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.")