1. ArrayExpress Query Interface Gonzalo Garc í a Lara January, 2003 1 / 24

2. 2 / 24 What is the Query Interface? A RRAY E XPRESS Q.I. View DB content in HTML Export DB content in XML Export Data Sets (to Expression Profiler)

3. 3 / 24 Where is it? EBI Web Site www.ebi.ac.uk/ arrayexpress/ query /entry impression machine Q.I.

4. 4 / 24 Query Interface Server Machine: impression Compaq Alphaserver ES40, 4 CPUs, 8GB RAM Server: Tomcat 4.0.1 Open source servlet engine implemented in java Java Virtual Machine: version 1.2.2 2 servers installed: Production and Test. Production server is monitered every 5 minutes and restarted automatically if it is down 193.62.196.98 /ebi/microarray/l/tools/tomcat/prod /usr/opt/java122/bin

5. 6 / TECH NOTE: Web Server Application server Servlet Engine Web server 5 / 24 FILE SYSTEM HTTP HTTP (HTML) picking a file

6. 6 / TECH NOTE: Servlet Engine Application server Servlet Engine Web server 6 / 24 HTTP HTTP (HTML) java computation in a single machine Servlets

7. 6 / TECH NOTE: Application Server Application server Servlet Engine Web server 7 / 24 HTTP HTTP (HTML) distributed computation GATE Enterprise Java Beans

8. 8 / 24 Static Server MAGE-ML Files download Expression matrices Spreadsheets describing Array Designs.

9. 9 / 24 Dynamic Server QueryFormServletResultListServletMAGEModelServlet Compliant with the 2.3 Servlet Specification

10. 10 / 24 Operation N www.ebi.ac.uk/arraye TOMCAT ORACLE 5 1.Wait request from client 2.Ask data to the database 3.Retrieve data 4.Render data in HTML form 5.Return result to client 4321 expressionimpression

11. 11 / 24 Internal Architecture TOMCAT servletsDBPoolCastorVelocity ORACLE HTTP (HTML) OQL java objects SQL*NET JDBC SQL

12. 12 / 24 “Manual” Software Concurrent Access to the Database: module DBPool Servlets Supporting classes

13. 13 / 24 Automatically generated SW Oracle Database Schema O-R mapping (oracle  java) Java classes to model MAGE objects Velocity templates used to produce HTML

14. XMI-DDL.tcl 14 / 24 java classes O-R mapping Automatic Generation I MAGE.xmi Description of the MAGE Object Model AE Database Schema Velocity Templates

15. 15 / 24 MAGE.xmi AE Database Schema Velocity Templates java classes O-R mapping Automatic Generation II MAGE.xmi abridged Abridge.MAGE.xmi.xsl MAGE-OM model in HTML Particular XSL scripts Description of the MAGE Object Model

16. 6 / TECH NOTE: XSL Transformation 16 / 24 XML Document XSL Stylesheet XSL Transformation Engine xalan XML, HTML, or text Document Another way to process XML files SOURCE DOCUMENT TRANSFORMATION SPECIFICATION OUTPUT DOCUMENT

17. 6 / TECH NOTE: XSL Example 17 / 24 Organization Person Snippet of a source XML document

18. 6 / TECH NOTE: XSL Example 18 / 24 <xsl:variable name=”SUBCLASS_NO" select="count(./subclasses/subclass )" /> 0"> XSL Stylesheet snippet to produce HTML table rows References to XML elements or attributes in source document HTML code

19. 6 / TECH NOTE: XSL Example 19 / 24 BioAssay 3 Contact 2 Snippet of resulting HTML code Data extracted from the source XML document BioAssay Contact 3 2 Snippet of resulting HTML file

20. 20 / 24 Can XSL be used to process MAGE-ML? BAD NEWS : - It works on top of SAX or DOM; cannot be faster. - It is pretty tedious. GOOD NEWS : - It is a true XML scripting language. - Automation of repetitive tasks (splitting files, information extraction)

21. 21 / 24 Other tasks Performance tunning, e.g. Memory consumption. User session tracking Multithreading problems

22. 22 / 24 Future 1.Web Server 2.Servlet Engine 3.Application Server Current system is in a rather “2.5” status EJB ServersTomcat(s) EBI Apache Servers EBI SystemsMicroarray responsability

23. 23 / 24 Some useful links Tomcat Servlet Engine http://jakarta.apache.org/tomcat Castor Object-Relational mapping http://castor.exolab.org Velocity HTML generation http://jakarta.apache.org/velocity Xalan XSL Transformation Engine http://xml.apache.org/xalan-j/index.html

24. 24 / 24 Questions ?