Databases and the Weblibvolume2.xyz/biotechnology/semester5/bioinformatics/databasesto… ·...

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Databases and the Web

An Introduction

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Why is ‘Databases on the

Web’ Important?

� Databases are established technology

for managing large amounts of data

� The Web is a good way to present

information

� Separating data management from

presentation improves efficiency

�updating

� finding information

Credit: Netskills

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Examples of Websites

Using Databases

� Organizational information services

�employee directories

� Booking & scheduling

�airlines, university courses signup

� Electronic commerce

� Website automation� www.yahoo.com

� www.webmonkey.com

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How to Integrate Databases

and the Web?

� Databases

� Integration tools

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Databases

� Database

� an organized collection of data– paper-based

� DBMS (database management system)– software to enable user to create and maintain databases

� Relational database

� organizes data into tables

� RDBMS

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Examples of RDBMS

� MS Access

� desktop

� MySQL, mSQL

� mid-range

� Oracle, Sybase, MS SQL Server

� large enterprise

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How to Integrate Databases

and the Web?

� Databases

� MS Access

� MySQL, mSQL

� Oracle, Sybase, MS SQL Server

� Integration tools

� PHP or CGI, Servlets, JSP, ASP etc.

� “Middleware”: e.g. ColdFusion

http://www.allaire.com/

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Application Interface to

Databases� CGI

� Perl DBI

� Perl DBD (DBD::mysql)

� ASP

� ODBC (Open DataBase Connectivity)– A standard for the MS world

� ODBC driver comes with database– MySQL supplies MyODBC

� Servlets/JSP — JDBC

DBI

DBD::mysql DBD::oracle

CGI

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Relational Databases

� Databases that organize data into tables� Each table has

– A name

(For identification)

– One or more columns

(For attributes or fields)

– Rows

(For entries or records)

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Relational Database Design

� Logical database design

� Physical database design

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Logical Database Design

(Entity-relationship modeling)

� Identify and model the entities

� Identify and model the relationships

between the entities

� Identify and model the attributes

� Create unique identifier for each entity

� Normalize

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Terminology

Term Definition

Entity A thing (person, place, event, etc.) which exists

outside of the database and is represented in it

Attribute Describes the properties of a particular entity

Relationship Describes the associations between two or more

entities

Normalization Prevents inefficiency by ensuring no duplicated data

in multiple tables

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Physical Database Design

� Entities become tables

� Attributes become columns

choose appropriate data type for each

column

� Unique identifiers become primary keys

� Relationships are modeled as foreign keys

Foreign keys can be primary keys from other

tables

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Structured Query Language (SQL)

Standard language for working with relational databases

� a type of ‘natural’ language

� We are going to use Oracle on Borg for the examples we will do in the class/tutorials and for assignment-4.

� If you want to use something else, you are free to do so. However, note that in that case it will be your responsibility to solve any problems that may come upG

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Structured Query Language (SQL)

Standard language for working with relational databases

� A type of ‘natural’ language

� You may not have to write any code

� There are tools for that e.g Access query tool

� But necessary to understand basics, as SQL is common to all nearly all the tools covered today

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Two Categories of SQL Statement

1. Data manipulation

• SELECT, INSERT, DELETE

2. Data definition

• CREATE DATABASE, DROP DATABASE

• CREATE TABLE, DROP TABLE

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SQL Statement: INSERT

INSERT INTO table

(col1, col2, col3, ...)

VALUES (‘text1’,’text2’...,num1,..);

mysql> INSERT INTO employee

-> (firstname, lastname, address,em_id)

-> VALUES(‘John’,’Doe’,’Somewhere’,1);

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SQL Statement: DELETE

DELETE FROM table

WHERE condition;

mysql> DELETE FROM employee

-> WHERE lastname=‘Jones’;

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SQL Statement: SELECT

SELECT column_list

FROM table

WHERE condition;

mysql> SELECT * from course;

mysql> SELECT description

-> FROM course

-> WHERE title LIKE ‘Using%’;

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Use SELECT to join tables

SELECT table1.colx, table2.coly...

FROM table1, table2

WHERE condition;

mysql> SELECT course.title, course.description,

-> teacher.name

-> FROM course, teacher

-> WHERE course.teacher_ID=teacher.teacher_ID;

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Reference

Programming the Perl DBIhttp://www.oreilly.com/catalog/perldbi/chapter/ch04.html

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The End

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Aside: Middleware

Adapted from Introduction to Distributed Systems: Slides for CSCI 3171 Lectures by E. W. Grundke

References:

� [TvS] A. Tanenbaum and M. van SteenDistributed Systems: Principles and Paradigms, Prentice-Hall (2002)

<URL:http://www.prenhall.com/divisions/esm/app/author_tanenbaum/custom/dist_sys_1e/>

� [CDK] G. Coulouris, J. Dollimore and T. KindbergDistributed System: Concepts and Design, Addison-Wesley (2001)

<URL:http://www.cdk3.net/ig/beida/index.html>

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Layered Protocols: IPLayers, interfaces, and protocols in the Internet model.

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Layered Protocols: OSILayers, interfaces, and protocols in the OSI model.

2-1

TvS 2.2

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Middleware Protocols

An adapted reference model for networked communication.

2-5

TvS 2.6

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Middleware

A software layer that

� masks the heterogeneity of systems

� provides a convenient programming abstraction

� provides protocols for providing general-purpose

services to more specific applications, e.g.

� authentication protocols

� authorization protocols

� distributed commit protocols

� distributed locking protocols

� high-level communication protocols

– remote procedure calls (RPC)

– remote method invocation (RMI)

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MiddlewareGeneral structure of a distributed system as middleware.

1-22

TvS 1.24

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Middleware and Openness

In an open middleware-based distributed system, the protocols

used by each middleware layer should be the same, as well as

the interfaces they offer to applications.

1.23

TvS 1.25

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Middleware programming models�Remote Calls

� remote Procedure Calls (RPC)

� distributed objects and Remote Method Invocation (RMI)

� e.g. Java RMI

�Common Object Request Broker Architecture (CORBA)

� cross-language RMI

�Other programming models

� remote event notification

� remote SQL access

� distributed transaction processingCDK Ch 1 End of Aside