# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Cystic_Fibrosis"

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

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

# Review subdirectories and check if any matches cystic fibrosis phenotype
cohorts = [d for d in os.listdir(tcga_root_dir) if os.path.isdir(os.path.join(tcga_root_dir, d))]

# No suitable cohort exists for cystic fibrosis in TCGA
# Record this in metadata and exit
validate_and_save_cohort_info(
    is_final=False,
    cohort="TCGA",
    info_path=json_path, 
    is_gene_available=False,
    is_trait_available=False
)