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Reading tomcat server.xml in junit test case

I am using java 7, and tomcat 7. I am writing few tests for my application in jUnit which uses tomcat/conf/server.xml for jndi. Here is the maven suggest folder structure.
src
|___test
|___java
| |___Testcase.java
|___resources
|___conf
|___server.xml
My sample server.xml would look like this,
<Resource name="jdbc/junit_db"
type="javax.sql.DataSource"
factory="org.apache.tomcat.dbcp.dbcp.BasicDataSourceFactory"
driverClassName="com.mysql.jdbc.Driver"
url="jdbc:mysql://localhost:3306/junit_db?zeroDateTimeBehavior=round&autoReconnect=true&dumpQueriesOnException=true"
username="root"
password="password"
maxIdle="0"
minIdle="0"
initialSize="1"
maxWait="5000"
maxActive="50"
loginTimeout="1000"
minEvictableIdleTimeMillis="2000"
timeBetweenEvictionRunsMillis="5000"
validationQuery="SELECT 1"
testOnBorrow="true"
testOnReturn="true"
testWhileIdle="false"
logAbandoned="true"
removeAbandoned="true"
poolPreparedStatements="true"
maxOpenPreparedStatements="10000"
accessToUnderlyingConnectionAllowed="false"
defaultAutoCommit="false"
defaultReadOnly="false"
defaultTransactionIsolation="4"/>
<Resource name="jdbc/junit_hive_db"
type="javax.sql.DataSource"
factory="com.office.hive.HiveDataSourceFactory"
driverClassName="org.apache.hive.jdbc.HiveDriver"
url="jdbc:hive2://localhost:10000/default?zeroDateTimeBehavior=round"
username=""
password="" />
I want to load this server.xml into the IntialContext before running jUnit test cases. How to achieve this?

Followed this link, it has solution for loading jndi into initialcontext manually.
http://www.alexecollins.com/tomcat-context-junit-rule/

Give TomcatJNDI a try. When fed with Tomcat's configuration files it will deliver all JNDI based objects that are declared in these files as soon as they are looked up. The code to achieve this is for example
TomcatJNDI tomcatJNDI = new TomcatJNDI();
tomcatJNDI.processServerXml(serverXmlFile)
tomcatJNDI.processContextXml(contextXmlFile);
tomcatJNDI.start();
Then you can lookup the objects as you are used to:
DataSource ds = (DataSource) InitialContext.doLookup("java:comp/env/path/to/datasource")
More about TomcatJNDI can be found here.

java.sql.SQLException: Connection has already been closed

We are getting java.sql.SQLException: Connection has already been closed. exception intermittently while performing a transaction. We are using tomcat 7.X and below is the configuration.
<Context docBase="ROOT" reloadable="true" antiJARLocking="true">
<Resource
name="jdbc/DS"
auth="Container"
type="javax.sql.DataSource"
driverClassName="org.postgresql.Driver"
url="jdbc:postgresql://XXXXXXX"
factory="org.apache.tomcat.jdbc.pool.DataSourceFactory"
username="XXXXXX"
password="XXXXXX"
maxActive="20"
maxIdle="3"
minIdle="3"
maxWait="10000"
removeAbandoned="true"/>
</Context>
Probably we are missing some configuration or property here that is causing the issue.
Please suggest a way fix this issue or help to find out the root cause.

Following configuration worked for me
<Context context="ROOT" debug="0" reloadable="false" useHttpOnly="true" cacheMaxSize="40960" cacheTTL="60000" cachingAllowed="true" antiJARLocking="true">
<Resource name="XYZ" auth="Container"
description="Exchange DB Connection"
dataSourceClassName="org.postgresql.ds.PGSimpleDataSource"
dataSource.serverName="XXXXX"
dataSource.databaseName="XXXX"
dataSource.portNumber="XXXX"
dataSource.user="xyz"
dataSource.password="xyz"
maximumPoolSize="20"
minimumIdle="5"
connectionTimeout="300000"
factory="com.zaxxer.hikari.HikariJNDIFactory"
registerMbeans="true"
type="javax.sql.DataSource" />
The key value here is connectionTimeout.
The factory which you are currently using has a default timeout, after that it forces session to close.
The connection timeout value above worked for me , for your application scenarios you'll have to experiment a bit to get the right value.

add below value:
removeAbandonedTimeout="600"

When is the tag I added in context.xml gets read?

In the context.xml of Tomcat I added the following tag :
<Resource name="jdbc/MyDatasource" auth="Container" type="javax.sql.DataSource"
driverClassName="org.apache.derby.jdbc.ClientDriver"
url="jdbc:derby://localhost:1527/my_database;create=true"
username="me" password="me"
maxActive="20" maxIdle="10" maxWait="-1" />
When does the following tag gets read ? Is it read when i start the server ?

This configuration is read when the application is deployed. If you have auto-deploy enabled, Tomcat will deploy your webapp during startup.

connecting to derby database with tomcat as the server

How do i connect to derby database (that comes with the netbeans) ? I am using Tomcat as the server. Earlier i used the following statements to connect to the derby database,but then i used glassfish as the server.
Context context = new InitialContext();
DataSource ds = (DataSource)context.lookup("java:comp/env/jdbc/PollDatasource");
Connection connection = ds.getConnection();
But now using Tomcat as the server i am unaware how to do this.
Note : Tomcat and Derby are pre installed with netbeans IDE that i am using currently

In Tomcat find conf/context.xml, then edit and write something like this:
<Resource name="jdbc/PollDatasource" auth="Container" type="javax.sql.DataSource"
driverClassName="com.YourDriver"
url="jdbc:derby://localhost:1527/nameOfTheDatabase;create=true"
username="username" password="password" maxActive="20"
maxIdle="10" maxWait="-1" />
Note 1: With the above URL the driver will be org.apache.derby.jdbc.ClientDriver
Note 2 : You can also add the above information in META-INF/context.xml of your project. This becomes application specific.If you add the information in tomcat's context.xml that becomes global.
Note 3: Download the jar from this website.Download db-derby-10.9.1.0-bin.zip.It contains many files, including derby.jar and derbyclient.jar (along with much documentation).derbyclient.jar contains our friend org.apache.derby.jdbc.ClientDriver.class. derby.jar contains org.apache.derby.jdbc.EmbeddedDriver. Keep the downloaded jar in lib folder of Tomcat.
and in your application web.xml "resource-ref":
<resource-ref>
<description>my connection</description>
<res-ref-name>jdbc/PollDatasource</res-ref-name>
<res-type>javax.sql.DataSource</res-type>
<res-auth>Container</res-auth>
</resource-ref>
You may want to look at these questions :
Isn't it necessary to mention the name of archive in the Resource tag?
When is the tag I added in context.xml gets read?
What are steps followed in the look-up? what is looked first web.xml or context.xml?

You need to:
1) Copy your derbyclient-*.jar to ${TOMCAT_HOME}/lib.
2) Edit your server.xml and add the following lines to the section GlobalNamingResources:
<Resource auth="Container"
driverClassName="org.apache.derby.jdbc.EmbeddedDriver"
maxActive="8" maxIdle="4"
name="jdbc/my-ds" type="javax.sql.DataSource"
url="jdbc:derby:mydb;create=true"
username="myuser" password="mypassword" />
3) In your context definition, add:
<Context docBase="myapp"
path="/myapp"
reloadable="true"
...>
<ResourceLink name="jdbc/my-ds"
global="jdbc/my-ds"
type="javax.sql.DataSource" />
</Context>
4) Restart Tomcat.

The example you have requires JNDI. See the relevant tomcat versions docs on setting that up.
Or use a connection string, here's a page from derby docs http://db.apache.org/derby/integrate/plugin_help/derby_app.html

Extra Information in JNDI Definition

I'm developing a web application and it is to be deployed on Apache Tomcat 6.0. Application will be connecting a lot of databases (almost 25) so in order to manage the Connections, I'm using a context.xml file located under META-INF. So far so good, and here is what a Resource Definition looks like:
<Resource
name="jdbc/XX"
auth="Container"
type="javax.sql.DataSource"
username="XXX"
password="XXX"
driverClassName="oracle.jdbc.driver.OracleDriver"
url="jdbc:oracle:thin:XXXX"
maxActive="8"
maxIdle="4"/>
Given this definition, a Connection object is created correctly.
What I'd like to know is if I am able to add extra information in this definition, such as projectName, and reach it from the context(or somewhere else). Something like the following:
<Resource
name="jdbc/XX"
auth="Container"
type="javax.sql.DataSource"
username="XXX"
password="XXX"
driverClassName="oracle.jdbc.driver.OracleDriver"
url="jdbc:oracle:thin:XXXX"
maxActive="8"
maxIdle="4"
projectName="Cool Project"/>
Any help is appreciated..

No, but you could define a naming convention and add an Environment element for each of your resource :
<Environment name="XX_projectName"
value="Cool Project"
type="java.lang.String"
override="false"/>
In your code, you would access it via
Context ctx = new InitialContext();
String projectName = (String) ctx.lookup("java:comp/env/XX_projectName");
See http://tomcat.apache.org/tomcat-7.0-doc/config/context.html#Environment%20Entries for details.