Python 培训之MySql

1. Install 

1.1 install mysql

      sudo apt-get install lamp-server^
        (tip: Set password)

1.2 install MySQLdb

   sudo apt-get install python-dev
2   sudo apt-get install libmysqlclient-dev
3   sudo apt-get install python-pip
4 　sudo pip install MySQL-python 

2. Commands

2.1 View

     mysql -u root -ppasswd
  　　show databases;
     use database;
     show tables;
     describe table;
     select * from table where colname = "##";
    (tip:count(*),limit;orderby;distinct,like)

2.2  Use

 create database ###;
 CREATE TABLE chem_gene
  (
  chem_gene_id int NOT NULL AUTO_INCREMENT,
    chemicalName varchar() NOT NULL,
    genesymbol varchar() NOT NULL,
    interaction text NOT NULL,
    interactionActions text NOT NULL,
   CONSTRAINT chem_gene PRIMARY KEY(chem_gene_id)
     ) ;
 insert into tablename values(##,###,###)

2.3. update && delete

     update ### set colname1=### where colname2=###;
     delete from tablename;
     delete from tablename where colname = ###;
     drop table tablename;
     drop database databasename;

2.4. coding

   create table (character set = utf8;)
   alter table ### convert to character set utf8;

2.5  create web user

   mysql -u root -ppasswd
   grant insert ,create,delete,select,drop,alter,index,update on dbname.* to username identified by "passwd";
   mysql -u username -ppasswd

 3. Mysql  Work with python 

3.1 sql script create database && create table

CREATE TABLE chem_gene
(
       chem_gene_id int NOT NULL AUTO_INCREMENT,
	chemicalName varchar(255) NOT NULL,
	chemicalID varchar(100) NOT NULL,
	casId varchar(100) NOT NULL,
	genesymbol varchar(100) NOT NULL,
	geneid varchar(100) NOT NULL,
	geneforms varchar(255) NOT NULL,
	organism varchar(100) NOT NULL,
	organismid varchar(100) NOT NULL,
	interaction text NOT NULL,
	interactionActions text NOT NULL,
	pubmedid varchar(100) NOT NULL,
	CONSTRAINT chem_gene PRIMARY KEY(chem_gene_id)
)
	character set = utf8;
(tip: mysql -u username -ppasswd -D dbname < ####.sql )

3.2. python  insert  by MySQLdb

#!/usr/bin/env/python
# -*- coding:UTF-8 -*-
from __future__ import print_function
import sys
import MySQLdb

fin = sys.argv[1]
table = sys.argv[2]

def mysql_conn(ip,user,passwd,db,port):
    try:
        conn = MySQLdb.connect(host=ip,user=user,
               passwd=passwd,db=db,port=port,charset='utf8')
        cur = conn.cursor()
        return conn,cur
    except MySQLdb.Error,e:
        print(e.args)
        sys.exit(1)

def insert_db(conn,cursor,command):
    try:
        cursor.execute(command)
        conn.commit()
    except MySQLdb.Error,e:
        print(e.args)
        sys.exit(1)

with open(fin) as input:
    conn,cur = mysql_conn("192.168.1.104","tcd_net","tcd_net","ctd_net",3308)
    for line in input:
        if not line.startswith("#"):
            content = line.strip().split("\t")
            out = tuple([""]+content)
            command = "insert into %s values%s;"%(table,out)
            print(command)
            try:
                insert_db(conn,cur,command)
            except:
                print("insert failed")
                sys.exit(1)
    conn.close()
    cur.close()
(tip: python ###.py ###.txt tablename )

3.3  python query  by MySQLdb

#!/usr/bin/env/python
# -*- coding:UTF-8 -*-
from __future__ import print_function
import MySQLdb
import sys

chem_name = sys.argv[1]

def mysql_connect():
    try:
        conn = MySQLdb.connect(host="localhost",user="tcd_net",
            passwd='tcd_net',db='ctd_net',port=3306,charset='utf8')
        cur = conn.cursor()
        return conn,cur
    except MySQLdb.Error,e:
        print(e.args)
        sys.exit(1)

def query_db(conn,cursor,command):
    try:
        cursor.execute(command)
        conn.commit()
        results = cursor.fetchall()
        return results
    except MySQLdb.Error,e:
        print(e.args)
        sys.exit(1)

def chem_gene_query(chem):
    conn,cur = mysql_connect()
    query_command = """select chemicalName,chemicalID,casId,
                   genesymbol,geneid,geneforms,organism,organismid,interaction,
                  interactionActions,pubmedid from chem_gene where chemicalName = "%s";"""%chem
    chem_gene_result = query_db(conn,cur,query_command)
    for res in chem_gene_result:
        print("\t".join(res))

chem_gene_query(chem_name)

(tip: python ###.py chem_name)

4. Mysql import && dump

    mysql -u root -ppasswd -D dbname < ****.sql
    mysqldump -u root -ppasswd dbname > ****.sql 

5..Mysql config

sudo service  mysql status/start/restart/stop
 /etc/mysql/my.cnf
[client]
port =
socket = /var/run/mysqld/mysqld.sock
[mysqld]
user = mysql
port =
datadir = /var/lib/mysql
bind-address = 0.0.0.0