# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Osteoporosis"

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

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

# 1. Check if suitable directory exists for Osteoporosis
# No suitable directory found in TCGA dataset since TCGA is a cancer database
# and osteoporosis is not a cancer condition

# Mark data as unavailable since no relevant cohort exists
is_gene_available = False 
is_trait_available = False

# Record this information
validate_and_save_cohort_info(
    is_final=False,
    cohort="TCGA",
    info_path=json_path,
    is_gene_available=is_gene_available,
    is_trait_available=is_trait_available
)