#5 Nimbus-branch LIMS jar problems

[Tony DeBat]

This bug refers to branches/seqware-lims/nimbus-branch as of revision 2341.

Following the instructions in branches/seqware-lims/nimbus-branch/README to deploy the SeqWareLIMS to Tomcat 6.0.13 fails due to extra and missing jars.

1. The included webapps/SeqWareLIMS/WEB-INF/lib/servlet-api.jar collides with the servlet-api.jar that is part of Tomcat. It's likely that this is needed by SeqWare LIMS at compile time, but should not be included in the SeqWareLIMS.war? This problem is similar to ID: 3221042.

2. The jar commons-dbcp-1.4.jar is missing. Without it the following error is produced:

...
Mar 22, 2011 12:29:05 PM org.apache.catalina.core.NamingContextListener addResource
WARNING: Failed to register in JMX: javax.naming.NamingException: Could not load resource factory class [Root exception is java.lang.ClassNotFoundException: org.apache.commons.dbcp.BasicDataSourceFactory]
[SeqWareLIMS] ERROR [2011/03/22 12:29:06] | Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dataSource' defined in ServletContext resource [/WEB-INF/config/applicationContext.xml]: Invocation of init method failed; nested exception is javax.naming.NamingException: Could not load resource factory class [Root exception is java.lang.ClassNotFoundException: org.apache.commons.dbcp.BasicDataSourceFactory]
Caused by:
javax.naming.NamingException: Could not load resource factory class [Root exception is java.lang.ClassNotFoundException: org.apache.commons.dbcp.BasicDataSourceFactory]
...

3. The jar commons-pool-1.5.5.jar is missing. Without it the following error is produced:

...
Mar 22, 2011 12:34:17 PM org.apache.tomcat.util.modeler.Registry registerComponent
SEVERE: Null component Catalina:type=JspMonitor,name=jsp,WebModule=//localhost/SeqWareLIMS,J2EEApplication=none,J2EEServer=none
Mar 22, 2011 12:34:17 PM org.apache.catalina.startup.HostConfig deployDescriptor
SEVERE: Error deploying configuration descriptor SeqWareLIMS.xml
java.lang.NoClassDefFoundError: org/apache/commons/pool/KeyedObjectPoolFactory
...

[Tony DeBat]

The commons-dbcp and commons-pool were already added to the war by some previous change. I excluded servlet-api.jar from the war.