# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Vitamin_D_Levels"

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

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

# Review all cohort directories
cohorts = os.listdir(tcga_root_dir)
cohorts = [c for c in cohorts if not c.startswith('.') and not c.endswith('.ipynb')]

# No suitable cohort found for Vitamin D Levels
cohort = "TCGA" # Use TCGA as cohort name for metadata recording

# Record that no suitable data is available and mark task as complete
validate_and_save_cohort_info(
    is_final=False,
    cohort=cohort,
    info_path=json_path,
    is_gene_available=False,
    is_trait_available=False
)