File size: 30,481 Bytes
84a242a
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
import torch
from torch.utils.data import Dataset
import os
import glob
from pathlib import Path
from sklearn.model_selection import train_test_split
from tools.subgraph_sampler import ProteinSubgraphSampler
from .pdb_processor import PDBProcessor
from .cache_manager import CacheManager
import random
import threading
from collections import OrderedDict

class ProteinDataset(Dataset):
    def __init__(self, train=True, data_path=None, pdb_path=None, cache_path=None, transform=None, **kwargs):
        self.train = train
        self.data_path = data_path
        self.pdb_path = pdb_path or "dataset/rcsb/human"  # Default PDB path
        self.cache_path = cache_path or "dataset/protein_cache"  # Default cache path
        self.transform = transform
        
        # New parameters for on-the-fly processing
        self.enable_pdb_processing = kwargs.get('enable_pdb_processing', True)
        self.force_pdb_processing = kwargs.get('force_pdb_processing', False)  # Force PDB processing even if .pt files exist
        
        # Subgraph sampling parameters
        self.min_nodes = kwargs.get('min_nodes', 10)
        self.max_nodes = kwargs.get('max_nodes', 100)

        # Initialize components
        self.subgraph_sampler = ProteinSubgraphSampler(
            min_nodes=self.min_nodes,
            max_nodes=self.max_nodes
        )
        
        # Initialize PDB processor and cache manager
        self.pdb_processor = None  # Lazy initialization
        self.cache_manager = CacheManager(self.cache_path)
        
        # Determine data source and index files
        self._determine_data_source()
        self.file_paths = self._get_file_paths()
        self.protein_ids = self._generate_protein_ids()
        
        # Split the dataset
        self.seed = kwargs.get('seed', 42)
        self._create_data_splits()

        # Improved memory management for multiprocessing
        self.cache_size = kwargs.get('cache_size', 512)  # Reduced default for multiprocessing
        self.enable_cache = kwargs.get('enable_cache', True)
        self.preload_cache = kwargs.get('preload_cache', False)
        
        # Thread-safe cache using OrderedDict (LRU)
        self._cache_lock = threading.Lock()
        self._cache = OrderedDict()
        
        # Worker-specific settings
        self._worker_id = None
        self._is_main_process = True
        
        # Statistics
        self._pdb_processed_count = 0
        self._cache_hit_count = 0
        self._pt_file_count = 0
        self._failed_files = set()  # Track files that failed to process
        self._valid_files = None  # Cache of validated files
        
        # Error handling options
        self.skip_invalid_files = kwargs.get('skip_invalid_files', True)
        self.validate_on_init = kwargs.get('validate_on_init', False)  # Pre-validate files during init
        self.max_retry_attempts = kwargs.get('max_retry_attempts', 1)
        
        # ESM-C configuration
        self.esm_use_cpu = kwargs.get('esm_use_cpu', False)
        if self.esm_use_cpu:
            os.environ['ESM_USE_CPU'] = 'true'
            print("Dataset: Configured ESM-C to use CPU only")
        
        # Pre-validate files if requested
        if self.validate_on_init and self.use_pdb_files:
            self._validate_pdb_files()
    
    def __getstate__(self):
        """Custom pickling - exclude locks and worker-specific state."""
        state = self.__dict__.copy()
        # Remove unpickleable entries
        del state['_cache_lock']
        # Reset worker-specific state for new process
        state['_worker_id'] = None
        state['_is_main_process'] = False  # Workers are not main process
        return state
    
    def __setstate__(self, state):
        """Custom unpickling - restore state and create new lock."""
        self.__dict__.update(state)
        # Create new lock in worker process
        self._cache_lock = threading.Lock()
        # Worker will determine its own ID later

    def _determine_data_source(self):
        """Determine whether to use preprocessed .pt files or PDB files."""
        self.use_pdb_files = False
        self.data_source_type = "unknown"
        
        # Check if we should force PDB processing
        if self.force_pdb_processing:
            if os.path.exists(self.pdb_path):
                self.use_pdb_files = True
                self.data_source_type = "pdb_forced"
                print(f"Dataset: Forced PDB processing from {self.pdb_path}")
            else:
                raise ValueError(f"PDB path not found: {self.pdb_path}")
        
        # Check for preprocessed .pt files first (backward compatibility)
        elif self.data_path and os.path.exists(self.data_path):
            pt_files = glob.glob(os.path.join(self.data_path, "*.pt"))
            if pt_files:
                self.use_pdb_files = False
                self.data_source_type = "preprocessed"
                print(f"Dataset: Using preprocessed .pt files from {self.data_path}")
                return
        
        # Fall back to PDB files if enabled
        if self.enable_pdb_processing and os.path.exists(self.pdb_path):
            pdb_files = glob.glob(os.path.join(self.pdb_path, "*.pdb"))
            if pdb_files:
                self.use_pdb_files = True
                self.data_source_type = "pdb_fallback"
                print(f"Dataset: Using PDB files from {self.pdb_path} (no preprocessed files found)")
            else:
                raise ValueError(f"No PDB files found in {self.pdb_path}")
        else:
            if not self.enable_pdb_processing:
                raise ValueError(f"No preprocessed files found in {self.data_path} and PDB processing is disabled")
            else:
                raise ValueError(f"No data files found in {self.data_path} or {self.pdb_path}")

    def _get_file_paths(self):
        """Get all protein file paths based on determined data source."""
        file_paths = []
        
        if self.use_pdb_files:
            # Use PDB files
            if os.path.exists(self.pdb_path):
                pattern = '*.pdb'
                file_paths.extend(glob.glob(os.path.join(self.pdb_path, pattern)))
        else:
            # Use preprocessed .pt files
            if self.data_path and os.path.exists(self.data_path):
                pattern = '*.pt'
                file_paths.extend(glob.glob(os.path.join(self.data_path, pattern)))
            
        # Sort for consistent ordering
        file_paths.sort()
        print(f"Dataset: Found {len(file_paths)} files ({self.data_source_type})")
        return file_paths
    
    def _generate_protein_ids(self):
        """Generate protein IDs from file names"""
        protein_ids = []
        for file_path in self.file_paths:
            filename = Path(file_path).stem  # Get filename without extension
            
            # Handle different filename patterns
            if self.use_pdb_files:
                # For PDB files, use the filename directly
                protein_ids.append(filename)
            else:
                # For .pt files, remove 'pytorch_graph_' prefix if present
                if filename.startswith('pytorch_graph_'):
                    protein_id = filename[len('pytorch_graph_'):]
                else:
                    protein_id = filename
                protein_ids.append(protein_id)
                
        return protein_ids
    
    def _create_data_splits(self):
        """Create train/test splits and select files based on self.train"""
        if not hasattr(self, 'file_paths') or not self.file_paths:
            raise ValueError("File paths are not initialized. Please check data_path.")
        
        # Split the dataset into train and test sets
        train_files, test_files = train_test_split(
            self.file_paths, test_size=0.1, random_state=self.seed)
        
        # if self.train:
        #     self.file_paths = train_files
        # else:
        #     self.file_paths = test_files
        
        # Regenerate protein IDs after split
        self.protein_ids = self._generate_protein_ids()
    
    def _validate_pdb_files(self):
        """Pre-validate PDB files to identify problematic ones."""
        if not self.use_pdb_files:
            return
        
        print(f"Dataset: Pre-validating {len(self.file_paths)} PDB files...")
        valid_files = []
        failed_files = []
        
        for i, file_path in enumerate(self.file_paths):
            if i % 50 == 0:
                print(f"Dataset: Validation progress: {i}/{len(self.file_paths)}")
            
            try:
                if self._is_pdb_file_valid(file_path):
                    valid_files.append(file_path)
                else:
                    failed_files.append(file_path)
                    self._failed_files.add(file_path)
            except Exception as e:
                print(f"Dataset: Validation failed for {file_path}: {e}")
                failed_files.append(file_path)
                self._failed_files.add(file_path)
        
        print(f"Dataset: Validation complete - Valid: {len(valid_files)}, Failed: {len(failed_files)}")
        
        if failed_files:
            print(f"Dataset: Failed files: {[Path(f).name for f in failed_files[:10]]}" + 
                  (f" (and {len(failed_files)-10} more)" if len(failed_files) > 10 else ""))
        
        # Update file paths to only include valid files
        if self.skip_invalid_files:
            self.file_paths = valid_files
            self.protein_ids = self._generate_protein_ids()
            print(f"Dataset: Using {len(self.file_paths)} valid files after filtering")
    
    def _is_pdb_file_valid(self, pdb_file_path):
        """Quick validation check for PDB file without full processing."""
        try:
            from Bio.PDB import PDBParser
            import numpy as np
            
            parser = PDBParser(QUIET=True)
            structure = parser.get_structure("test", pdb_file_path)
            
            # Check if we have any valid chains with coordinates
            valid_residues = 0
            for model in structure:
                for chain in model:
                    for residue in chain:
                        if residue.has_id("CA"):
                            ca_atom = residue["CA"]
                            coords = ca_atom.get_coord()
                            
                            # Check for NaN or infinite coordinates
                            if np.any(np.isnan(coords)) or np.any(np.isinf(coords)):
                                print(f"Dataset: Invalid coordinates in {pdb_file_path}: {coords}")
                                return False
                            
                            valid_residues += 1
                            
                            # Early exit if we have enough valid residues
                            if valid_residues >= self.min_nodes:
                                return True
            
            if valid_residues < self.min_nodes:
                print(f"Dataset: Too few valid residues in {pdb_file_path}: {valid_residues} < {self.min_nodes}")
                return False
            
            return True
            
        except Exception as e:
            print(f"Dataset: Validation error for {pdb_file_path}: {e}")
            return False

    def _get_worker_info(self):
        """Get current worker information for multiprocessing awareness"""
        try:
            import torch.utils.data as data
            worker_info = data.get_worker_info()
            if worker_info is not None:
                self._worker_id = worker_info.id
                self._is_main_process = False
                # Adjust cache size per worker
                self.cache_size = max(32, self.cache_size // worker_info.num_workers)
            return worker_info
        except:
            return None

    def _get_pdb_processor(self):
        """Get PDB processor with lazy initialization."""
        if self.pdb_processor is None:
            self.pdb_processor = PDBProcessor()
        return self.pdb_processor

    def _load_single_graph(self, file_path):
        """Load a single protein graph with improved thread-safe caching"""
        if not self.enable_cache:
            return self._load_from_disk(file_path)
        
        # Get worker info on first access
        if self._worker_id is None:
            self._get_worker_info()
        
        # Thread-safe cache access
        with self._cache_lock:
            # Check cache first
            if file_path in self._cache:
                # Move to end (most recently used)
                graph_data = self._cache.pop(file_path)
                self._cache[file_path] = graph_data
                return graph_data
        
        # Load from disk if not in cache
        graph_data = self._load_from_disk(file_path)
        
        if graph_data is not None and self.enable_cache:
            self._add_to_cache(file_path, graph_data)
        
        return graph_data
    
    def _load_from_disk(self, file_path):
        """Load graph data from disk or process PDB file on-demand."""
        try:
            if self.use_pdb_files:
                return self._load_from_pdb(file_path)
            else:
                return self._load_from_pt_file(file_path)
                
        except Exception as e:
            print(f"Error loading {file_path}: {e}")
            return None
    
    def _load_from_pt_file(self, file_path):
        """Load graph data from preprocessed .pt file."""
        try:
            graph_data = torch.load(file_path, map_location='cpu')
            
            self._pt_file_count += 1
            return graph_data
            
        except Exception as e:
            print(f"Error loading .pt file {file_path}: {e}")
            return None
    
    def _load_from_pdb(self, pdb_file_path):
        """Load graph data from PDB file with persistent caching."""
        try:
            # Check persistent cache first
            if self.cache_manager.exists(pdb_file_path):
                graph_data = self.cache_manager.load(pdb_file_path)
                if graph_data is not None:
                    self._cache_hit_count += 1
                    return graph_data
            
            # Process PDB file on-the-fly
            print(f"Processing PDB file on-the-fly: {pdb_file_path}")
            processor = self._get_pdb_processor()
            graph_data = processor.process_pdb_file(pdb_file_path)
            
            if graph_data is not None:
                # Save to persistent cache
                self.cache_manager.save(pdb_file_path, graph_data)
                self._pdb_processed_count += 1
                return graph_data
            else:
                print(f"Failed to process PDB file: {pdb_file_path}")
                return None
                
        except Exception as e:
            print(f"Error processing PDB file {pdb_file_path}: {e}")
            return None
        
    def _add_to_cache(self, file_path, graph_data):
        """Add graph to cache with thread-safe LRU eviction"""
        if self.cache_size <= 0:
            # Cache is disabled
            return
            
        with self._cache_lock:
            # Remove oldest items if cache is full
            while len(self._cache) >= self.cache_size:
                if self._cache:  # Check if cache is not empty before popitem
                    self._cache.popitem(last=False)  # Remove oldest (FIFO)
                else:
                    break  # Exit if cache becomes empty
            
            # Add new item (will be most recent)
            self._cache[file_path] = graph_data

    def clear_cache(self):
        """Clear the cache to free memory"""
        with self._cache_lock:
            self._cache.clear()

    def get_cache_info(self):
        """Get cache statistics"""
        with self._cache_lock:
            basic_info = {
                'cache_size': len(self._cache),
                'max_cache_size': self.cache_size,
                'worker_id': self._worker_id,
                'is_main_process': self._is_main_process,
                'cache_enabled': self.enable_cache,
                'data_source_type': self.data_source_type,
                'use_pdb_files': self.use_pdb_files,
                'pdb_processed_count': self._pdb_processed_count,
                'cache_hit_count': self._cache_hit_count,
                'pt_file_count': self._pt_file_count
            }
            
            # Add persistent cache info if using PDB files
            if self.use_pdb_files:
                persistent_cache_info = self.cache_manager.get_cache_stats()
                basic_info.update({
                    'persistent_cache': persistent_cache_info
                })
            
            return basic_info
    
    def get_processing_stats(self):
        """Get detailed processing statistics."""
        return {
            'data_source': self.data_source_type,
            'total_files': len(self.file_paths),
            'failed_files_count': len(self._failed_files),
            'failed_files': [Path(f).name for f in list(self._failed_files)[:10]],  # Show first 10
            'pdb_processed_on_fly': self._pdb_processed_count,
            'persistent_cache_hits': self._cache_hit_count,
            'pt_files_loaded': self._pt_file_count,
            'success_rate': (len(self.file_paths) - len(self._failed_files)) / len(self.file_paths) if len(self.file_paths) > 0 else 0,
            'cache_manager_stats': self.cache_manager.get_cache_stats() if self.use_pdb_files else None
        }
    
    def get_failed_files(self):
        """Get list of files that failed to process."""
        return list(self._failed_files)
    
    def clear_failed_files(self):
        """Clear the list of failed files (useful for retrying)."""
        self._failed_files.clear()
        print("Dataset: Cleared failed files list")

    def warm_cache(self, num_samples=None):
        """Pre-load a subset of the dataset into cache"""
        if not self.enable_cache or not self._is_main_process:
            return
        
        num_samples = num_samples or min(self.cache_size, len(self.file_paths))
        print(f"Warming cache with {num_samples} samples...")
        
        # Load a random subset for better distribution
        indices = random.sample(range(len(self.file_paths)), num_samples)
        
        for i, idx in enumerate(indices):
            file_path = self.file_paths[idx]
            self._load_single_graph(file_path)
            
            if (i + 1) % 50 == 0:
                print(f"Cache warming progress: {i + 1}/{num_samples}")
        
        print(f"Cache warmed. Current cache info: {self.get_cache_info()}")

    def __len__(self):
        # Return dataset size
        return len(self.file_paths)

    def _data_to_dict(self, data_obj):
        """Convert PyTorch Geometric Data object to dictionary format for subgraph sampler."""
        from torch_geometric.data import Data
        
        if isinstance(data_obj, Data):
            return {
                'node_features': data_obj.x,
                'edge_index': data_obj.edge_index, 
                'edge_attr': data_obj.edge_attr,
                'node_pos': data_obj.pos,
                'num_nodes': data_obj.x.shape[0] if data_obj.x is not None else 0
            }
        else:
            # Already dictionary format
            return data_obj
    
    def _dict_to_data(self, dict_obj):
        """Convert dictionary format back to PyTorch Geometric Data object."""
        from torch_geometric.data import Data
        
        if isinstance(dict_obj, dict):
            return Data(
                x=dict_obj['node_features'],
                edge_index=dict_obj['edge_index'],
                edge_attr=dict_obj['edge_attr'],
                pos=dict_obj['node_pos']
            )
        else:
            # Already Data object
            return dict_obj
    
    def _get_num_nodes(self, graph_obj):
        """Get number of nodes from either Data object or dictionary."""
        from torch_geometric.data import Data
        
        if isinstance(graph_obj, Data):
            return graph_obj.x.shape[0] if graph_obj.x is not None else 0
        else:
            return graph_obj.get('num_nodes', graph_obj['node_features'].shape[0])

    def __getitem__(self, idx):
        """Load protein graph on-demand and generate two contrastive views with robust error handling."""
        max_attempts = len(self.file_paths)  # Maximum attempts to find a valid sample
        attempt = 0
        
        while attempt < max_attempts:
            try:
                # Get current file (with wraparound if we've tried many times)
                current_idx = (idx + attempt) % len(self.file_paths)
                file_path = self.file_paths[current_idx]
                protein_id = self.protein_ids[current_idx]
                
                # Skip files that we know have failed before
                if self.skip_invalid_files and file_path in self._failed_files:
                    attempt += 1
                    continue
                
                # Check graph file existence, skip to debug
                pt_file_path = '/'.join(file_path.split('/')[:-2]) + '/graph_cache/protein_pdb_files/' + 'pytorch_graph_' + protein_id + '.pt'
                if os.path.exists(pt_file_path) and not self.force_pdb_processing:
                    return {
                        'load_error': False
                    }

                # Load graph data
                protein_graph = self._load_single_graph(file_path)
                
                if protein_graph is None:
                    # Mark this file as failed and try next
                    self._failed_files.add(file_path)
                    print(f"Dataset: Marking {Path(file_path).name} as failed, trying next file...")
                    attempt += 1
                    continue
                
                # Validate graph data
                if not self._validate_graph_data(protein_graph):
                    self._failed_files.add(file_path)
                    print(f"Dataset: Graph validation failed for {Path(file_path).name}, trying next file...")
                    attempt += 1
                    continue
                
                # Check if graph is large enough for subgraph sampling
                num_nodes = self._get_num_nodes(protein_graph)
                if num_nodes < self.min_nodes:
                    self._failed_files.add(file_path)
                    print(f"Dataset: Graph too small for {Path(file_path).name} ({num_nodes} < {self.min_nodes}), trying next file...")
                    attempt += 1
                    continue
                
                # Generate two contrastive views
                view1, view2, sampling_strategy, noise_applied = self._generate_contrastive_views(protein_graph)
                
                # Validate views
                if view1 is None or view2 is None:
                    print(f"Dataset: Failed to generate views for {Path(file_path).name}, trying next file...")
                    attempt += 1
                    continue
                
                # Successfully created a valid sample
                return {
                    'protein_graph': protein_graph,
                    'protein_id': protein_id,
                    'idx': current_idx,
                    'file_path': file_path,
                    'load_error': False,
                    'view1': view1,
                    'view2': view2,
                    'sampling_strategy': sampling_strategy,
                    'noise_applied': noise_applied,
                    'attempts_needed': attempt + 1
                }
                
            except Exception as e:
                print(f"Dataset: Unexpected error processing {self.file_paths[(idx + attempt) % len(self.file_paths)]}: {e}")
                attempt += 1
                continue
        
        # If we get here, we couldn't find any valid sample after many attempts
        print(f"Dataset: Could not find valid sample after {max_attempts} attempts starting from idx {idx}")
        
        # Return a dummy sample to prevent DataLoader from crashing
        return self._create_dummy_sample(idx)
    
    def _validate_graph_data(self, graph_data):
        """Validate that graph data is complete and has no NaN/infinite values."""
        try:
            if graph_data is None:
                return False
            
            # Check for NaN or infinite values
            import torch
            
            # Check node features
            if torch.any(torch.isnan(graph_data.x)) or torch.any(torch.isinf(graph_data.x)):
                print("Dataset: NaN/Inf found in node_features")
                return False
            
            # Check node positions
            if torch.any(torch.isnan(graph_data.pos)) or torch.any(torch.isinf(graph_data.pos)):
                print("Dataset: NaN/Inf found in node_pos")
                return False
            
            # Check edge attributes if present
            if graph_data.edge_attr is not None:
                if torch.any(torch.isnan(graph_data.edge_attr)) or torch.any(torch.isinf(graph_data.edge_attr)):
                    print("Dataset: NaN/Inf found in edge_attr")
                    return False
            
            # Check tensor shapes are consistent
            num_nodes = graph_data.x.shape[0]
            if graph_data.pos.shape[0] != num_nodes:
                print(f"Dataset: Inconsistent shapes - features: {graph_data.x.shape}, pos: {graph_data.pos.shape}")
                return False
            
            return True
            
        except Exception as e:
            print(f"Dataset: Error validating graph data: {e}")
            return False
    
    def _generate_contrastive_views(self, protein_graph):
        """Generate two contrastive views with error handling."""
        try:
            num_nodes = protein_graph.x.shape[0]
            can_sample_subgraph = num_nodes >= self.min_nodes
            
            # Generate two contrastive views with sampling probabilities
            a = getattr(self, 'complete_graph_percent', 0)
            complete_prob = a / 100.0
            seq_prob = (50 - 0.5 * a) / 100.0
            dist_prob = seq_prob
            
            rand_val = random.random()
            
            # Convert Data object to dictionary for subgraph sampler compatibility
            protein_graph_dict = self._data_to_dict(protein_graph)
            
            if not can_sample_subgraph or rand_val < complete_prob:
                # Use complete graph for both views
                view1_dict = self.subgraph_sampler.apply_noise(protein_graph_dict, "identity")
                view2_dict = self.subgraph_sampler.apply_noise(protein_graph_dict, "identity")
                sampling_strategy = 'complete' if can_sample_subgraph else 'complete_forced'
            elif rand_val < complete_prob + seq_prob:
                # Sequential sampling for both views
                view1_dict = self.subgraph_sampler.sample_sequential_subgraph(protein_graph_dict)
                view2_dict = self.subgraph_sampler.sample_sequential_subgraph(protein_graph_dict)
                sampling_strategy = 'sequential'
            else:
                # Distance-based sampling for both views  
                view1_dict = self.subgraph_sampler.sample_distance_subgraph(protein_graph_dict)
                view2_dict = self.subgraph_sampler.sample_distance_subgraph(protein_graph_dict)
                sampling_strategy = 'distance'
            
            # Convert back to Data objects
            view1 = self._dict_to_data(view1_dict)
            view2 = self._dict_to_data(view2_dict)            # Validate views before applying noise
            if not self._validate_graph_data(view1) or not self._validate_graph_data(view2):
                print("Dataset: Invalid views generated during subgraph sampling")
                return None, None, sampling_strategy, 'none'
            
            # Apply noise transformations
            apply_masking = random.random() < 0.5
            
            if apply_masking:
                view1_dict = self._data_to_dict(view1)
                view2_dict = self._data_to_dict(view2)
                view1_dict = self.subgraph_sampler.apply_noise(view1_dict, "random_edge_masking", edge_mask_prob=0.15)
                view2_dict = self.subgraph_sampler.apply_noise(view2_dict, "random_edge_masking", edge_mask_prob=0.15)
                view1 = self._dict_to_data(view1_dict)
                view2 = self._dict_to_data(view2_dict)
                noise_applied = 'masking'
            else:
                view1_dict = self._data_to_dict(view1)
                view2_dict = self._data_to_dict(view2)
                view1_dict = self.subgraph_sampler.apply_noise(view1_dict, "identity")
                view2_dict = self.subgraph_sampler.apply_noise(view2_dict, "identity")
                view1 = self._dict_to_data(view1_dict)
                view2 = self._dict_to_data(view2_dict)
                noise_applied = 'identity'
            
            # Final validation of views
            if not self._validate_graph_data(view1) or not self._validate_graph_data(view2):
                print("Dataset: Invalid views after noise application")
                return None, None, sampling_strategy, noise_applied
            
            return view1, view2, sampling_strategy, noise_applied
            
        except Exception as e:
            print(f"Dataset: Error generating contrastive views: {e}")
            return None, None, 'error', 'none'
    
    def _create_dummy_sample(self, idx):
        """Create a dummy sample when all else fails to prevent DataLoader crashes."""
        return {
            'protein_graph': None,
            'protein_id': f'dummy_{idx}',
            'idx': idx,
            'file_path': 'dummy',
            'load_error': True,
            'view1': None,
            'view2': None,
            'sampling_strategy': 'dummy',
            'noise_applied': 'none',
            'attempts_needed': -1
        }