Python och Perl

1
Python och Perl

• Lecture 3
• API and DBMS-connections.

2
Why use a DBMS?(DBMS Database management
system, e.g. MySQL, Oracle, Access)

• We have extracted a huge data amounts from flat
  files (databanks)
• That takes a lot of time.
• Same information and repeated queries.
• Solution
• Store data in a DBMS
• only needs to extract data once.
• only needs to read in the data once.
• We can put an index on any values we want
• (compare Hash)

3
Requirements for Python/Perl and DBMS hook up

• A database server (e.g. MySQL-server)
• A client for interaction with the database
  server (e.g. mysql-client)
• An API (Application Programming Interface)
• Perl uses DBI (database independent interface)
• Python uses the module MySQLdb
• Driver
• Perl uses mysql
• Python MySQLdb module has a built in driver.

4
Overview of system
Python script, using API. import MySQLdb
MySQL-server, with databases
API
Python-MySQLdb is a module for MySQL which uses
the API-syntax standard.
Perl-DBI is a generic API and requires a
complementing driver for every type of database
server.
5
How to apply

• Connect , connect()
• Prepare generisc query, prepare()
• Execute query with specific values, execute()
• Retrieve result, fetch()
• It is possible to iterate over both 4. and 3.

6
Example - Perl

• use DBI
• ( user, password) ( "student, "student)
• database "biolabdb"
• driver "mysql"
• data_source "DBIdriverdatabase"
• data_source ska ha 3 värden, moduldrivrutindat
  abas
• step 1.
• dbh DBI-gtconnect( data_source, user,
  password )
• step 2.
• statement "SELECT ID FROM keywords WHERE
  keyword?
• sth dbh-gtprepare( statement )
• step 3.
• sth-gtexecute( Membrane )
• step 4.
• _at_result sth-gtfetchall_array()

7
Example - Python

• import MySQLdb
• step 1.
• connection MySQLdb.connect(user"student", \
• passwd"student",db"biolabdb")
• step 2.
• cursor connection.cursor()
• statement "SELECT ID " \
• "FROM keywords " \
• "WHERE keywords
• step 3.
• cursor.execute( statement, Membrane) step 3.
• step 4.
• result cursor.fetchall() step 4.
• print result