Access OpenWorm Semantic Database via Python

Access OpenWorm Semantic Database via Python (1).ipynb

{
 "metadata": {
  "name": "Access OpenWorm Semantic Database via Python"
 },
 "nbformat": 3,
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 "worksheets": [
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   "cells": [
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "A simple example of using a [Python MySQL library](https://github.com/PyMySQL/PyMySQL) to access the [OpenWorm Semantic Database](http://www.interintelligence.org/openworm/)."
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!sudo pip install PyMySQL",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "Downloading/unpacking PyMySQL\r\n"
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "  Downloading PyMySQL-0.5.tar.gz\r\n"
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "  Running setup.py egg_info for package PyMySQL\r\n"
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "    \r\nInstalling collected packages: PyMySQL\r\n  Running setup.py install for PyMySQL\r\n"
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "    \r\n"
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "Successfully installed PyMySQL\r\nCleaning up...\r\n"
      }
     ],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "#!/usr/bin/env python\n\nimport pymysql\n\n#conn = pymysql.connect(host='127.0.0.1', unix_socket='/tmp/mysql.sock', user='root', passwd=None, db='mysql')\n\nconn = pymysql.connect(host='my01.winhost.com', port=3306, user='openworm', passwd='openworm', db='mysql_31129_celegans')\n   \ncur = conn.cursor()\n\ncur.execute(\"SELECT DISTINCT EnID1 FROM tblrelationship LIMIT 5\")\n\n# print cur.description\n\n# r = cur.fetchall()\n# print r\n# ...or...\nfor r in cur.fetchall():\n   print(r)\n\ncur.close()\nconn.close()",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "(39L,)\n(48L,)\n(49L,)\n(40L,)\n(41L,)\n"
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "",
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}