# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Substance_Use_Disorder"

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

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

# Get list of available cohorts
available_cohorts = [d for d in os.listdir(tcga_root_dir) 
                    if os.path.isdir(os.path.join(tcga_root_dir, d)) and not d.startswith('.')]

# Check for directories related to substance use disorder
substance_related_dirs = [d for d in available_cohorts 
                         if any(term in d.lower() for term in ['substance', 'addiction', 'drug', 'alcohol'])]

# Since no relevant directories found, record this and end processing
clinical_df = None
genetic_df = None

validate_and_save_cohort_info(
    is_final=False,
    cohort='TCGA',
    info_path=json_path,
    is_gene_available=False,
    is_trait_available=False
)