# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Gaucher_Disease"

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

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

# No relevant cohort exists for Gaucher Disease in TCGA dataset
is_gene_available = False  # No gene expression data available
is_trait_available = False # No trait data available

# Record that this trait needs to be skipped due to lack of relevant data
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
)

# Exit further processing since no suitable data exists
print("No suitable TCGA cohort found for Gaucher Disease. Skipping this trait.")