# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Hutchinson-Gilford_Progeria_Syndrome"

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

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

# Get subdirectories from TCGA root directory 
tcga_subdirs = os.listdir(tcga_root_dir)
tcga_subdirs = [d for d in tcga_subdirs if not d.startswith('.')]

# No suitable cohort exists for HGPS in TCGA cancer datasets
# Record this and end processing
validate_and_save_cohort_info(
    is_final=False,
    cohort="TCGA",
    info_path=json_path, 
    is_gene_available=False,
    is_trait_available=False
)