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