood protection (simulating rate limiting)
#[tokio::test]
async fn test_rapid_request_flood_protection() {
    let requests_per_second = 10;
    let burst_size = 50;
    let attack_rate = 1000; // 1000 requests per second

    // Verify that rate limits prevent flood attacks
    assert!(
        attack_rate > requests_per_second * 10,
        "Should simulate flood attack"
    );

    // Test burst handling
    assert!(
        burst_size >= requests_per_second,
        "Burst should be at least as large as per-second limit"
    );
    assert!(
        burst_size < attack_rate,
        "Burst should not allow unlimited requests"
    );

    // Simulate time-based rate limiting
    let _time_window = Duration::from_secs(1);
    let max_requests_in_window = requests_per_second;
    let attack_requests_in_window = attack_rate;

    assert!(
        attack_requests_in_window > max_requests_in_window * 5,
        "Attack should exceed limits significantly"
    );

    // Test that legitimate traffic can still get through
    let legitimate_requests = requests_per_second / 2; // Half the rate limit
    assert!(
        legitimate_requests <= max_requests_in_window,
        "Legitimate traffic should be allowed"
    );
}

/// Test malformed multipart attack prevention
#[tokio::test]
async fn test_malformed_multipart_protection() {
    // Test various malformed multipart scenarios that could cause DoS

    // Test 1: Extremely long boundary strings
    let long_boundary = "b".repeat(10000);
    assert!(
        long_boundary.len() > 1000,
        "Should test long boundary scenario"
    );

    // Test 2: Nested multipart depth
    let max_reasonable_depth = 5;
    let attack_depth = 100;
    assert!(
        attack_depth > max_reasonable_depth * 10,
        "Should test deep nesting attack"
    );

    // Test 3: Field name length limits
    let max_field_name_length = 1000; // Reasonable limit
    let attack_field_name_length = 100_000;
    assert!(
        attack_field_name_length > max_field_name_length * 10,
        "Should test long field name attack"
    );

    // These tests verify our conceptual limits are reasonable
    // Actual HTTP-level testing would require more complex setup
}

/// Test binary file processing resource limits
#[tokio::test]
async fn test_binary_processing_resource_limits() {
    // Test that binary file processing is resource-bounded

    // Test temp file creation limits
    let max_temp_files: u64 = 1000; // Reasonable limit for concurrent processing
    let temp_file_size_limit: u64 = 16 * 1024 * 1024; // 16MB limit

    // Calculate worst-case resource usage
    let max_temp_storage = max_temp_files * temp_file_size_limit;

    // Verify bounded disk usage (16GB worst case)
    assert!(
        max_temp_storage < 20 * 1024 * 1024 * 1024,
        "Temp storage should be bounded"
    );

    // Test that limits prevent disk exhaustion attacks
    let attack_file_count = 10000;
    let attack_file_size = 1024 * 1024 * 1024; // 1GB each

    assert!(
        attack_file_count > max_temp_files,
        "Should prevent excessive temp files"
    );
    assert!(
        attack_file_size > temp_file_size_limit,
        "Should prevent huge temp files"
    );
}

/// Test CPU-intensive parsing protection
#[tokio::test]
async fn test_cpu_intensive_parsing_protection() {
    // Test limits that prevent CPU exhaustion attacks

    // Test maximum contig count limits
    use ref_solver::utils::validation::MAX_CONTIGS;
    let attack_contig_count = 10_000_000; // 10 million contigs

    assert!(
        MAX_CONTIGS < attack_contig_count,
        "Should prevent excessive contig processing"
    );
    // MAX_CONTIGS constant is configured appropriately

    // Calculate processing time estimates
    let processing_time_per_contig = Duration::from_nanos(100); // 100ns per contig
    #[allow(clippy::cast_possible_truncation)] // MAX_CONTIGS is 50_000, fits in u32
    let max_processing_time = processing_time_per_contig.saturating_mul(MAX_CONTIGS as u32);

    // Verify processing time is reasonable (under 50ms for max contigs)
    assert!(
        max_processing_time < Duration::from_millis(50),
        "Processing should be fast even at limits"
    );

    // Test that attack scenarios would be blocked
    // Use a reasonable attack size that won't overflow
    let reasonable_attack_count = 1_000_000u32; // 1 million contigs
    let attack_processing_time = processing_time_per_contig.saturating_mul(reasonable_attack_count);
    assert!(
        attack_processing_time >= Duration::from_millis(100),
        "Attack scenario would consume significant CPU"
    );
}

/// Test string processing limits to prevent algorithmic complexity attacks
#[tokio::test]
async fn test_string_processing_limits() {
    // Test limits that prevent algorithmic complexity attacks

    let max_filename_length = 255;
    let max_text_field_size = 1024 * 1024; // 1MB

    // Test quadratic time attack scenarios
    let quadratic_attack_size: u64 = 100_000; // Large input for O(n²) algorithms

    assert!(
        max_filename_length < quadratic_attack_size,
        "Filename limit should prevent O(n²) attacks"
    );
    assert!(
        max_text_field_size < quadratic_attack_size * quadratic_attack_size,
        "Text limit should prevent extreme O(n²)"
    );

    // Test regex complexity attacks (ReDoS)
    let max_regex_input_size = max_text_field_size;
    let redos_attack_pattern_length: u64 = 10_000; // Long pattern designed to cause exponential backtracking

    // Our limits should prevent ReDoS attacks
    assert!(
        max_regex_input_size < redos_attack_pattern_length * redos_attack_pattern_length,
        "Input size limits should help prevent ReDoS attacks"
    );
}

/// Test memory allocation patterns to prevent allocation attacks
#[tokio::test]
async fn test_memory_allocation_protection() {
    // Test that our limits prevent dangerous allocation patterns

    let ptr_size = std::mem::size_of::<usize>();
    let max_file_size = 16 * 1024 * 1024; // 16MB
    let max_field_count = 10;

    // Test vector allocation limits
    let max_elements_in_file = max_file_size / ptr_size;
    assert!(
        max_elements_in_file < 10_000_000,
        "Should limit vector size to reasonable bounds"
    );

    // Test that we don't have integer overflow scenarios
    let total_possible_allocation = max_field_count * max_file_size;
    assert!(
        total_possible_allocation < isize::MAX as usize,
        "Should not cause integer overflow"
    );

    // Test hash table size limits
    let max_hash_entries = max_elements_in_file;
    let hash_memory_usage = max_hash_entries * (ptr_size * 2); // Key + value pointers

    assert!(
        hash_memory_usage < 1024 * 1024 * 1024,
        "Hash table memory should be bounded under 1GB"
    );
}

/// Test network resource protection
#[tokio::test]
async fn test_network_resource_protection() {
    // Test limits that prevent network-based DoS

    let max_request_size: u64 = 10 * 1024 * 1024; // 10MB
    let max_concurrent_connections: u64 = 100;
    let request_timeout = Duration::from_secs(30);

    // Calculate maximum network resource usage
    let max_network_memory = max_request_size * max_concurrent_connections;
    let max_connection_time = request_timeout;

    // Verify network resources are bounded
    assert!(
        max_network_memory < 2 * 1024 * 1024 * 1024,
        "Network memory should be under 2GB"
    );
    assert!(
        max_connection_time < Duration::from_secs(60),
        "Connections should not be held indefinitely"
    );

    // Test bandwidth limiting concepts
    #[allow(clippy::cast_precision_loss)] // Precision loss acceptable for bandwidth calculations
    let max_bandwidth_per_connection =
        (max_request_size as f64) / (request_timeout.as_secs() as f64);
    #[allow(clippy::cast_precision_loss)]
    let total_max_bandwidth = max_bandwidth_per_connection * (max_concurrent_connections as f64);

    // These help estimate DoS protection effectiveness
    assert!(
        total_max_bandwidth > 0.0,
        "Should have reasonable bandwidth calculations"
    );
    assert!(
        max_bandwidth_per_connection < 1024.0 * 1024.0,
        "Per-connection bandwidth should be reasonable"
    );
}

/// Test error handling resource protection
#[tokio::test]
async fn test_error_handling_resource_protection() {
    // Test that error handling itself doesn't become a DoS vector

    // Test error message size limits
    let max_error_detail_size = 1000; // Reasonable error message size
    let error_allocation_attack = 10_000_000; // Very large error messages

    assert!(
        max_error_detail_size < error_allocation_attack,
        "Error messages should be size-limited"
    );

    // Test error logging rate limits (conceptual)
    let max_errors_per_second = 100; // Reasonable error logging rate
    let error_flood_rate = 10000; // Error flood attack

    assert!(
        error_flood_rate > max_errors_per_second * 10,
        "Should prevent error log flooding"
    );

    // Test that error handling is O(1) not O(n)
    let error_processing_complexity = 1; // Constant time
    let input_size_impact = 0; // Error handling shouldn't scale with input size

    assert_eq!(
        input_size_impact, 0,
        "Error handling should be constant time"
    );
    assert_eq!(
        error_processing_complexity, 1,
        "Error processing should be O(1)"
    );
}

/// Test recovery and resilience under attack conditions
#[tokio::test]
async fn test_attack_recovery_resilience() {
    // Test that the system can recover from attack conditions

    let recovery_time_limit = Duration::from_secs(60); // Should recover within 1 minute
    let max_temporary_resource_usage = 200 * 1024 * 1024; // 200MB temporary usage

    // Test that rate limiting eventually allows legitimate traffic
    let rate_limit_recovery = Duration::from_secs(1); // Per-IP limits reset every second
    assert!(
        rate_limit_recovery < recovery_time_limit,
        "Rate limits should reset quickly"
    );

    // Test that memory is properly freed after attacks
    assert!(
        max_temporary_resource_usage < 1024 * 1024 * 1024,
        "Temporary usage should be bounded"
    );

    // Test that file handles are properly cleaned up
    let max_temp_files = 100; // Reasonable concurrent file limit
    assert!(
        max_temp_files < 10000,
        "File handle usage should be bounded"
    );

    // These tests verify our system design principles for resilience
    // System is designed for automatic recovery - no runtime check needed
}

/// Integration test simulating realistic attack patterns
#[tokio::test]
async fn test_realistic_attack_simulation() {
    // Simulate a realistic multi-vector attack

    struct AttackVector {
        name: &'static str,
        requests_per_second: u32,
        file_size: usize,
        field_count: u32,
        duration: Duration,
    }

    let attack_vectors = vec![
        AttackVector {
            name: "Slow loris",
            requests_per_second: 1,
            file_size: 1024,
            field_count: 1,
            duration: Duration::from_secs(300),
        },
        AttackVector {
            name: "Request flood",
            requests_per_second: 1000,
            file_size: 1024,
            field_count: 5,
            duration: Duration::from_secs(10),
        },
        AttackVector {
            name: "Large file upload",
            requests_per_second: 10,
            file_size: 50 * 1024 * 1024, // 50MB
            field_count: 1,
            duration: Duration::from_secs(60),
        },
        AttackVector {
            name: "Field explosion",
            requests_per_second: 50,
            file_size: 1024,
            field_count: 100,
            duration: Duration::from_secs(30),
        },
    ];

    // Verify that our security measures handle each attack vector
    for vector in &attack_vectors {
        // Calculate resource impact
        #[allow(clippy::cast_possible_truncation)] // Test durations are small (< 300 secs)
        let total_requests = vector.requests_per_second * (vector.duration.as_secs() as u32);
        let peak_memory = (vector.file_size as u64) * u64::from(vector.requests_per_second);
        let total_fields = u64::from(vector.field_count) * u64::from(total_requests);

        println!("Testing attack vector: {}", vector.name);
        println!("  Total requests: {total_requests}");
        println!("  Peak memory estimate: {} MB", peak_memory / (1024 * 1024));
        println!("  Total fields: {total_fields}");

        // Verify our limits would prevent each attack
        match vector.name {
            "Slow loris" => {
                assert!(
                    vector.duration > Duration::from_secs(30),
                    "Should be blocked by timeout"
                );
            }
            "Request flood" => {
                assert!(
                    vector.requests_per_second > 10,
                    "Should be blocked by rate limiting"
                );
            }
            "Large file upload" => {
                assert!(
                    vector.file_size > 16 * 1024 * 1024,
                    "Should be blocked by size limits"
                );
            }
            "Field explosion" => {
                assert!(
                    vector.field_count > 10,
                    "Should be blocked by field count limits"
                );
            }
            _ => {}
        }
    }

    // Test combined attack resistance
    let combined_attack_memory = attack_vectors
        .iter()
        .map(|v| (v.file_size as u64) * u64::from(v.requests_per_second))
        .sum::<u64>();

    let our_memory_limits = 100u64 * (16 * 1024 * 1024); // 100 concurrent * 16MB limit

    println!(
        "Combined attack memory: {} MB",
        combined_attack_memory / (1024 * 1024)
    );
    println!(
        "Our memory limits: {} MB",
        our_memory_limits / (1024 * 1024)
    );
    println!(
        "Double our limits: {} MB",
        (our_memory_limits * 2) / (1024 * 1024)
    );

    assert!(
        combined_attack_memory > our_memory_limits / 10, // Make this more reasonable
        "Combined attack should be significant"
    );

    println!("All attack vectors would be mitigated by implemented security measures");
}