# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Alopecia"

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

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

# 1. Review subdirectories for matching trait data
subdirs = [d for d in os.listdir(tcga_root_dir) if os.path.isdir(os.path.join(tcga_root_dir, d))]

# No suitable directory exists for age-related macular degeneration
# Mark data as unavailable 
cohort = "TCGA_no_suitable_cohort"

# Record unavailability and end preprocessing
validate_and_save_cohort_info(
    is_final=False,
    cohort=cohort, 
    info_path=json_path,
    is_gene_available=False,
    is_trait_available=False
)