Relational Database

CISC/QCSE 810some materials from Software Carpentry

Introduction

Text files have a long and useful history for storing files they are human-readable they can always be imported into new

formats simple to write reading routines in

any language

Limitations of Text Files 1

No meta-data experimental/simulation data has

conditions/parameters attached If your file names are like

"results_s10_n5_p43.txt", you should consider recording results in a database

Limitations of Text Files 2

Redundancy (and error) One way to include meta-data is to add extra

columns to your text files

"Any duplication will eventually lead to errors"

Extra columns of constants are extremely expensive, largely wasted space, and don't scale well as you add new meta-data

Limitations of Text Files 3

Searching and subsetting searching for matching entries in a

text file is cumbersome grep is fine for some easy matches,

but not for searches like "“Find all experiments done with the Mark VII that had yields greater than 30%, that didn't use cadmium disulfide as a reagant”

Non-text files

Collections of documents need be both stored and searched graphic images: index by date,

source, resolution, format, processing done, comments

video clips: same

Relational Databases

Relational Databases are data repositories that can help store relations between different types of dataAllows you to focus on one aspect of data modeling at a time reduce redundancy improve search

Getting Started

A database is a collection of zero or more tables, each of which: Has a name Stores a single relation (i.e., a set of information

of a particular kind)

Each table has a fixed set of named columns All the values in a column have the same type

Each table has zero or more rows Also called records

SQL Interface, DBMS

Interact with database management system (DBMS) using a specialized language called SQL Every vendor implements its own

extensions to the standard Table, database names are not case

sensitive: gravity, Gravity and GRAVITY are considered the same

Data can be case sensitive

Building vs Querying

Most time with database is spent querying generating graphs, tables from subsets of

data

Still need to build it in the first place! record-by-record table-by-table Perl/Python program to do fancy file-to-

database upload

Create a Database

Database is a grouped collection of tables CREATE DATABASE <database

name>

Creating a Table

To create a table, specify its name, and the names and types of its columns

CREATE TABLE Person(Login TEXT NOT NULL,LastName TEXT NOT NULL,FirstName TEXT NOT NULL

); The expression NOT NULL means that the value

must be present Data types are similar to C, Java types

To erase a table, use DROP TABLE name Very handy when you're first starting…

Filling in a Table

Adding records manually INSERT INTO <table> VALUES (….)INSERT INTO Person VALUES("skol", "Kovalevskaya", "Sofia");

Adding from a file LOAD DATA LOCAL INFILE

Filling in a Table 2

For anything more complicated, you'll want to write a script in some other language that does the uploading for you, through tailored "insert" commandse.g. experiment just finished check for existing experiment w/same

conditions create new record for experiment if necessary get new experiment ID (or old if it exists) upload results, with DB experimentID attached

Querying

Suppose we want to get everyone's name and login IDWrite a query that specifies what we want, and where to find it

SELECT Person.FirstName, Person.LastName, Person.Login

FROM Person;

Querying and Sorting

SELECT Person.FirstName, Person.LastName, Person.Login

FROM Person ORDER BY Person.Login;

Selection

Frequently only want a subset of data

SELECT FirstNameFROM Person WHERE Login = "skol"

Simple Joins

Getting project IDs from namesSELECT ProjectID, LastNameFROM Person, InvolvedWHERE Person.login = Involved.login

Query Joins w/3 Tables

More interesting query: what are the names of the projects is

Ivan involved in?

Far more to see!

Design of databases "normal forms" knowing the relationships between

your data tables

Efficient access of databases optimization of queries

Accessing an existing database

Download a MySQL clientTry to connect to 130.15.100.140 username aableson password

First steps

Create a database named for your Queen's NetIDTry some of the operations outlined in the MySQL tutorial skip the logging in with command

line, go straight to building tables, queries

Resources

MySQL Query Browser download http://dev.mysql.com/downloads/gui-tools/5.0.html

MySQL tutorial http://dev.mysql.com/doc/refman/5.0/en/tutorial.html tailored for command-line usage; can skip some if you're

using a GUI

MySQL reference http://dev.mysql.com/doc/refman/5.1/en/index.html