{
 "cells": [
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   "cell_type": "code",
   "execution_count": 1,
   "id": "461d7761",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T07:00:18.889703Z",
     "iopub.status.busy": "2025-03-25T07:00:18.889550Z",
     "iopub.status.idle": "2025-03-25T07:00:19.056212Z",
     "shell.execute_reply": "2025-03-25T07:00:19.055827Z"
    }
   },
   "outputs": [],
   "source": [
    "import sys\n",
    "import os\n",
    "sys.path.append(os.path.abspath(os.path.join(os.getcwd(), '../..')))\n",
    "\n",
    "# Path Configuration\n",
    "from tools.preprocess import *\n",
    "\n",
    "# Processing context\n",
    "trait = \"Bone_Density\"\n",
    "\n",
    "# Input paths\n",
    "tcga_root_dir = \"../../input/TCGA\"\n",
    "\n",
    "# Output paths\n",
    "out_data_file = \"../../output/preprocess/Bone_Density/TCGA.csv\"\n",
    "out_gene_data_file = \"../../output/preprocess/Bone_Density/gene_data/TCGA.csv\"\n",
    "out_clinical_data_file = \"../../output/preprocess/Bone_Density/clinical_data/TCGA.csv\"\n",
    "json_path = \"../../output/preprocess/Bone_Density/cohort_info.json\"\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b4e032e6",
   "metadata": {},
   "source": [
    "### Step 1: Initial Data Loading"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "427fe1ea",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T07:00:19.057737Z",
     "iopub.status.busy": "2025-03-25T07:00:19.057582Z",
     "iopub.status.idle": "2025-03-25T07:00:19.064119Z",
     "shell.execute_reply": "2025-03-25T07:00:19.063799Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "No suitable directory found in TCGA for Bone_Density.\n",
      "TCGA focuses on cancer types, not directly on bone density measurements.\n",
      "Skipping this trait as recommended in the guidelines.\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "False"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import os\n",
    "import pandas as pd\n",
    "\n",
    "# 1. Find the most relevant directory for Bone Density\n",
    "subdirectories = os.listdir(tcga_root_dir)\n",
    "target_trait = trait.lower().replace(\"_\", \" \")  # Convert to lowercase for case-insensitive matching\n",
    "\n",
    "# Words related to bone density that might appear in directory names\n",
    "bone_related_terms = [\"bone\", \"density\", \"osteoporosis\", \"skeletal\", \"osseous\"]\n",
    "\n",
    "# First try direct matches\n",
    "matched_dir = None\n",
    "for subdir in subdirectories:\n",
    "    subdir_lower = subdir.lower()\n",
    "    # Check if any bone-related term is in the directory name\n",
    "    if any(term in subdir_lower for term in bone_related_terms):\n",
    "        matched_dir = subdir\n",
    "        break\n",
    "\n",
    "# If no direct match found, look specifically for Sarcoma as it may include bone sarcomas\n",
    "if not matched_dir:\n",
    "    for subdir in subdirectories:\n",
    "        if \"sarcoma_(sarc)\" in subdir.lower():\n",
    "            matched_dir = subdir\n",
    "            break\n",
    "\n",
    "# No suitable directory found - we should skip this trait\n",
    "print(f\"No suitable directory found in TCGA for {trait}.\")\n",
    "print(\"TCGA focuses on cancer types, not directly on bone density measurements.\")\n",
    "print(\"Skipping this trait as recommended in the guidelines.\")\n",
    "\n",
    "validate_and_save_cohort_info(\n",
    "    is_final=False,\n",
    "    cohort=\"TCGA\",\n",
    "    info_path=json_path,\n",
    "    is_gene_available=False,\n",
    "    is_trait_available=False\n",
    ")"
   ]
  }
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