intermine/intermine — pull request #647 by julie-sullivan (2014-05-09 09:36:46+00:00)
Title: Remove unneeded dependencies on the ObjectStore

I created InterMine-model project that most other projects are now dependent on. Now InterMine-pathquery and the Java client are not dependent on the ObjectStore any more.

To do this I had to move some Util classes around and change just a little bit of code. Here are the details:

* Moved Utils to InterMine-model
* Some not used in InterMine model but needed by the Java client and the ObjectStore
* Didn’t need all of Util but it’s confusing to have two different Util classes different packages. Needs to be easy to find too.
* ``2.0 release notes`` - mines may have to update references to these classes in their Mine-webapp projects.
* Utils:
* StringUtil
* TypeUtil
* SAXParser
* StringConstructor
* Util
* methods moved from org.intermine.util.DynamicUtil
* getFriendlyName()
* decomposeClass()
* Moved JARs
* some duplicate JARs - json20110106.jar
* Some JARs not needed by InterMine-model but needed by unrelated, dependent projects
* Moved ConstraintOp to metadata
* ObjectStore and PathQuery both use
* Removed dependencies
* InterMine-API → Java client
* for XML parser helper classes
* Updated query handling to use JSON instead, JSON library already available
* Webapp & Webservice → Java client
* import org.intermine.webservice.client.exceptions.InternalErrorException a typo
* Java client → ObjectStore
* PathQuery → ObjectStore
* InterMineFastPathObject
* InterMineFastPathObject extends FastPathObject
* InterMineObject has ref to OS