# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Essential_Thrombocythemia"

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

# Output paths
out_data_file = "./output/preprocess/1/Essential_Thrombocythemia/TCGA.csv"
out_gene_data_file = "./output/preprocess/1/Essential_Thrombocythemia/gene_data/TCGA.csv"
out_clinical_data_file = "./output/preprocess/1/Essential_Thrombocythemia/clinical_data/TCGA.csv"
json_path = "./output/preprocess/1/Essential_Thrombocythemia/cohort_info.json"

import os
import pandas as pd

# 1. Identify subdirectories under tcga_root_dir
subdirectories = os.listdir(tcga_root_dir)

# Attempt to find a directory name relevant to "Essential Thrombocythemia" or synonyms
trait_subdir = None
search_terms = ["thrombocythemia", "essential_thrombocythemia", "et", "myeloproliferative"]
for d in subdirectories:
    d_lower = d.lower()
    if any(term in d_lower for term in search_terms):
        trait_subdir = d
        break

# 2. If none found, skip this trait
if not trait_subdir:
    print(f"No suitable subdirectory found for trait '{trait}'. Skipping...")
    is_gene_available = False
    is_trait_available = False
    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
    )
else:
    # This block is theoretically where we'd find and load files if the directory was found,
    # but for "Essential Thrombocythemia" there appears to be no matching directory.
    pass