gpl_main.ipynb

{
 "cells": [
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   "cell_type": "code",
   "execution_count": 6,
   "id": "41a9395c-0e12-4e7a-85b8-1eac4f02870d",
   "metadata": {},
   "outputs": [],
   "source": [
    "from Bio import Entrez\n",
    "import GEOparse\n",
    "import pandas as pd\n",
    "import os\n",
    "import preprocess_functions\n",
    "import insert_tables\n",
    "import mysql.connector\n",
    "from mysql.connector import errorcode"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "34bc052f-3e52-4a26-8946-0c12a9317bde",
   "metadata": {},
   "outputs": [],
   "source": [
    "gpl_path=\"/home/lmasa/GEO_Laura/data/gpl\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "4981165e-a2bf-462b-8b1d-8573872e930b",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "06-Jul-2024 13:30:43 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL94.annot: \n",
      "06-Jul-2024 13:30:43 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:43 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL571.annot: \n",
      "06-Jul-2024 13:30:43 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:43 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL570.annot: \n",
      "06-Jul-2024 13:30:43 DEBUG GEOparse - ANNOTATION: \n",
      "/home/lmasa/miniconda3/lib/python3.12/site-packages/GEOparse/GEOparse.py:401: DtypeWarning: Columns (12) have mixed types. Specify dtype option on import or set low_memory=False.\n",
      "  return read_csv(StringIO(data), index_col=None, sep=\"\\t\")\n",
      "06-Jul-2024 13:30:43 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL93.annot: \n",
      "06-Jul-2024 13:30:43 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:44 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL96.annot: \n",
      "06-Jul-2024 13:30:44 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:44 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL1426.annot: \n",
      "06-Jul-2024 13:30:44 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:44 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL201.annot: \n",
      "06-Jul-2024 13:30:44 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:44 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL8300.annot: \n",
      "06-Jul-2024 13:30:44 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:44 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL4191.annot: \n",
      "06-Jul-2024 13:30:44 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:44 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL97.annot: \n",
      "06-Jul-2024 13:30:44 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:44 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL10526.annot: \n",
      "06-Jul-2024 13:30:44 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:45 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL92.annot: \n",
      "06-Jul-2024 13:30:45 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:45 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL95.annot: \n",
      "06-Jul-2024 13:30:45 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:45 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL74.annot: \n",
      "06-Jul-2024 13:30:45 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:45 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL4133.annot: \n",
      "06-Jul-2024 13:30:45 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:45 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL80.annot: \n",
      "06-Jul-2024 13:30:45 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:45 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL10558.annot: \n",
      "06-Jul-2024 13:30:46 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:46 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL91.annot: \n",
      "06-Jul-2024 13:30:46 DEBUG GEOparse - ANNOTATION: \n",
      "06-Jul-2024 13:30:46 INFO GEOparse - Parsing /home/lmasa/GEO_Laura/data/gpl/GPL246.annot: \n",
      "06-Jul-2024 13:30:46 DEBUG GEOparse - ANNOTATION: \n"
     ]
    }
   ],
   "source": [
    "gpl_data=preprocess_functions.fetch_gpl_annot(gpl_path)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "23f1d834-caeb-4f0e-a28c-95d258f8ea53",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>gpl_id</th>\n",
       "      <th>gpl_title</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>GPL94</td>\n",
       "      <td>[HG_U95D] Affymetrix Human Genome U95D Array</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>GPL571</td>\n",
       "      <td>[HG-U133A_2] Affymetrix Human Genome U133A 2.0...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>GPL570</td>\n",
       "      <td>[HG-U133_Plus_2] Affymetrix Human Genome U133 ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GPL93</td>\n",
       "      <td>[HG_U95C] Affymetrix Human Genome U95C Array</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>GPL96</td>\n",
       "      <td>[HG-U133A] Affymetrix Human Genome U133A Array</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   gpl_id                                          gpl_title\n",
       "0   GPL94       [HG_U95D] Affymetrix Human Genome U95D Array\n",
       "1  GPL571  [HG-U133A_2] Affymetrix Human Genome U133A 2.0...\n",
       "2  GPL570  [HG-U133_Plus_2] Affymetrix Human Genome U133 ...\n",
       "3   GPL93       [HG_U95C] Affymetrix Human Genome U95C Array\n",
       "4   GPL96     [HG-U133A] Affymetrix Human Genome U133A Array"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gpl_data.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6389c1a1-c443-4774-bd9d-0fb65af45bee",
   "metadata": {},
   "outputs": [],
   "source": [
    "##Insert GPL data into database"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "d5785dba-71d0-4269-9ae7-b1968b8e9a19",
   "metadata": {},
   "outputs": [],
   "source": [
    "#The connection details needed to insert data into the database\n",
    "host = \"{host}\"  # Host where the MySQL server is located. Example: 'localhost' or '127.0.0.1'\n",
    "user = \"{user_name}\"  # Username for accessing the MySQL database. Example: 'root' or 'my_user'\n",
    "password = \"{password}\"  # Password for the MySQL user. Ensure to use a secure password for database access.\n",
    "database = \"{database}\"  # Name of the database to connect to. Example: 'disnet_biolayer'\n",
    "port = \"{port}\"  # Port number for the MySQL server. Default is 3306, but it may vary depending on the setup."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "b823d154-7c31-4aee-80b1-89bb933edb58",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Initialize the connection variable to None\n",
    "conn = None\n",
    "\n",
    "try:\n",
    "    # Attempt to establish a connection to the MySQL database\n",
    "    conn = mysql.connector.connect(\n",
    "        host=host,\n",
    "        user=user,\n",
    "        password=password,\n",
    "        database=database,\n",
    "        port=port\n",
    "    )\n",
    "        # Insert GPL data into the database\n",
    "        insert_tables.insert_gpl_main(conn, df)\n",
    "\n",
    "# Handle any MySQL errors that occur during the connection or insertion process\n",
    "except mysql.connector.Error as err:\n",
    "        print(f\"Error connecting to MySQL: {err}\")\n",
    "\n",
    "# Ensure the connection is closed properly even if an error occurs\n",
    "finally:\n",
    "        if conn and conn.is_connected():\n",
    "            conn.close()"
   ]
  }
 ],
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