# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Psoriasis"

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

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

# Review directories to find relevant cohort for Psoriasis
cohorts = os.listdir(tcga_root_dir)
cohorts = [d for d in cohorts if os.path.isdir(os.path.join(tcga_root_dir, d)) and d[0] != '.']

# No suitable cohort found for Psoriasis as it's not a cancer type covered by TCGA
validate_and_save_cohort_info(
    is_final=False,
    cohort="TCGA", 
    info_path=json_path,
    is_gene_available=False,
    is_trait_available=False
)