Developing Web Applications for Daycart

Ragu Bharadwaj,

Daylight CIS Inc

Several ways to create applications for Oracle.

Oracle forms
Using Excel & Access
Using ActiveX Controls available in Integrated Development Environments like Visual C++
Using Java & JDBC (Java DataBase Connectivity)

As the Oracle Daycart cartridge uses standard SQL all these methods can be used for Daycart application development.

We discuss one such methodology for web application development. Our method uses

XML(eXtensible Meta Language)
JSP(Java Server Pages) technology
XSLT (eXtensible Stylesheet Language).

In the process we'd like to

show the tools available for such a process
display the ease of application development with Daycart
point out the separation of content from display achieved by these methods

XML

XML is a way to present information in a containerized form. Information is presented just as in HTML, between tags. However only data & no presentation information is present. For example an address in XML is stored as

      <PERSONAL_INFO>
        <NAME>John Doe</NAME>
        <ADDRESS>
	  <STREET>
	    221, Pinehurst Ave.
	  </STREET>
	  <CITY>
	    San Diego
	  </CITY>
	  <STATE>
	    CA
	  </STATE>
	  <ZIP>
	    94210
	  </ZIP>
	</ADDRESS>
      </PERSONAL_INFO>

The above information may be presented as:

John Doe
221, Pinehurst Ave.
San Diego, CA 94210

when printed on top of an envelope. Or it could be represented as a bar code suitable for digital scanning. Or it could be represented as a LDAP record when inserted in an address database. Such conversion could be facilitated via:

XSLT

XSLT is a subset of XML
XSLT is a language with special constructs for converting an input XML file to HTML or other output.
Using XSLT requires an XSLT processor.
- An XSLT processor reads in an XML file and an XSLT file and alters the input XML using conversion instructions from the input XSLT file to present the input XML file. XSLT processors are available in C, C++, Java and many other languages
- We use the Xalan XSLT processor for our conversions. The processor is written in Java and is freely available from the Apache group.

So the idea is

to access a database for content
format its content into XML
Use XSLT stylesheets to convert that content to HTML, PDF or whatever format of output is expected

Accessing the database

Express the chemical query on a web page
Direct the query to the web server.
The web server invokes a CGI or server side application that
- queries the database
- formats its output into XML in preparation to pass the XML onto the XSLT processor.
Our server side application for this purpose resides in a JSP engine.
Pic
A JSP engine plugs into any standard web server such as
- Apache
- Microsoft IIS
- Netscape Server
It uses JDBC (the Java DataCase Connectivity API) to access the database. The JDBC API is a widely accepted and easy to use API to access SQL compliant databases.

A demo finally.

Expressing a chemical query on the web page

Daylight's languages like SMILES & SMARTS are a powerful way of expressing chemical structure and selection
The syntax for these languages leads to
- extremely compact strings that represent chemical structure
- extremely powerful ways to select chemical functionality
The languages themselves are easy to use by UNIX users familiar with regular expressions
However this isn't applicable to most chemists as they think in terms of chemical groups and are averse to non-graphical methods of chemical query.

Grins is a chemical editor family we have developed for such users. Grins occurs in the following flavors:

XVGrins, a XView-based app.
JavaGrins, a Java based app. Available forms:
- Currently available as a Netscape-only app that can do both SMILES & SMARTS.
- It is also in beta development as an IE capable app. This form requires the Java Plugin, a freely available plugin for Internet Explorer, made & distributed by Sun Microsystems
- In either case, integrating the editor into a web page is very easy & takes about 3 lines of JavaScript code in the web page.
PCGrins, a PC-based app which runs on Microsoft NT, & Windows 2000

While multiple technologies are used, generating a new app is fairly easy. This is because:

developing apps can be clearly separated into
- data generation and
- conversion of data into presentation
The data generation code is very simple in Java. e.g. the source code for the TCM JSP
The presentation is very easy to manipulate and change. This is because altering presentation involves altering the XSLT stylesheet only. This process
- doesn't need a recompile
- doesn't affect data retrieval and therefore doesn't create new bugs