# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Longevity"

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

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

# Review directory names for longevity relevance
directories = [d for d in os.listdir(tcga_root_dir) if os.path.isdir(os.path.join(tcga_root_dir, d))]

# None of the cancer cohorts in TCGA are directly relevant to studying longevity
# Mark task as completed by recording no suitable data was found
validate_and_save_cohort_info(
    is_final=False,
    cohort="TCGA", 
    info_path=json_path,
    is_gene_available=False,
    is_trait_available=False
)