ArrayExpressArrayExpress Query Interface Query Interface

Gonzalo García Lara

January, 2003

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What is the What is the Query InterfaceQuery Interface??

ARRAYEXPRESS

Q.I.

• View DB content in HTML

• Export DB content in XML

• Export Data Sets (to Expression Profiler)

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Where is it?Where is it?

EBI Web Site

www.ebi.ac.uk/arrayexpress/query/entry

impressionmachine

Q.I.

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Query Interface ServerQuery Interface Server

• Machine: impressionCompaq 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

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TECH NOTE:

Web ServerWeb Server Application server

Servlet Engine

Web server

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FILESYSTEM

HTTP

HTTP

HTTP (HTML)

picking a file

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TECH NOTE:

Servlet EngineServlet Engine Application server

Servlet Engine

Web server

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HTTP

HTTP (HTML)

java computationin a single machine

Servlets

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TECH NOTE:

Application ServerApplication Server Application server

Servlet Engine

Web server

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HTTP

HTTPHTTP (HTML)

distributed computation

GATE

Enterprise Java Beans

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Static ServerStatic Server

• MAGE-ML Files download

• Expression matrices

• Spreadsheets describing Array Designs.

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Dynamic ServerDynamic Server

QueryFormServlet ResultListServlet MAGEModelServlet

Compliant with the 2.3 Servlet Specification

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OperationOperation

Nwww.ebi.ac.uk/arraye

TOMCAT ORACLE

5

1. Wait request from client2. Ask data to the database3. Retrieve data4. Render data in HTML form5. Return result to client

4 3

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1

expressionimpression

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Internal ArchitectureInternal Architecture

TOMCAT

servlets DBPool

CastorVelocity ORACLE

HTTP

HTTP

(HTML)

OQL

OQL

java objects

SQL*NET

JDBC

SQL

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““Manual” Manual” SoftwareSoftware

• Concurrent Access to the Database: module DBPool

• Servlets

• Supporting classes

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Automatically generated SWAutomatically generated SW

• Oracle Database Schema

• O-R mapping (oracle java)

• Java classes to model MAGE objects

• Velocity templates used to produce HTML

XMI-DDL.tcl

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javaclasses

O-Rmapping

Automatic Generation IAutomatic Generation I

MAGE.xmi

Description of the MAGE Object Model

AE

DatabaseSchema

VelocityTemplates

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MAGE.xmi AE

DatabaseSchema

VelocityTemplates

javaclasses

O-Rmapping

Automatic Generation IIAutomatic Generation II

MAGE.xmiabridged

Abridge.MAGE.xmi.xsl

MAGE-OMmodel

in HTML

Particular XSL scriptsDescription of the MAGE Object Model

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XSL TransformationXSL Transformation

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XML Document

XSL Stylesheet

XSL Transformation

Engine

xalan

XML,HTML,or textDocument

Another way to process XML files

SOURCE DOCUMENT

TRANSFORMATION SPECIFICATION

OUTPUT DOCUMENT

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XSL ExampleXSL Example

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<mage-class name="Contact" superclass="Identifiable”> <subclasses> <subclass>Organization</subclass> <subclass>Person</subclass> </subclasses> <attributes> <field name="URI" type="String"/> <field name="address" type="String"/> <field name="phone” type="String"/></attributes> <associations> <link name="roles" type="composite" target-class="OntologyEntry"/> </associations></mage-class>

Snippet of a source XML document

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XSL ExampleXSL Example

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<xsl:template match="mage-class">

<xsl:variable name=”SUBCLASS_NO" select="count( ./subclasses/subclass )" />

<xsl:if test="$SUBCLASS_NO > 0"> <tr> <td align="left"> <xsl:value-of select="@name" /> </td> <td align="center"> <xsl:value-of select="$SUBCLASS_NO" /> </td> </tr> </xsl:if>

</xsl:template>

XSL Stylesheet snippet to produce HTML table rows

References to XMLelements or attributesin source document

HTML code

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XSL ExampleXSL Example

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<tr> <td align="left"> BioAssay </td> <td align="center"> 3 </td> </tr> <tr> <td align="left"> Contact </td> <td align="center"> 2 </td> </tr>

Snippet of resulting HTML code

Data extracted fromthe source XML document

BioAssay

Contact

3

2

Snippet of resulting HTML file

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Can XSL be used to process MAGE-ML?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)

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Other tasksOther tasks

• Performance tunning, e.g. Memory consumption.

• User session tracking

• Multithreading problems

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FutureFuture

1. Web Server2. Servlet Engine3. Application Server

Current system is in a rather “2.5” status

EJB ServersTomcat(s)

EBI Apache Servers

EBI Systems Microarray responsability

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Some useful linksSome useful links

Tomcat Servlet Enginehttp://jakarta.apache.org/tomcat

Castor Object-Relational mappinghttp://castor.exolab.org

Velocity HTML generationhttp://jakarta.apache.org/velocity

Xalan XSL Transformation Enginehttp://xml.apache.org/xalan-j/index.html

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QuestionsQuestions

?