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    "execution": {
     "iopub.execute_input": "2025-03-25T07:56:53.310912Z",
     "iopub.status.busy": "2025-03-25T07:56:53.310813Z",
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     "shell.execute_reply": "2025-03-25T07:56:53.469704Z"
    }
   },
   "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 = \"Melanoma\"\n",
    "cohort = \"GSE189631\"\n",
    "\n",
    "# Input paths\n",
    "in_trait_dir = \"../../input/GEO/Melanoma\"\n",
    "in_cohort_dir = \"../../input/GEO/Melanoma/GSE189631\"\n",
    "\n",
    "# Output paths\n",
    "out_data_file = \"../../output/preprocess/Melanoma/GSE189631.csv\"\n",
    "out_gene_data_file = \"../../output/preprocess/Melanoma/gene_data/GSE189631.csv\"\n",
    "out_clinical_data_file = \"../../output/preprocess/Melanoma/clinical_data/GSE189631.csv\"\n",
    "json_path = \"../../output/preprocess/Melanoma/cohort_info.json\"\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4953c8df",
   "metadata": {},
   "source": [
    "### Step 1: Initial Data Loading"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "d49ef9f0",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T07:56:53.471451Z",
     "iopub.status.busy": "2025-03-25T07:56:53.471307Z",
     "iopub.status.idle": "2025-03-25T07:56:53.476993Z",
     "shell.execute_reply": "2025-03-25T07:56:53.476726Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Files in the directory:\n",
      "[]\n",
      "Warning: Could not find a SOFT file. Using the first .gz file as fallback.\n",
      "Warning: Could not find a matrix file. Using the second .gz file as fallback if available.\n",
      "SOFT file: None\n",
      "Matrix file: None\n",
      "Could not find necessary files for processing.\n"
     ]
    }
   ],
   "source": [
    "# 1. Check what files are actually in the directory\n",
    "import os\n",
    "print(\"Files in the directory:\")\n",
    "files = os.listdir(in_cohort_dir)\n",
    "print(files)\n",
    "\n",
    "# 2. Find appropriate files with more flexible pattern matching\n",
    "soft_file = None\n",
    "matrix_file = None\n",
    "\n",
    "for file in files:\n",
    "    file_path = os.path.join(in_cohort_dir, file)\n",
    "    # Look for files that might contain SOFT or matrix data with various possible extensions\n",
    "    if 'soft' in file.lower() or 'family' in file.lower() or file.endswith('.soft.gz'):\n",
    "        soft_file = file_path\n",
    "    if 'matrix' in file.lower() or file.endswith('.txt.gz') or file.endswith('.tsv.gz'):\n",
    "        matrix_file = file_path\n",
    "\n",
    "if not soft_file:\n",
    "    print(\"Warning: Could not find a SOFT file. Using the first .gz file as fallback.\")\n",
    "    gz_files = [f for f in files if f.endswith('.gz')]\n",
    "    if gz_files:\n",
    "        soft_file = os.path.join(in_cohort_dir, gz_files[0])\n",
    "\n",
    "if not matrix_file:\n",
    "    print(\"Warning: Could not find a matrix file. Using the second .gz file as fallback if available.\")\n",
    "    gz_files = [f for f in files if f.endswith('.gz')]\n",
    "    if len(gz_files) > 1 and soft_file != os.path.join(in_cohort_dir, gz_files[1]):\n",
    "        matrix_file = os.path.join(in_cohort_dir, gz_files[1])\n",
    "    elif len(gz_files) == 1 and not soft_file:\n",
    "        matrix_file = os.path.join(in_cohort_dir, gz_files[0])\n",
    "\n",
    "print(f\"SOFT file: {soft_file}\")\n",
    "print(f\"Matrix file: {matrix_file}\")\n",
    "\n",
    "# 3. Read files if found\n",
    "if soft_file and matrix_file:\n",
    "    # Read the matrix file to obtain background information and sample characteristics data\n",
    "    background_prefixes = ['!Series_title', '!Series_summary', '!Series_overall_design']\n",
    "    clinical_prefixes = ['!Sample_geo_accession', '!Sample_characteristics_ch1']\n",
    "    \n",
    "    try:\n",
    "        background_info, clinical_data = get_background_and_clinical_data(matrix_file, background_prefixes, clinical_prefixes)\n",
    "        \n",
    "        # Obtain the sample characteristics dictionary from the clinical dataframe\n",
    "        sample_characteristics_dict = get_unique_values_by_row(clinical_data)\n",
    "        \n",
    "        # Explicitly print out all the background information and the sample characteristics dictionary\n",
    "        print(\"Background Information:\")\n",
    "        print(background_info)\n",
    "        print(\"Sample Characteristics Dictionary:\")\n",
    "        print(sample_characteristics_dict)\n",
    "    except Exception as e:\n",
    "        print(f\"Error processing files: {e}\")\n",
    "        # Try swapping files if first attempt fails\n",
    "        print(\"Trying to swap SOFT and matrix files...\")\n",
    "        temp = soft_file\n",
    "        soft_file = matrix_file\n",
    "        matrix_file = temp\n",
    "        try:\n",
    "            background_info, clinical_data = get_background_and_clinical_data(matrix_file, background_prefixes, clinical_prefixes)\n",
    "            sample_characteristics_dict = get_unique_values_by_row(clinical_data)\n",
    "            print(\"Background Information:\")\n",
    "            print(background_info)\n",
    "            print(\"Sample Characteristics Dictionary:\")\n",
    "            print(sample_characteristics_dict)\n",
    "        except Exception as e:\n",
    "            print(f\"Still error after swapping: {e}\")\n",
    "else:\n",
    "    print(\"Could not find necessary files for processing.\")"
   ]
  }
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