UVa ITC Research Computing Support

Fall, 2002

Presented by the

Research Computing Support GroupDavid Drake, Kathy Gerber, Ed Hall, Tim F. Jost Tolson

Overview of Research Hardware, Software, Support & Storage: Tuesday, September 10, 3:30 PM

Statistical Software – Thursday, September 12, 3:30 PM Mathematical & Visualization Software – Tuesday, September 17, 3:30 PM High Performance Computing – Thursday, September 19, 3:30 PM FEMLAB Seminar: Multiphysics Modeling – Friday, Sept. 27 at 10:00 AM Introduction to IDL – Wednesday, October 9 at Noon

Database-Based Webpages – Wednesday, October 23 at 3 pm Maple 8 – Wednesday, November 20 at 3 pm

Database-Driven Webpages

By: David Drake

Research Computing Support Center

Phone: 243-8800 || Fax: 243-8765

E-Mail: Res-Consult@Virginia.EDU

http://www.itc.Virginia.edu/researchers

Databases and the Web

I. Databases in the Abstract

II. Creating Databases using Relational DataBase Management Systems (RDBMSs)

III. Databases and Web Interfaces

I. Databases in the Abstract

A. Definition

B. Normalization

C. Structure

D. Language

I. A. Definition

• A database is an organized collection of data whose content must be quickly and easily– Accessed

– Managed

– Updated

• A relational database is one whose data are split up into tables, sometimes called relations

• First Normal Form (1NF)– All attributes are single valued & non-repeating

• Second Normal Form (2NF)– Must be 1NF & must have primary key– Each non-primary key attribute must be functionally

dependent on primary key

• Third Normal form (3NF)– Must be 2NF– Each non-primary key attribute must be dependent only

on primary key

I. B. Normalization(read logical organization)

I. C. 1. Tables (Relations)

• Each column constitutes an attribute

• Each row constitutes a record or tuple

Attribute 1(column 1)

Attribute 2(column 2)

Record 1(tuple 1)

Record 2(tuple 2)

• Primary– An attribute or group of attributes which

uniquely identifies each record in a table– May not be a Null value

• Foreign– used primarily for enforcing referential

integrity, but also for establishing relationships between the two tables

I. C. 2. Keys

• One-to-one (1-to-1)

• One-to-many (1-to-M or 1-to-)

• Many-to-Many (M-to-M or -to-)

I. C. 3. Relationships

I. D. Structured Query Language(SQL)

• Pronounce “Sequel” or “Ess Que Ell”

• Industry standard language of (Relational) Databases

• Allows for complete– Table Creation, Deletion, Editing– Data extraction (Queries)– Database management & administration

II. Creating Databasesusing RDBMSs

A. Microsoft Access– Creating Tables– Entering, Importing, Editing, & Viewing Data– Defining Relationships– Constructing Queries

B. MySQL … (Documentation)– Where to put it (servers at UVa)– Ditto MS Access

C. Others– mSQL, PostGreSQL, Oracle, DB2, Informix, Sybase,

Empress, Adabas (available with StarOffice), ….

III. Databases and Web Interfaces(What you need to get started)

A. Requirements for a Database Web Interface

B. Where to Put Your Database and ScriptsC. Server-Side Scripting Languages

• ASP• Cold Fusion• Perl• PHP

III. A. Requirements for a Database Web Interface

• Your database (Access, MySQL)

• A Web server with appropriate RDBMS

• A way of connecting the two(Common Gateway Interface [CGI] scripts and SQL)

• Security concerns

III. B. Where to Put Your Databaseand Scripts

• Academic side of UVa– Access

• ESERVICES es-web1 (web.virginia.edu)

– MySQL• MySQL server (dbm1.itc.virginia.edu)• Home directory (www.people – accessible through blue.unix),

faculty, curry, avery, minerva (www.virginia.edu), jm.acs (www.itc.virginia.edu)

• Medical side of UVa– See the

UVa Health System’s Web Development Center

Active Server Pages (ASP)

• When a browser calls an ASP document, the ASP Server reads the .asp document and

1. Substitutes appropriate files for the (server-side) include statements

2. Runs the ASP code (see the VBScript and JScript Tutorial and Language References as well as the ASP Guide)

3. Returns the resulting HTML code to the browser

• Example (code, copy of database)

ASP Key Points (1)

• ASP code enclosed in: <% VBScript code %>• Everything outside is HTML• The result of the combined HTML and ASP code

must be a “standard” HTML document, e.g.:– <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Final//EN">

<html><head><title>Miracle Drug Study</title><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><meta name="Description" content=""><meta name="Keywords" content=""><link rel=STYLESHEET type="text/css" href=""></head><body></body></html>

ASP Key Points (2)

• Connect with database:– Create connection object:

• set conn = Server.CreateObject("ADODB.Connection")

– Open connection:• conn.open("Provider=Microsoft.Jet.OLEDB.4.0;Data

Source=f:\web\database\rescomp\study.mdb")

• Submit a (read-only) Query:– Generate SQL statement:

• SQL = "SELECT FirstName, LastName, DOB, Gender FROM Patients WHERE Gender = '" & Gender & "' ORDER BY FirstName DESC"

• set Patients = conn.execute(SQL)

ASP Key Points (3)

• Move through the data records:– do while NOT Patients.eof

Name = Patients(0) & " " & Patients(1)Patients.MoveNext

loop

• Add to or edit table:– Create and open Record Set object:

• set RS = Server.CreateObject("ADODB.Recordset")RS.Open “table name", conn, , adLockOptimistic, adCmdTable(where adLockOptimistic = 3, adCmdTable = 2)

ASP Key Points (4)

• Add to or edit table (continued):– Create new record, Edit, & Update:

• RS.AddNewRS(“Dosage”) = 200RS.Update

– Or Find desired record, Edit, & Update :• do while NOT RS.eof

if RS(“ID”) = 7 thenRS(“Dosage”) = 200RS.Update

elseRS.MoveNext

end ifloop

ASP Key Points (5)

• Clean up (free server resources) when done:– Queries:

• Patients.Closeset Patients = nothing

– Record Sets:• RS.Close

set RS = nothing

– The Connection:• conn.close

set conn = nothing

ASP Security

• Apart from various Internet Information Services (IIS – Window’s Web service) security holes (for viruses and worms), security is quite good.

• Use https:// … if you want to protect content over the internet – this provides Secure Socket Layer (SSL) security

ASP Resources

• ITC-Training Workshops– ASP Introduction

• Microsoft’s– ASP Guide– VBScript and JScript Language References

• ITC-Desktop’s examples• WebMonkey’s tutorial• Beginning ASP Databases by Kauffman (Wrox)• Professional Active Server Pages 3.0 by Homer (Wrox)

ColdFusion

• Easy-to-learn Server-Side Scripting Language: CFML, or Cold Fusion Markup Language, is embedded in HTML code

• CF code is enclosed in or by CF tags:– <CFtagname CF code >– <Cftagname > CF Code </Cftagname >

• Documents must end in .cfm• ColdFusion is Case Insensitive• Example (code, copy of database)

ColdFusion Key Points (1)

• All #variables# are enclosed in # signs

• HTML output which includes of CF variables must be surrounded by CF output tags; e.g.:– <CFset height = “tall”>

<CFoutput>The <B>#height#</B> boy fell.<CFoutput>

ColdFusion Key Points (1)

• Connect with database and run query simultaneously:– <CFQUERY Name="Patients" dbtype="dynamic"

connectstring="#DBdriver# #DBfile#">SELECT ID, FirstName, LastName FROM PatientsORDER BY FirstName</CFQUERY>

Where the variables are defined beforehand:– <CFset Dbdriver = "Driver={MICROSOFT ACCESS DRIVER (*.mdb)};

UID=admin; PWD=; dbq=">

– <CFset Dbfile = "f:\web\database\rescomp\study.mdb">

ColdFusion Key Points (2)

• Access Query Results– <SELECT name="PatientID">

<CFoutput QUERY="Patients"><OPTION value=#ID#>#FirstName# #LastName#

</CFoutput></SELECT>

• Insert Data from a Form– If a HTML form submits variables to be inserted, do so directly

using CFinsert:• <CFinsert tablename="Treatment" dbtype="dynamic"

connectstring="#DBdriver# #DBfile#">

All variables in the form object (e.g. Form.var1) that match attributes in the table are inserted into the table automatically

ColdFusion Key Points (3)

• Insert Data using Cfquery (SQL):– <CFquery name="Treatment" dbtype="dynamic"

connectstring="#DBdriver# #DBfile#">INSERT into TreatmentVALUES (#PatientID#, #EventID#, Now(), #Dosage(mg)#, #Severity#, #Time#)</CFquery>

• Other Data editing features also available– see Macromedia’s documentation webpage (find the

ColdFusion Markup Language Reference and Quick Reference pdf files at the bottom of the documentation webpage)

Cold Fusion Resources

• ITC-Training Workshops– Cold Fusion Introduction

• Allaire/Macromedia’s Documentation Web page – Developing CF Applications– CFML Reference– CFML Quick Reference

• ITC-Desktop’s examples• WebMonkey’s tutorial• Security links page• Programming Cold Fusion by Brooks-Bilson (O’Reilly)• Cold Fusion 5 Web Applications Construction Kit (4th Ed.)

by Forta (Macromedia Press)

Practical Extraction andReport Language (Perl)

• Ubiquitous– Originally designed to be a better general

purpose tool than a Unix shell, it has grown and spread to be supported from Windows to Macintosh to VMS.

• Powerful but Cryptic

• Example (code)

Perl Key Points (1)

• The file itself must end in “.cgi” or “.pl”• File must have “other” read and execute

permission (chmod o+rx filename.pl)• First line must specify the location of the Perl

engine (The DBI module will not work for “#!/usr/local/bin /perl[5]” – see below):– #!/uva/bin/perl -w

• First printed line must be the following if you want its response to go to a browser:– print "Content-type: text/html\n\n";

Perl Key Points (2)

Modules• You *must* use the DBI module which

allows you to interface with the database (see DBI link 1 & DBI link 2)– use DBI;

• You can & should also make use of the CGI module, esp. for parameter passing– use CGI;

Perl Key Points (3)

• Set the usual parameters:– my $hostname = "dbm1.itc.virginia.edu";

my $username = "dld5s"; # "my" defines a local variablemy $password = “…"; # fill inmy $database = $username . "_study"; # = dld5s_studymy $data_source = "DBI:mysql:$database:$hostname";

• Connect to the database:– my $dbh = DBI->connect($data_source, $username, $password)

or die "Can't connect to $data_source: $DBI::errstr\n";

Perl Key Points (4)

• Define the SQL statement and execute– my $SQL = "SELECT FirstName, LastName, DOB, Gender

FROM Patients WHERE Gender = '$Gender' ORDER BY FirstName DESC";my $sth = $dbh->prepare($SQL)or die "Unable to prepare $SQL: dbh->errstr\n";$sth->execute or die "Unable to execute query: $dbh->errstr\n";

• Clean up– $sth->finish;

$dbh->disconnect;

Perl Security

• Perl/MySQL can be made secure apart from one serious flaw as implemented at UVa:– Because web files must be readable by the world (unix

permissions), anyone with an account on the server where you run the php code can see the code, including your MySQL $password!

– A couple of exceptions to this flaw are as follows:• If you secure your server so that there are no other users on it• (It may** be possible to compile Perl scripts into binary

executables using perlcc. Then you must hide or remove your source code containing the MySQL password)

• One other possible poor to fair workaround: use .htaccess to password protect your php directory (limited access)

– See the passwords link, security links page

Perl Resources

• ITC-Training Workshops– Perl Programming Introduction– Perl Programming for the Web

• Perl Documentation (UVa currently has 5.6, but 5.8 exists)– Overview, Built-in functions, Data types, Regular expressions, …– Modules: DBI(1), CGI

• WebMonkey’s Tutorial, etc.• MySQL and PERL for the Web by DuBois (New Riders)• Learning Perl by Schwartz & Christiansen (O’Reilly)• Programming Perl by Wall, Orwant, & Christiansen

(O’Reilly)• Programming the Perl DBI: Database Programming with

Perl by Descartes, Bunce, & Mui (Editor) (O’Reilly)

PHP: Hypertext Preprocessor (PHP)

• HTML embedding scripting language (see the PHP online manual

• When a browser calls a PHP document, the Server reads the PHP document and– Runs the PHP code– Returns the resulting HTML code to the

browser

• Example (code)

PHP Key Points (1)

• Filename must end in .php or .phtml• File must have “other” read permission

(chmod o+r filename.phtml)• PHP code enclosed in <?php PHP code ?>

or <? PHP code ?>• Everything outside is HTML• Output is (generally) to a browser requiring

standard HTML

PHP Key Points (2)

Connecting with RDBMS and editing, adding, and deleting databases therein are all done through PHP functions

• Connect with MySQL RDBMS– mysql_connect($hostName, $userName, $password) or

die("Unable to connect to host $hostName");

• Connect with database– mysql_select_db($dbName) or die("Unable to select

database $dbName");

PHP Key Points (3)

Queries: Nearly all table interaction and management is done through queries:

• Basic information searches– $SQL = "SELECT FirstName, LastName, DOB,

Gender FROM Patients WHERE Gender = '$Gender‘ ORDER BY FirstName DESC";$Patients = mysql_query($SQL);

• Editing, adding, and deleting records and tables– $SQL = "INSERT INTO Patients (FirstName,

LastName) VALUES('$firstName', '$lastName')";$Patients = mysql_query($SQL);

PHP Key Points (4)

• Looping through and extracting results– $numPatients = mysql_numrows($Patients);– For ($I-0; $I<$numPatients; $I++) {

$lastName = mysql_result($Patients, $I, “LastName”);

…}

• Cleaning up: close the database connection– mysql_close();

PHP/MySQL Security

• The same problems as PHP occur with Perl if you run it as a Perl or CGI script. – See the passwords link

PHP Resources

• ITC-Training Workshops– PHP and MySQL

• PHP Documentation• ITC-Desktop’s examples• PHP’s Tutorial• WebMonkey’s Tutorial• PHP and MySQL Web Development by Welling

& Thomson (SAMS)• Beginning PHP4 by Blan, Choi, et. al (Wrox)

(Other) Books

• Beginning ASP Databases by Kauffman (Wrox)• Professional Active Server Pages 3.0 by Homer (Wrox)• Programming Cold Fusion by Brooks-Bilson (O’reilly)• Cold Fusion 5 Web Applications Construction Kit (4th Ed.) by Forta (Macromedia

Press)• MySQL by DuBois (New Riders)• MySQL and PERL for the Web by DuBois (New Riders)• MySQL & mSQL byYarger, Reese, & King• PHP and MySQL Web Development by Welling & Thomson (SAMS)• Beginning PHP4 by Blan, Choi, et. al (Wrox)• Learning Perl by Schwartz & Christiansen (O’Reilly)• Programming Perl by Wall, Orwant, & Christiansen (O’Reilly)• Programming the Perl DBI: Database Programming with Perl by Descartes, Bunce,

& Mui (Editor) (O’Reilly)• SQL-99 Complete, Really by Gulutzan & Pelzer (R&D Books)