# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Schizophrenia"

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

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

# Since TCGA only contains cancer datasets, and schizophrenia is not a cancer,
# we know there won't be suitable data - record unavailability and exit
validate_and_save_cohort_info(
    is_final=False, 
    cohort="TCGA",
    info_path=json_path,
    is_gene_available=False,
    is_trait_available=False
)

# Return empty dataframes to avoid errors in subsequent code
clinical_df = pd.DataFrame()
genetic_df = pd.DataFrame()