# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Rheumatoid_Arthritis"

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

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

# Review available cohorts for asthma relevance
tcga_dirs = os.listdir(tcga_root_dir)
# Filter out non-directory files
tcga_dirs = [d for d in tcga_dirs if os.path.isdir(os.path.join(tcga_root_dir, d))]

# For asthma trait, none of the TCGA cancer cohorts are directly relevant
print(f"No suitable TCGA cancer cohort was found for the trait: {trait}")

# Save cohort info to mark this trait as completed
_ = validate_and_save_cohort_info(
    is_final=False,
    cohort="TCGA",
    info_path=json_path,
    is_gene_available=False, 
    is_trait_available=False
)
# Exit preprocessing as no suitable data exists
clinical_df = None
genetic_df = None