| import json | |
| import os | |
| import sys | |
| # Assume running from Spec-RAG/ or using relative path | |
| input_path = "data/val.jsonl" | |
| output_path = "data/test_spectra.jsonl" | |
| num_samples = 50 | |
| # If paths don't exist, try absolute | |
| if not os.path.exists(input_path): | |
| # Try relative to script | |
| script_dir = os.path.dirname(os.path.abspath(__file__)) | |
| input_path = os.path.join(script_dir, "../data/val.jsonl") | |
| output_path = os.path.join(script_dir, "../data/test_spectra.jsonl") | |
| if not os.path.exists(input_path): | |
| print(f"Error: {input_path} does not exist.") | |
| sys.exit(1) | |
| print(f"Reading from {input_path}...") | |
| with open(input_path, "r") as f_in, open(output_path, "w") as f_out: | |
| count = 0 | |
| for line in f_in: | |
| line = line.strip() | |
| if not line: continue | |
| if count >= num_samples: | |
| break | |
| try: | |
| data = json.loads(line) | |
| # Keep only necessary fields for inference (peaks) and reference (smiles) | |
| new_data = { | |
| "spectrum_id": data.get("spectrum_id", f"spec_{count}"), | |
| "peaks": data.get("peaks", []), | |
| "smiles": data.get("smiles", "") # Keep ground truth for evaluation | |
| } | |
| f_out.write(json.dumps(new_data) + "\n") | |
| count += 1 | |
| except json.JSONDecodeError: | |
| continue | |
| print(f"Created {output_path} with {count} samples.") | |