# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Obstructive_sleep_apnea"

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

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

# Check for OSA-related directory in TCGA
# Since TCGA is focused on cancer, no directory is related to OSA
is_gene_available = False  
is_trait_available = False

# Mark task as completed and save info about data unavailability
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
)