YOKOFAKUN: 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

YOKOFAKUN

16 September 2010

Using MongoDB with Apache Tomcat, searching for Pubmed articles