A custom JSP tag for mediawiki

I'm pretty happy with the following custom JSP tag for mediawiki I wrote last week (http://code.google.com/p/code915/source/browse/trunk/charpak/src/WEB-INF/src/fr/inserm/umr915/charpak/j2ee/tags/MediaWikiTag.java). For a given title, it calls the mediawiki api to test if an article exists in a mediawiki installation. In my case, this system will be useful to let my users write some custom annotations to some records from our database.

<u915:mediawiki title="${geneName}" preload="Template:Gene"/>

If the article does exist on the mediawiki installation a simple hyperlink is created. If the article does not exist, an hyperlink for creating/editing the new article is displayed with a predload option: Preloading wikitext presents the user with a partially created page rather than a blank page, possibly with inline instructions for content organization..For example, in the following web application, the blue and red icons point to some existing articles or some articles to be created:

Internals

This custom tag calls the mediawiki api (e.g api.php?action=query&format=xml&titles=Charles+Darwin )and get the XML response as a DOM document. An XPath expression is then evaluated to test if an attribute '@missing' was declared for the given article.

boolean pageFound=false;
String termUTF8 = URLEncoder.encode(term,"UTF-8");
URL url=new URL(baseurl+"/api.php?action=query&format=xml&titles="+termUTF8);
URLConnection con=url.openConnection();
in=con.getInputStream();
Document dom=this.domBuilder.parse(in);
Element e=(Element)this.xpathPage.evaluate(dom,XPathConstants.NODE);
if(e!=null && e.getAttributeNode("missing")==null)
{
pageFound=true;
}
in.close();

That's it,
Pierre

Using MongoDB with Apache Tomcat, searching for Pubmed articles

The current post continues the previous one titled "
MongoDB and NCBI pubmed: Inserting, searching and updating. My notebook.".

Here I've used the Java API for MongoDB/BSON in Apache Tomcat, the java servlet container to search and display some pubmed papers stored in mongo via a web interface. At the end the result looks like this:

The servlet

The servlet uses the JAVA API for mongo.

• An instance of Mongo is created and it connects to the mongodb server
• We obtain an object DB from the server for the database 'pubmed'
• we get an object DBCollection from the database
• If the user provided a valid pmid, the new query is created:
  BasicDBObject query=new BasicDBObject("_id",Long.parseLong(pmid))
  and it is used to search the collection
  BObject article=collection.findOne(query);
• If the article was found, it was injected in the request and forwarded to the JSP named 'article.jsp'

File: src/WEB-INF/src/fr/inserm/umr915/biomongo/BioMongoServlet.java

package fr.inserm.umr915.biomongo;

import java.io.IOException;
import javax.servlet.ServletConfig;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import com.mongodb.BasicDBObject;
import com.mongodb.DB;
import com.mongodb.DBCollection;
import com.mongodb.DBObject;
import com.mongodb.Mongo;
import com.mongodb.ServerAddress;

@SuppressWarnings("serial")
public class BioMongoServlet extends HttpServlet
{
/** mongodb host */
private String mongoHost=ServerAddress.defaultHost();
/** mongodb port */
private int mongoPort=ServerAddress.defaultPort();

@Override
public void init(ServletConfig config) throws ServletException {
super.init(config);
String param=config.getInitParameter("mongo.port");
if(param!=null) this.mongoPort=Integer.parseInt(param);
param=config.getInitParameter("mongo.host");
if(param!=null) this.mongoHost=param;
}

@Override
protected void service(HttpServletRequest req, HttpServletResponse res)
throws ServletException, IOException
{
Mongo mongo=null;
try {
//connect to mongo
mongo = new Mongo(this.mongoHost,this.mongoPort);
//get the database pubmed
DB database=mongo.getDB("pubmed");
if(database==null) throw new ServletException("canot get database");
//get the collection 'articles'
DBCollection col = database.getCollection("articles");
if(col==null) throw new ServletException("canot get collection");
//get the query parameter 'pmid'
String pmid=req.getParameter("pmid");
String jspPage="/WEB-INF/jsp/index.jsp";
//if pmid exist and looks like a number
if(pmid!=null && pmid.matches("[0-9]+"))
{
//find
DBObject article=col.findOne(new BasicDBObject("_id",Long.parseLong(pmid)));
if(article==null)
{
req.setAttribute("message", "Cannot find pmid:"+pmid);
}
else
{
jspPage="/WEB-INF/jsp/article.jsp";
req.setAttribute("article",article);
}
}
req.getRequestDispatcher(jspPage).forward(req, res);
}
catch(ServletException e)
{
throw e;
}
catch(IOException e)
{
throw e;
}
catch(Exception e)
{
throw new ServletException(e);
}
finally
{
//cleanup mongo
if(mongo!=null)
{
mongo.close();
}
mongo=null;
}
}
}

article.jsp

article.jsp displays the article. As this object is an instance of BasicDBObject (that is to say a Map and/or a List) it was very easy to use it with the JSP technology and the Java Standard Tag Library (JSTL).

File: ./src/WEB-INF/jsp/article.jsp

<%@page contentType="text/html" %>
<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core" %>
<%@ taglib prefix="mongo" tagdir="/WEB-INF/tags" %>
<% out.clearBuffer(); %><html><head>
<title>PMID:<c:out value="${param['pmid']}" escapeXml="true"/></title>
</head>
<body>
<h1>PMID:<c:out value="${param['pmid']}" escapeXml="true"/></h1>
<h2><c:out value="${article.title}" escapeXml="true"/></h2>
<dl>
<dt>Date</dt><dd><mongo:dbobject object="${article.created}"/></dd>
<dt>Authors</dt><dd><ul><c:forEach var="author" items="${article.authors}">
<li>
<mongo:dbobject object="${author}"/>
</li>
</c:forEach></ul></dd>
<dt>Journal</dt><dd><mongo:dbobject object="${article.journal}"/></dd>
<dt>Mesh</dt><dd><ul><c:forEach var="term" items="${article.mesh}">
<li>
<c:out value="${term}" escapeXml="true"/>
</li>
</c:forEach></ul></dd>
</dl>


</body>
</html>

dbobject.tag

The previous JSP page calls a custom tag file <mongo:dbobject> which make a 'pretty display' of a BSON object by serializing it with com.mongodb.util.JSON.serialize(Object o)

File: ./src/WEB-INF/tags/dbobject.tag

<%@ tag language="java" pageEncoding="UTF-8"%>
<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core" %>
<%@ taglib prefix="fn" uri="http://java.sun.com/jsp/jstl/functions" %>
<%@tag import="com.mongodb.util.JSON"%>
<%@tag import="com.mongodb.DBObject"%>
<%@attribute name="object" required="true" rtexprvalue="true" type="java.lang.Object"%>
<c:set var="bson"><%= JSON.serialize(this.object) %></c:set>

<div style="background-color:lightgray;"><c:out escapeXml="true" value="${bson}"/></div>

Other Files

index.jsp

a simple form for searching an article.

File: ./src/WEB-INF/jsp/index.jsp

<%@page contentType="text/html" %>
<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core" %>
<% out.clearBuffer(); %><html><head>
<title>Search PMID</title>
</head>
<body>
<form method="GET" action="${pageContext.request.contextPath}/biomongo" >
<div style=" position:absolute;width:400px;height:100px;left:50%;top:50%;margin-left:-100px;margin-top:-50px;">
<c:if test="${not empty message}">
<div style="text-align:center; color:red;"><c:out value="${message}" escapeXml="true"/></div>
</c:if>
<input name="pmid"/><input type="submit"/>
</div>
</form></body>
</html>

web.xml

the deployement descriptor.

File: ./src/WEB-INF/web.xml

<?xml version="1.0" encoding="UTF-8"?>
<web-app xmlns="http://java.sun.com/xml/ns/javaee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd"
version="2.5">

<description>Biomongo Servlet</description>
<display-name>Biomongo</display-name>


<servlet>
<display-name>Biomongo Servlet</display-name>
<servlet-name>biomongo</servlet-name>
<servlet-class>fr.inserm.umr915.biomongo.BioMongoServlet</servlet-class>

<load-on-startup>1</load-on-startup>
</servlet>

<servlet-mapping>
<servlet-name>biomongo</servlet-name>
<url-pattern>/biomongo</url-pattern>
</servlet-mapping>


<jsp-config>
<taglib>
<taglib-uri>http://java.sun.com/jstl/fmt</taglib-uri>
<taglib-location>/WEB-INF/tld/fmt.tld</taglib-location>
</taglib>


<taglib>
<taglib-uri>http://java.sun.com/jstl/core</taglib-uri>
<taglib-location>/WEB-INF/tld/c.tld</taglib-location>
</taglib>



<taglib>
<taglib-uri>http://java.sun.com/jstl/sql</taglib-uri>
<taglib-location>/WEB-INF/tld/sql.tld</taglib-location>
</taglib>



<taglib>
<taglib-uri>http://java.sun.com/jstl/x</taglib-uri>
<taglib-location>/WEB-INF/tld/x.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>http://java.sun.com/jstl/functions</taglib-uri>
<taglib-location>/WEB-INF/tld/fn.tld</taglib-location>
</taglib>


</jsp-config>

</web-app>

An ANT file for building the project

File: build.xml

<?xml version="1.0" encoding="UTF-8"?>
<project default="biomongo">
<property file="build.properties"/>
<property name="root.dir" value="."/>

<property file="${rootdir}/build.properties"/>


<path id="mongo.path">
<pathelement location="${mongodb.lib}"/>
</path>

<path id="servlet.path">
<pathelement location="${tomcat.servlet.api}"/>
<pathelement location="${tomcat.jsp.api}"/>
</path>


<target name="biomongo">
<property name="base.dir" value="${root.dir}/biomongo"/>
<mkdir dir="${base.dir}/src/WEB-INF/lib"/>
<mkdir dir="${base.dir}/src/WEB-INF/classes"/>

<copy todir="${base.dir}/src/WEB-INF/lib" includeEmptyDirs="false">
<fileset file="${mongodb.lib}"/>
<fileset dir="${taglib.dir}/lib" includes="*.jar"/>
</copy>

<copy todir="${base.dir}/src/WEB-INF/tld" includeEmptyDirs="false">
<fileset dir="${taglib.dir}/tld" includes="*.tld"/>
</copy>


<javac srcdir="${base.dir}/src/WEB-INF/src"
destdir="${base.dir}/src/WEB-INF/classes"
debug="true"
source="1.6"
target="1.6">
<classpath>
<path refid="mongo.path"/>
<path refid="servlet.path"/>
</classpath>
<sourcepath>
<pathelement location="${base.dir}/src/WEB-INF/src"/>
</sourcepath>
<include name="**/BioMongoServlet.java"/>
</javac>

<jar destfile="${tomcat.dir}/webapps/biomongo.war"
basedir="${base.dir}/src">
</jar>

</target>

</project>

Result

That's it.

Pierre

My fNotebook: Apache Tomcat / Bioinformatics

Hi all,
here is how I installed created and installed today a web application based on JSP (Java Server Page) and running on tomcat.

A prior knowledge on how deploying a web application with tomcat is required so this post is more a notebook than a tutorial.

First download tomcat 6.0, extract it:

wget -q "http://apache.cict.fr/tomcat/tomcat-6/v6.0.14/bin/apache-tomcat-6.0.14.tar.gz"
tar xfz apache-tomcat-6.0.14.tar.gz

Fetch the mysql java connector, extract it, and move in into the tomcat 'lib' folder

wget -q "ftp://ftp.inria.fr/pub/MySQL/Downloads/Connector-J/mysql-connector-java-5.1.5.tar.gz"
tar xfz mysql-connector-java-5.1.5.tar.gz
mv mysql-connector-java-5.1.5/mysql-connector-java-5.1.5-bin.jar apache-tomcat-6.0.14/lib/

I need the java standard template library JSTL library. I fetch and extract it.

wget "http://people.apache.org/builds/jakarta-taglibs/nightly/projects/standard/jakarta-taglibs-standard-20060823.tar.gz"
tar xfz jakarta-taglibs-standard-20060823.tar.gz

I create a database of snp.

mysql -u root -p -D test -e 'create table snp(chrom varchar(10) ,chromStart int not null,chromEnd int not null,name varchar(20) unique not null)'

I fill this database with a few snp from dbsnp@ucsc

mysql -N --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg18 -e 'select chrom,chromStart,chromEnd,name from snp126 where chrom="chrM" ' |\
gawk -F ' ' '{printf("insert into test.snp(chrom,chromStart,chromEnd,name) values (\"%s\",%s,%s,\"%s\");\n",$1,$2,$3,$4);}' |\
mysql -u login -p

I add a mysql connection pool in apache. In apache-tomcat-6.0.14/conf/context.xml , I add the following code just before the last tag </Context>

<Resource name="jdbc/MYSQL" auth="Container" type="javax.sql.DataSource"
maxActive="100" maxIdle="30" maxWait="10000"
username="login" password="yourpassword" driverClassName="com.mysql.jdbc.Driver"
url="jdbc:mysql://localhost:3306/test?autoReconnect=true"/>

we also need to setup a few properties before running tomcat:

export JAVA_HOME /usr/your-path/java1.6
export CATALINA_HOME=${PWD}/apache-tomcat-6.0.14
export CATALINA_BASE=${PWD}/apache-tomcat-6.0.14

we can now run tomcat.

./apache-tomcat-6.0.14/bin/startup.sh
Using CATALINA_BASE: /home/pierre/tmp/TOMCAT/apache-tomcat-6.0.14
Using CATALINA_HOME: /home/pierre/tmp/TOMCAT/apache-tomcat-6.0.14
Using CATALINA_TMPDIR: /home/pierre/tmp/TOMCAT/apache-tomcat-6.0.14/temp
Using JRE_HOME: /usr/your-path/java1.6/jre

we then create a few new directories

mkdir -p ./src/jsp
mkdir -p ./src/org/lindenb/jsp

We create a first JSP Custom TAG in src/org/lindenb/jsp/Anchor2DbSNP.java. This custom JSP tag will be used to create a automatic anchor to dbSNP.

package org.lindenb.jsp;
import javax.servlet.jsp.*;
import javax.servlet.jsp.tagext.*;
import java.util.regex.*;

/**
* This is a simple printing a link to dbSNP.
*/
public class Anchor2DbSNP extends BodyTagSupport
{
static private final Pattern RS_PATTERN=Pattern.compile("rs[0-9]+");

public int doEndTag() throws JspException
{
try
{
BodyContent bodyContent= getBodyContent();
if(bodyContent==null) return EVAL_PAGE;
String input=bodyContent.getString().trim().toLowerCase();
if(RS_PATTERN.matcher(input).matches())
{
getPreviousOut().print(
"<a href='http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs="+
input.substring(2)+
"'>"+
input+
"</a>"
);
}
else
{
getPreviousOut().print(input);
}
} catch(java.io.IOException err)
{
throw new JspException(err);
}
return EVAL_PAGE;
}
}

Another two custom tags will be used to display a simple genomic map in SVG.

Here is src/org/lindenb/jsp/ChromosomeTag.java

package org.lindenb.jsp;
import javax.servlet.jsp.*;
import javax.servlet.jsp.tagext.*;
import java.util.regex.*;
import java.util.*;

public class ChromosomeTag extends BodyTagSupport
{
private static class Position
{
int position=0;
String name=null;
public Position(int position,String name)
{
this.position=position;
this.name=name;
}
}

private Vector<Position> items= null;
private int svgWidth=500;
private int itemHeight=20;


public int doStartTag() throws JspException
{
items= new Vector<Position>();
return EVAL_BODY_INCLUDE;
}

public void addPosition(int position,String name)
{
if(position<0 || name==null) return;
this.items.addElement(new Position(position,name));
}

public int doEndTag() throws JspException
{
//if(this.items.isEmpty()) return EVAL_PAGE;
int max=0;
int min=Integer.MAX_VALUE;
for(Position p:this.items)
{
max=Math.max(p.position,max);
min=Math.min(p.position,min);
}
try
{
JspWriter out= pageContext.getOut();
out.write("<svg xmlns:xlink='http://www.w3.org/1999/xlink' xmlns='http://www.w3.org/2000/svg' width='"+svgWidth+"' height='"+ (this.items.size()*itemHeight)+"' style='font-size:"+(itemHeight-10)+"pt;stroke-width:1;'>");
out.write("<rect x='0' y='0' width='"+svgWidth+"' height='"+ (this.items.size()*itemHeight)+"' style='fill:white; stroke:gray;'/>");
int y=0;
for(Position p:this.items)
{
int x= (int)(((p.position-min)/(float)(max-min))*(svgWidth-200))+100;
out.write("<line x1='"+x+"' y1='"+y+"' x2='"+x+"' y2='"+(y+itemHeight)+"' style='stroke:blue;'/>");

out.write("<line x1='0' y1='"+y+"' x2='"+svgWidth+"' y2='"+(y)+"' style='stroke:gray;'/>");

out.write("<text x='"+(x+4)+"' y='"+(y+5+itemHeight/2)+"' >"+p.name+"</text>");
y+=itemHeight;
}

out.write("</svg>");

}
catch(java.io.IOException err)
{
throw new JspException(err);
}
items=null;
return EVAL_PAGE;
}

public void release()
{
items=null;
}
}

and

src/org/lindenb/jsp/ChromItemTag.java

package org.lindenb.jsp;
import javax.servlet.jsp.*;
import javax.servlet.jsp.tagext.*;
import java.util.regex.*;


public class ChromItemTag extends BodyTagSupport
{
private int position=-1;
private String name="";

public void setPosition(int position) { this.position= position;}


public int doEndTag() throws JspException
{
BodyContent bodyContent= getBodyContent();
if(bodyContent!=null) this.name =bodyContent.getString().trim();
if(this.name==null || name.length()==0) this.name=String.valueOf(this.position);
Tag parent= findAncestorWithClass(this,ChromosomeTag.class);
if(parent==null) return EVAL_PAGE;
ChromosomeTag ct= ChromosomeTag.class.cast(parent);
ct.addPosition(this.position+20,this.name);
return EVAL_PAGE;
}

public void release()
{
name=null;
position=-1;
}
}

the file src/bio.tld is the file used to declare the three custom tags.

<?xml version="1.0" encoding="ISO-8859-1" ?>
<taglib xmlns="http://java.sun.com/xml/ns/j2ee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-jsptaglibrary_2_0.xsd"
version="2.0">

<description>Bioinfo JSP TAG library</description>
<display-name>Bioinfo</display-name>
<tlib-version>1.1</tlib-version>
<short-name>bio</short-name>
<uri>http://jsp.lindenb.org</uri>

<tag>
<name>rs</name>
<tag-class>org.lindenb.jsp.Anchor2DbSNP</tag-class>
<body-content>JSP</body-content>
<info>display a link to dbSNP</info>
</tag>

<tag>
<name>chrom</name>
<tag-class>org.lindenb.jsp.ChromosomeTag</tag-class>
<body-content>JSP</body-content>
<info>svg map</info>
</tag>

<tag>
<name>item</name>
<tag-class>org.lindenb.jsp.ChromItemTag</tag-class>
<body-content>JSP</body-content>
<info>svg item</info>
<attribute>
<name>position</name>
<required>true</required>
<rtexprvalue>true</rtexprvalue>
</attribute>
</tag>


</taglib>

the file cat src/jsp/page.jsp is our JSP. It displays a SVG map and a table of a few SNP. It uses the JSTL and our custom tags.

<jsp:root
xmlns:jsp="http://java.sun.com/JSP/Page"
xmlns:c="http://java.sun.com/jsp/jstl/core"
xmlns:sql="http://java.sun.com/jsp/jstl/sql"
xmlns:bio="http://jsp.lindenb.org"

version="2.0">
<jsp:directive.page contentType="text/xml; charset=iso-8859-1"/>
<jsp:output doctype-root-element="html"
doctype-public="-//W3C//DTD XHTML 1.0 Strict//EN"
doctype-system="http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"
omit-xml-declaration="true"
/>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>JSP Tutorial For Bioinformatics</title>
<!-- <meta http-equiv="Content-Type" content="application/xhtml+xml; charset=iso-8859-1" /> -->
</head>
<body>
<sql:query var="snps" dataSource="jdbc/MYSQL">select * from snp limit 10</sql:query>
<bio:chrom>
<c:forEach var="row" items="${snps.rows}">

<bio:item position="${row.chromStart}"><c:out value="${row.name}"/></bio:item>
</c:forEach>
</bio:chrom>

<sql:query var="snps" dataSource="jdbc/MYSQL">select * from snp limit 10</sql:query>
<table>
<tr><th>Position</th><th>Name</th></tr>
<c:forEach var="row" items="${snps.rows}">
<tr>
<td><c:out value="${row.chrom}"/>:<c:out value="${row.chromStart}"/>-<c:out value="${row.chromEnd}"/></td>
<td><bio:rs><c:out value="${row.name}"/></bio:rs></td>
</tr>
</c:forEach>
</table>
</body>
</html>
</jsp:root>

Tomcat needs src/web.xml as a descriptor to learn how to deploy this web application.

<?xml version="1.0" encoding="ISO-8859-1"?>
<web-app
xmlns="http://java.sun.com/xml/ns/javaee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd"
version="2.5">
<display-name>Application Name</display-name>
<description>Application Description</description>


<taglib>
<taglib-uri>http://jsp.lindenb.org</taglib-uri>
<taglib-location>/WEB-INF/bio.tld</taglib-location>
</taglib>

<!-- see http://www.developer.com/java/ejb/article.php/1447551 -->
<taglib>
<taglib-uri>http://java.sun.com/jstl/fmt</taglib-uri>
<taglib-location>/WEB-INF/fmt.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>http://java.sun.com/jstl/fmt-rt</taglib-uri>
<taglib-location>/WEB-INF/fmt-rt.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>http://java.sun.com/jstl/core</taglib-uri>
<taglib-location>/WEB-INF/c.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>http://java.sun.com/jstl/core-rt</taglib-uri>
<taglib-location>/WEB-INF/c-rt.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>http://java.sun.com/jstl/sql</taglib-uri>
<taglib-location>/WEB-INF/sql.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>http://java.sun.com/jstl/sql-rt</taglib-uri>
<taglib-location>/WEB-INF/sql-rt.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>http://java.sun.com/jstl/x</taglib-uri>
<taglib-location>/WEB-INF/x.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>http://java.sun.com/jstl/x-rt</taglib-uri>
<taglib-location>/WEB-INF/x-rt.tld</taglib-location>
</taglib>


</web-app>

and we finally need src/build.xml to build all this stuff with ant.

<?xml version="1.0" encoding="ISO-8859-1"?>
<project name="Test" default="install" basedir=".">
<property name="tomcat.home" value="../apache-tomcat-6.0.14"/>
<property name="jstl.home" value="../jakarta-taglibs/standard"/>
<property name="webapps" value="${tomcat.home}/webapps"/>

<target name="compile">
<javac destdir="." srcdir="." debug="on">
<include name="org/lindenb/jsp/*.java"/>
<classpath>
<pathelement location="${jstl.home}/lib/jstl.jar"/>
<pathelement location="${jstl.home}/lib/standard.jar"/>
<pathelement location="${tomcat.home}/lib/servlet-api.jar"/>
<pathelement location="${tomcat.home}/lib/jsp-api.jar"/>
</classpath>
</javac>

<jar destfile="bio.jar"
basedir="."
includes="org/**"

/>

</target>

<target name="install" depends="compile">
<!-- yes, I know there is also war task... -->
<zip destfile="${webapps}/test.war">
<zipfileset dir="jsp" includes="*.jsp"/>
<zipfileset dir="." includes="web.xml" prefix="WEB-INF"/>
<zipfileset dir="${jstl.home}/tld" includes="*.tld" prefix="WEB-INF"/>
<zipfileset dir="." includes="*.tld" prefix="WEB-INF"/>
<zipfileset dir="${jstl.home}/lib" includes="*.jar" prefix="WEB-INF/lib"/>
<zipfileset dir="." includes="bio.jar" prefix="WEB-INF/lib"/>
</zip>
</target>

</project>

let's build this application. It creates a web archive (war) in the webapps folder of tomcat.

ant
Buildfile: build.xml

compile:
[jar] Building jar: /home/pierre/tmp/TOMCAT/src/bio.jar

install:
[zip] Building zip: /home/pierre/tmp/TOMCAT/apache-tomcat-6.0.14/webapps/test.war

BUILD SUCCESSFUL
Total time: 1 second

When you open "http://localhost:8080/test/page.jsp" you should get the following screen:

Pierre