Update to latest version of 3-rd party software

[Nicklas Nordborg]

It is now over 2 years since we last checked many of the included 3-rd party software. Since then some have been updated with bug fixes and performance enhancements. I think it is time to go through the list and se what is new and if there is something we can benefit from.

[Nicklas Nordborg]

(In [5029]) References #1353: Update to latest version of 3-rd party software

Updated log4j: 1.2.14 --> 1.2.15

[Nicklas Nordborg]

(In [5030]) References #1353: Update to latest version of 3-rd party software

Updated JDOM: 1.0 --> 1.1.1 Update Xerces: 2.9.0 --> 2.9.1

[Nicklas Nordborg]

(In [5031]) References #1353: Update to latest version of 3-rd party software

Updated JAI: 1.1.2 --> 1.1.3

[Nicklas Nordborg]

(In [5032]) References #1353: Update to latest version of 3-rd party software

Updated MySQL JDBC driver: 5.1.6--> 5.1.8 Updated PostgreSQL JDBC driver: 8.3.603 --> 8.4.701

[Nicklas Nordborg]

(In [5033]) References #1353: Update to latest version of 3-rd party software

Updated JFreeChart: 1.0.3 --> 1.0.13

[Nicklas Nordborg]

(In [5034]) References #1353: Update to latest version of 3-rd party software

Updated SvnAnt?: 1.2.0.RC1 --> 1.2.1

[Nicklas Nordborg]

I have tried to update Axis2 to version 1.5 (from version 1.3). There are several changes in JAR files. Some have gone, some have been updated and some new ones. Unfortunately, it seems like there is a bug that is preventing us from using 1.5. The bug is described here:

​http://issues.apache.org/jira/browse/AXIS2-4370

and results in the following exception when trying to access the information for an experiment (which has "PublicationDate?" as a date field).

java.lang.NumberFormatException: date string can not be less than 19 charactors
        at org.apache.axis2.databinding.utils.ConverterUtil.convertToDateTime(ConverterUtil.java:993)
        at org.apache.axis2.databinding.typemapping.SimpleTypeMapper.makeDate(SimpleTypeMapper.java:313)
        at org.apache.axis2.databinding.typemapping.SimpleTypeMapper.getSimpleTypeObject(SimpleTypeMapper.java:114)
        at org.apache.axis2.databinding.utils.BeanUtil.deserialize(BeanUtil.java:397)
        at org.apache.axis2.databinding.utils.BeanUtil.processObject(BeanUtil.java:682)
        at org.apache.axis2.databinding.utils.BeanUtil.ProcessElement(BeanUtil.java:601)
        at org.apache.axis2.databinding.utils.BeanUtil.deserialize(BeanUtil.java:562)
        at org.apache.axis2.rpc.client.RPCServiceClient.invokeBlocking(RPCServiceClient.java:104)
        at net.sf.basedb.ws.client.AbstractRPCClient.invokeBlocking(AbstractRPCClient.java:88)
        at net.sf.basedb.ws.client.AbstractRPCClient.invokeBlocking(AbstractRPCClient.java:94)
        at net.sf.basedb.ws.client.ExperimentClient.getExperiments(ExperimentClient.java:92)
        at TestWebservices.test_getRawDataInExperiment(TestWebservices.java:386)
        at TestWebservices.test_all(TestWebservices.java:146)
        at TestWebservices.main(TestWebservices.java:73)