# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Atrial_Fibrillation"

# Input paths
tcga_root_dir = "../DATA/TCGA"

# Output paths
out_data_file = "./output/preprocess/3/Atrial_Fibrillation/TCGA.csv"
out_gene_data_file = "./output/preprocess/3/Atrial_Fibrillation/gene_data/TCGA.csv"
out_clinical_data_file = "./output/preprocess/3/Atrial_Fibrillation/clinical_data/TCGA.csv"
json_path = "./output/preprocess/3/Atrial_Fibrillation/cohort_info.json"

# Review available TCGA cohorts to find one relevant to atrial fibrillation
cohorts = os.listdir(tcga_root_dir)
cohorts = [c for c in cohorts if not c.startswith('.') and not c.endswith('.ipynb')]

# No suitable cohort found for atrial fibrillation
# Document this and mark the task as completed
validate_and_save_cohort_info(
    is_final=False,
    cohort="TCGA", 
    info_path=json_path,
    is_gene_available=False,
    is_trait_available=False
)